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CALOOSAHATCHEE ESTUARY AND CHARLOTTE HARBOR 

CONCEPTUAL MODEL 

A: Model Leads

Tomma Barnes, South Florida Water Management District 

Darren Rumbold, South Florida Water Management District 

Mark Salvato, U.S. Fish & Wildlife Service 

B: Introduction 

The Caloosahatchee Estuary and Charlotte Harbor are located on the lower west coast of

Florida. The Caloosahatchee River was originally a shallow, meandering river with headwaters in

the proximity of Lake Hicpochee and tidal influence almost to La Belle. To accommodate 

navigation, flood control, and land reclamation needs, the freshwater portion of the river was 

reconfigured into a canal known as C-43. Many canals were constructed along the banks of the

river in support of the many agricultural communities associated with the river. In addition, three

lock-and-dam structures (S-77, S-78, and S-79) were added to control flow and stage height. The 

Caloosahatchee River watershed includes the adjacent basins drained by the river from the

Charlotte Harbor estuarine system which includes San Carlos Bay, Matlacha Pass, Pine Island

Sound and the estuaries and nearshore waters associated with Sanibel Island, Captiva, North 

Captiva and the Immokalee Rise areas 

Today, the Caloosahatchee River extends 105 km from Lake Okeechobee to San Carlos 

Bay. The freshwater portion ranges from 50 m to 130 m in width and 6 m to 9 m in depth. Many

of the original bends remain as oxbows along both sides of the canal. The width of the estuarine 

portion is irregular, from 160 m in the upper portion to 2,500 m downstream at San Carlos Bay

(Scarlatos 1988). The narrow section extends from Franklin Lock and Dam to Beautiful Island.

This area has an average depth of 6 m, and the area downstream of Beautiful Island has an

average depth of 1.5 m (Scarlatos 1988). The pattern and period of flow of the Caloosahatchee 

River is highly variable based on demand (Drew and Schomer 1984). 

The tidal Caloosahatchee basin includes portions of Lee and Charlotte Counties. The 

estuary between Franklin Lock and Shell Point is 42 km long and is bordered by Fort Myers on 

the southern shore and Cape Coral on the northern shore. Water discharges from the 

Caloosahatchee pass Shell Point and enter the Gulf of Mexico at San Carlos Bay. Because of the 

long and narrow configuration of the estuary, changes in wind, tide, runoff, or precipitation can

have effects on estuarine features such as flow, water depth, salinity, and turbidity. Therefore, due 

to the dynamic nature of the estuary, characterization of the system is difficult. 

Major changes in the hydrology of the Caloosahatchee watershed are the result of 

significant modifications in land and canal development, as well as water management policy.

Adverse ecological impacts in the estuary have occurred as a result of hydrological changes in the 

timing, distribution, quality, and volume of fresh water released into the estuary from the 

watershed and Lake Okeechobee (SFWMD 1999). Despite these impacts, the Caloosahatchee 

Estuary continues to be an important environmental and economic resource. Understanding how

this system responds to stressors will provide a basis for well-informed management decisions. 

Charlotte Harbor is America’s 17th largest and Florida’s second largest open water 

estuary. It has a broad barrier island chain, large parts of which are in public ownership: its 

mangrove shoreline is largely intact and in public management. The Harbor is dominated by 

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rivers that flow into the coastal areas. Unlike other estuaries in Southwest Florida that are most

influenced by the Gulf of Mexico, Charlotte Harbor’s special characteristics are created by large

rivers, such as the Caloosahatchee. Large fluctuations of seasons strongly affect the salinity and

water characteristics in Charlotte Harbor. 

Geographically, the watershed stretches from the headwaters of the Peace River in Polk 

County to the southern end of Estero Bay in Lee County, a distance of more than 100 miles. 

The model boundary for the Caloosahatchee Estuary and Charlotte Harbor Conceptual 

Model extends east to the S-79 structure. This is the final downstream structure and marks the

beginning of the Caloosahatchee Estuary. Also known as the W.P. Franklin Lock and Dam, this 

structure maintains specified water levels upstream, regulates freshwater discharge into the

estuary, and acts as an impediment to saltwater intrusion to the river. From there, the model

extends southwest to the northern boundary of Estero Bay and into the Gulf of Mexico through

Big Carlos Pass and includes a freshwater plume that extends approximately 3 miles offshore.

The area of Bokeelia, at the northern end of Pine Island serves as the northern boundary. The 

model's western boundary extends 3 miles offshore of Sanibel and Captiva Islands, making a turn

through Captiva Pass. 

C: External Drivers and Ecological Stressors 

External Drivers 

Water Management 

Water Management practices have resulted in drastic hydrologic and habitat alterations to 

the Caloosahatchee Estuary and Charlotte Harbor systems in order to convey more watershed 

runoff and include regulatory releases from Lake Okeechobee. These changes have caused large 

fluctuations in the volume, timing, and frequency of freshwater inflow to the estuary and have 

had an overwhelming impact on the ecology of the estuarine systems through the alteration of 

salinity zonation. 

Natural Phenomenon

Sea level rise is an important natural phenomenon that is causing the inland movement of

marine conditions into the estuary transition zone (Tampa Bay Regional Planning Council, 1993,

Wanless et al. 1994, Meeder et al. 1996,). Sea level has been rising along Florida's west coast and 

is projected to rise at an accelerated rate because of global warming (Tampa Bay Regional 

Planning Council, 1993). The inland movement of marine conditions due to sea level rise is

happening independent from societal-driven stressors. 

Growth & Development 

Changes in land use of a result of increased growth and development along with 

agricultural demands have led to loss and fragmentation of coastal and shoreline habitat, and

changes in water use and an increase in water demands. Decreased water quality, resulting from 

an increased input of nutrients and dissolved organics into the system, has also had an effect on 

this urban and agriculture pressure. 

An additional ecological stressor is that placed on the natural systems by boating and

fishing pressures. The need for navigation from the east coast through Lake Okeechobee to the 

west coast has resulted in the dredging and the channelization of the original Caloosahatchee

River to the current C-43 canal. The continued channelization of the C-43 has had a profound 

impact in decreasing the amount of submerged aquatic vegetation within the estuary. Furthermore 

increases in manatee mortality and decreases in native fish populations have been a consequence 

of both boating activity in the estuary and harbor as well as fishing pressures. 

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Ecological Stressors 

Altered Hydrology & Freshwater Flow

Altered hydrology and freshwater flow is one of the predominate stressors of the system

and takes the form of excessive water withdrawals (demand) and over drainage. This causes

changes in the timing and quality of the watershed runoff to the estuary and harbor, which now 

includes regulatory releases from Lake Okeechobee. These alterations result from providing flood 

protection and water supply to a growing agriculture and urban population. The altered hydrology

is facilitated by the physical changes made in the watershed, which include the development of a 

complex network of secondary canals, enlargement of C-43 to convey more water, and the

addition of three water control structures on C-43, which connect the canal to Lake Okeechobee. 

Accompanying these hydrologic changes is a decrease in water quality, marked by increases in 

turbidity and nutrient loading, changes in water residence time in the estuary, and alteration in the 

natural salinity regime. 

Altered estuarine and harbor salinity has resulted from man-made hydrological 

modifications that have dramatically altered the natural quantity, quality, timing, and distribution 

of flows to the estuary, often without proper regard to the biological integrity of the estuary 

(Haunert et al., 2000). During the wet season, rainfall runoff that was historically retained within

the undeveloped watershed now reaches the river in greater volume and less time (USCOE,

1957). Additionally, the construction of S-79 has confined the estuary by restricting

freshwater/low salinity waters from the upper reaches of the estuary during the dry season.

Alterations in the delivery of freshwater at S-79 cause salinity to vary widely in time and space 

(USCOE, 1957). Rapid and unnatural fluctuations in salinity have contributed to major impacts 

on submerged plant abundance and distribution, including a loss of the natural gradient of grass 

species between Downtown Fort Myers and the mouth of the Caloosahatchee River. 

The estuarine flora and fauna are sensitive to freshwater releases and disruption of the 

volume, distribution, circulation, and temporal patterns of freshwater discharges could place 

severe stress on the entire ecosystem. "Such salinity patterns affect productivity, population

distribution, community composition, predator-prey interactions, and food web structure in the

inshore marine habitat. In many ways, salinity is a master ecological variable that controls

important aspects of community structure and food web organization in coastal systems" (Myers

and Ewel, 1990). 

Habitat Alteration and Loss 

Habitat alterations to the estuary and harbor have also impacted the presence and 

abundance of species historically found within the system. These alterations include conversion 

of wetlands, dredging of channels and spoil disposal, changes in shoreline, snagging of navigation

hazards, and decrease in spatial extent of the estuaries through construction of barriers (such as S79) (Harris et al. 1983). The addition of the Intracoastal Waterway and the Sanibel Causeway

altered water flow and habitat (Harris, et al. 1983). Changes in the physical dimension of the 

estuary, which resulted from the addition of S-79, reduced (or eliminated) the upstream 

oligohaline portion of the estuary, especially during the dry season (Chamberlain and Doering 

1998a). This salinity zone is an important nursery area, feeding area, and refugia for juvenile 

stages of desirable sport and commercial fishes. Construction and operation of the water control 

structures may interfere with migrations patterns of many estuarine species, by acting as a barrier

between the freshwater and saline water habitats and have historically resulted in deaths of 

manatees attempting to pass through these structures. 

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Changes in Water Quality & Increased Sediment Contaminants 

Nutrients and dissolved organics enter the system as a result of anthropogenic activities 

in the watershed. The greatest loadings come from agricultural runoff facilitated by water 

management practices, urban runoff, and point source discharges to the estuary from sewage 

treatment plants (Post, Buckley, Schuh, and Jernigan and W. Dexter Bender and Associates, Inc 

1999, Drew and Schomer 1984). In addition, atmospheric deposition contributes to nitrogen

loading (Squires et al. 1998). These constituents lead to increased phytoplankton production and 

interact with altered salinity patterns, increased water color, and sediment loading to reduce light 

penetration. This can lead to declines in submerged plant abundance. Increases in areas of low 

dissolved oxygen and shifts in species composition of benthic invertebrates to more pollution

tolerant organisms are linked to increased nutrient levels (Barbour et al. 1996). 

Toxins which include pesticides, fungicides, herbicides, coliforms from sewage treatment 

plants, oils, greases, mercury, and other heavy metals such as copper and zinc can be introduced

into the system from urban development, agricultural practices, and boating. Direct toxic effects 

have been documented in other south Florida systems on zooplankton and fish. Indirect effects 

can occur through the process of bioaccumulation or biomagnification through the food web,

increasing the toxic load to top predators (Day et al. 1989). Studies in the Caloosahatchee 

Watershed have been unable to detect serious contamination of sediments with toxins (La Rose 

and McPherson 1983, Fernandez. et al. 1999). It is recommended that monitoring be continued. 

Boating and Fishing Pressure 

Boating pressure is a stressor to the estuary through direct impacts such as seagrass

scarring, sediment resuspension, wake erosion, and construction of boating channels. In addition,

boat collisions are the leading cause of human-related manatee mortality (W. Dexter Bender and

Associates 1995). Fishing pressure from sport and commercial fisheries has impacted standing 

stocks of many species (Post, Buckley, Schuh, and Jernigan, Inc. 1999) and in turn impacted

those species that depend on fish as their primary food source. Recent resource trends for local

fisheries show some increase as a result of changes in the management process (Muller et al. 

1996, McMichael 1997). 

D: Ecological Attributes 

Eight attributes have been identified in the Caloosahatchee Estuary and Charlotte Harbor 

as the biological or ecological indicators of environmental stress. 

Submerged Aquatic Vegetation Community Structure, and Function 

Submerged Aquatic Vegetation (SAV), for the purpose of this conceptual model, include 

only the vascular underwater plants that live throughout the estuary and in near-coast waters. 

SAV play several roles in maintaining an estuary's health. They provide habitat and nursery

grounds for many fish and invertebrate communities and are especially important in benthic

based primary productivity. SAV and the organisms that live on them are important food sources 

in the estuarine system. Manatees, waterfowl and wading birds rely heavily on seagrass systems

as forage areas. SAV help maintain water clarity by trapping fine sediments and they improve 

water quality by taking up large quantities of nutrients that would otherwise accelerate the 

eutrophication of the estuarine system. 

Tape grass (Vallisneria americana) is the dominant submerged aquatic vegetation in the

upper Caloosahatchee Estuary and occurs in well-defined beds in shallow water. Vallisneria

americana is an important habitat for a variety of freshwater and estuarine invertebrate and 

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vertebrate species, including some commercially and recreationally important fishes (Bortone and 

Turpin 1999). Additionally, it can serve as a food source for the Florida manatee (Trichechus 

manatus). Shoal grass (Halodule wrightii), turtle grass (Thalassia testudinum), and manatee grass 

(Syringodium filiforme) are the most common higher salinity grasses in the Caloosahatchee

Estuary and Charlotte Harbor. Argopectin sp., the bay scallop, prefers shoal and turtle grass beds. 

Increasing scallop populations to resemble historic distributions is currently a goal of the

Charlotte Harbor Estuarine Program (CHNEP 1999).

All species of SAV have a preferred and tolerable salinity range. They respond

unfavorably when salinity alterations exceed these ranges. Degraded water quality and physical

alterations, such as the Sanibel Causeway and the Intracoastal Waterway have also shown 

negative impacts to the seagrasses. The result has been a regional decrease of seagrass coverage 

(Chamberlain and Doering 1998a). This decline negatively impacts the fish and invertebrate

communities. It also causes destabilization of sediments and a shift in primary productivity from

benthic macrophytes to phytoplankton, both of which provide negative biofeedback to further

affect seagrass beds. 

Oyster Bar Community Structure, and Function 

Oysters are sensitive to salinity and siltation. They require salinity levels above 4-5 ppt 

(Loosanoff 1932) with an optimal salinity range between 14 and 28 ppt (Chanley 1958, Galtsoff 

1964) varying with geographical region. Higher salinity levels increase negative effects from

saltwater predators such as oyster drills (Hofstetter 1977, White and Wilson 1996) and the 

protozoan parasite Perkinsus marinus (Dermo) (Volety 1995), the primary oyster pathogen in the 

Gulf of Mexico (Soniat 1996). Dermo is estimated to have killed 80% of the oysters in a bed 

under optimal salinity and temperature within Chesapeake Bay (Andrews 1988). Presently,

increased oligohaline conditions have limited distribution of oysters in the Caloosahatchee 

estuarine systems. 

Oyster bars provide several important functions, including habitat and food for other 

species. Wells (1961) lists 303 species that depend on oyster bars either directly or indirectly. 

Individual oysters filter 4 to34 liters of water per hour, removing phytoplankton, particulate

organic carbon, sediments, pollutants, and microorganisms from the water column (Volety pers. 

com.). This process results in greater light penetration and promotes the growth of submerged

aquatic vegetation immediately downstream of the oyster bars. 

The epidemiology of Dermo disease coupled with physiological responses of oysters in 

relations to environmental and anthropogenic stress will yield critical information on conditions 

necessary for healthy oyster reefs. Salinity and water quality conditions that yield enhanced 

distribution of healthy oyster reefs can be used as hydrological targets for restoring and 

maintaining suitable salinity and water quality in the Caloosahatchee Estuary and Charlotte

Harbor. 

Mesohaline Benthic Community Structure and Function 

Open bottoms in the Caloosahatchee Estuary and Charlotte Harbor are composed of

mixtures of sand, mud, shell, and bedrock. Macroinvertebrates, including mollusks, are dominant

elements of both the estuarine and tidal river Caloosahatchee and Charlotte Harbor ecosystems. 

The number, diversity, dispersion, and condition of macroinvertebrates have been studied 

for decades, forming a large and robust body of information on adaptations of numerous phyla to

the physical and chemical conditions unique to estuaries. Numerous studies have demonstrated 

that spatial and temporal trends in macroinvertebrate attributes vary in consistent form with 

variations in river flow, current speed, salinity, dissolved oxygen, and foodstuffs such as 

particulate organic carbon, phytoplankton, macrophytes, and prey. In recent years, a variety of

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studies have been published which indicate the extent to which macroinvertebrate attributes can

be related specifically to independent variables such as freshwater inflow and salinity alterations. 

The mesohaline clams Rangia cuneata, (Bivalvia: Mactridae), and Polymesoda 

carolineata (Bivalvia: Corbiculidae), are commonly found associated with mud and sandy

bottoms in the Caloosahatchee Estuary. Both of these mollusks require lower salinities and can be

used as indicators of estuarine condition. Furthermore, because mollusks leave behind their shells 

upon death, it is possible to look at the death assemblage to construct historical salinity regimes.

Shell characteristics such as size, shape, and ornamentation vary according to salinity and can be 

used to construct historical salinity regimes. The death assemblage, which is sampled along with

live community, can be utilized as an indicator of conditions prior to recent alterations to the 

system and provide a useful target when compared with current conditions. 

Fisheries Community Structure and Function 

At least 70% of Florida's recreationally sought fishes depend on estuaries for at least part

of their life histories (Harris et al. 1983, Estevez 1998, Lindall 1973). Within the estuary, seagrass 

communities provide critical refugia for juvenile fish such as redfish, grouper, snook, and spotted 

seatrout. The decline in juvenile abundance and distribution of these and other species, along with

the overall decline in species richness may be related to a decline in this seagrass habitat and/or a

result of alterations in the salinity regime and the timing of the freshwater discharges. 

Commercial and recreational fishing pressure has also increased along the west coast of 

Florida. With this increase, there has been a decline in reported landings (Post, Buckley, Schuh, 

and Jernigan and W. Dexter Bender and Associates, Inc 1999). In Lee County clear evidence for 

this decrease can be seen with the spotted seatrout where there has been a decline on catch-perunit-effort from 1986 to 1995 (Bortone and Wilzbach, 1997). 

The blue crab fishery is the largest, year-round fishery in the upper and middle portion of 

the Caloosahatchee River and Charlotte Harbor. This commercial fishery is intensely fished 

virtually every day of the year by several hundred crab traps and will be able to provide fishery 

landings data that can be correlated to other estuarine components to provide evidence of the

overall productivity of the system. Blue crabs also move freely about the system are good 

monitors of localized changes in conditions relative to temperature, salinity and other water 

quality parameters. 

Manatee Demographics 

Manatees are a very visible and publicly appreciated feature of the Caloosahatchee

Estuary and Charlotte Harbor. They have been listed by the state and federal government as an

endangered species and are protected throughout their range. In the study area, the largest 

concentration of manatees is found in the upper tidal reaches of the Caloosahatchee Estuary, near 

the Orange River and the warm water outflow of the Florida Power and Light power generating

plant (USFWS, 1995). 

The Florida manatee is an opportunistic herbivore, feeding on a wide variety of plants.

Seagrasses, especially V. Americana, can be an important food resource for manatees in the 

Caloosahatchee Estuary. Other critical requirements for the manatee are warm water in winter

months and access to fresh water. They prefer waters with salinities less than 25 ppt, but can 

move freely between fresh and salt water (USFWS, 1999) 

Lee County leads the west coast of Florida in the total number of manatee deaths. Some 

of these deaths can be attributed to watercrafts, entanglement with crab lines, rope, or gill nets,

and ingestion of monofilament line or pieces of plastic. Lee County also leads all other west coast

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counties in the number of deaths in the categories of dependent calves, natural causes, and

undetermined. 

Shoreline Community Structure and Function 

In 1982 approximately 674,260 acres of mangrove forests occurred in Florida (Lewis et 

al., 1985). Approximately 2,995 acres of mangroves are found in the Lower Caloosahatchee 

River Subbasin (Post, Buckley, Schuh, and Jernigan and W. Dexter Bender and Associates, Inc 

1999). In the Caloosahatchee Estuary and Charlotte Harbor, mangroves support fish and macroinvertebrate communities by providing protected nursery areas for fishes, crustaceans, and 

shellfish, and food for a multitude of important commercial and recreational marine species such 

as snook, snapper, tarpon, jack, sheepshead, red drum, oyster, and shrimp (Harris et al. 1983, 

Lindall 1973). Mangrove roots act to trap sediments and prevent shoreline erosion and provide

attachment surfaces for various marine organisms. Additionally, mangrove forests provide habitat 

for a highly diverse population of birds (Odum et al. 1982). 

Mangrove shoreline habitats have decreased in spatial extent and in function. Large areas

of mangroves have been lost or fragmented through dredge-and-fill activities (National Safety

Council 1998, Estevez 1998). In addition, mangroves are sensitive to alterations in upland

drainage. In some areas, drainage for agricultural and urban development has reduced overland 

flows of freshwater to the mangroves. This results in an increased amount of concentrated runoff,

which in turn changes the salinity balance, reduces the flushing of detritus, and washes nutrients 

directly into the estuary without the benefit of filtration by the mangrove system (Estevez, 1998). 

Algal Blooms Community Structure & Function 

Periodic blooms of algae, including true algae, dinoflagellates, and cyanobacteria or bluegreen algae have been reported within the marine and freshwater portions of the Caloosahatchee

Estuary and Charlotte Harbor. In many instances these algal blooms are merely an aesthetic

nuisance, however certain species producing toxins that kill fish, invertebrates, birds and 

mammals (USGS 1988). Pigmented algal blooms that are toxic to the marine environment are 

referred to as “red tides”, while those produced by cyanobacteria in freshwater are termed

cyanobacterial blooms (USGS 1988). Florida red tide blooms typically begin in the Gulf of 

Mexico 40-80 miles offshore and move slowly with the prevailing ocean currents toward 

southwest Florida. As the bloom progresses, the density of red tide organisms increase to several 

million cells in each liter of sea water, and the effected area expands to many square miles. 

Red tides within Charlotte Harbor can and have presented to marine animals. Marine 

algal toxins, such as brevetoxin, bioaccumulate and are thereby magnified in the food chain, 

while anatoxins from freshwater cyanobacteria affect the nervous system. There have been 

several documented cases in the field where blooms of Karenia brevis, a brevetoxin that produces 

neurotoxins and the major species of harmful algal bloom in Gulf waters which causes red tides, 

have killed both vertebrate and invertebrate species. At least 17 invertebrate species normally 

present in Tampa Bay, Florida, have been recorded absent immediately after a red tide incidents 

(FMRI 2000). Various species of bivalve shellfish, especially oysters, clams and coquinas can

accumulate so much toxin that they become toxic to both marine animals and humans as well

(MML 2002). 

During two of the largest recorded red tide out breaks (1946–1947 and 1953–1955) in

southwest Florida catastrophic mortalities of marine animals were recorded (FMRI 2000). 

Among the affected organisms during these periods were reports of dead bottlenose dolphins 

(Tursiops truncatus), sea turtles, and numerous fish species. Because fish die quickly from

exposure and contact with red tides the toxins do not have time to build up in their tissue. Those 

fish exposes to lower and hence sub lethal concentrations of red tide may accumulate these toxins 

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in their body. Such bioaccumulation of toxins in fish eaten that then eaten by dolphins may a 

major factor in the marine mammals mortality in the study area. The largest red tide-associated

dolphin mortality involved more than 740 bottlenose dolphin strandings along the Atlantic coast 

from June 1987 to May 1988. Although other infections were present in examined dolphin 

carcasses, brevetoxin was suspected as the proximate cause of the mortality during this mass 

stranding. 

Along with toxin effects, algal blooms negatively influence aquatic organisms by 

depleting dissolved oxygen concentrations in the water through their proliferation, death, decay 

and nightly respiration (USGS 1988). Although coastal pollution has enhanced red tide blooms in

other areas of the world, the Florida red tides represent a natural phenomenon not caused by

pollution. These blooms serve a purpose in the ecology of Florida Gulf coastal regions (MML 

2000). 

Wading Birds Community Structure & Function 

A number of ecological factors are negatively influencing wading bird species in the 

Caloosahatchee Estuary and Charlotte Harbor, chief among these are loss of shoreline habitat, 

decreased availability of SAV and fish within the mangroves and littoral zones as well as 

potential influence from increased nutrients and contaminant runoff. 

Environmental contaminants, such as pesticides and heavy metals, used for agricultural

and urban needs throughout much of South Florida pose a variety of potential threats to fauna, as 

they can be concentrated in organisms through food webs in the Caloosahatchee Estuary and 

Charlotte Harbor regions. These bioaccumulated toxins can have significant effects on the health

of populations of macroinvertebrates and fish, and ultimately on the survival of wading bird 

species. Contaminants can also significantly affect aquatic fauna without being bioaccumulated,

particularly for those species with gills or permeable surfaces exposed to water. 

Many bird species can be affected by algal toxins (USGS 1988). Most reports of 

mortality are from die-offs that occur in conjunction with a bloom that had worked its way into 

that specie’s food chain. During a long duration outbreak of K. brevis red tide on the Florida west 

coast between October 1973 to May 1974, large numbers of aquatic birds, particularly doublecrested cormorants, Phalacrocorax auritus, red-breasted mergansers, Mergus merganser, and 

lesser scaup, Aythya affinis, were found moribund or dead in red tide areas. Over an eight-week

period several thousand lesser scaup died (FMRI 2000). 

E: Ecological Effects 

Loss of Shoreline Habitat and Function 

Relationship of loss of shoreline habitat and function and shoreline community structure 

and function. The ecological functionality of shoreline habitat in the Caloosahatchee Estuary and 

Charlotte Harbor systems is predominantly composed of mangrove habitat. Urbanization and 

shoreline development have resulted in the extensive loss of mangrove habitat along the

Caloosahatchee Estuary and within Charlotte Harbor. Among the ecological functions carried out

by mangroves are land formation (Warming, 1925; Davis, 1940), sediment stabilization, primary 

productivity, filtration of land runoff, absorption and recharge floodwaters. The mangroves also

serve as habitats and nurseries providing food and cover for a multitude of native fish and wildlife 

(MacNae, 1968, Odum et al., 1982; Harris et al., 1983; Dawes 1998). These functions help to 

maintain water quality, recycle nutrients, and control erosion (Harris et al., 1983). In south 

Florida, mangroves have been destroyed by dredge-fill operations to create real estate, and port

and industrial facilities. Mangrove destruction results in a chain of reactions that affect estuarine 

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and off shore production. In the Tampa Bay estuarine system, one similar in structure and 

function to the Caloosahatchee, 44% of the mangrove and salt marsh land has been lost due to 

construction and resultant turbidity from runoff and pollution (Lewis and Estevez 1988). This loss 

in the Tampa Bay Estuary has been linked to declines in fin fish and commercial shrimping in the

region (Dawes 1998). 

Relationship of loss of shoreline habitat and function and wading bird community 

structure and function. Mangroves, the dominant shoreline habitat for the lower Caloosahatchee

Estuary and Charlotte Harbor, carry out a number of ecological functions; in particular this 

ecosystem serves as primary habitat and nursery grounds for both wading birds species and their 

various prey organisms such as estuarine invertebrates and fish. Productivity in the shoreline 

mangrove systems are also depressed as a result of diminished upland flows of freshwater to the 

mangroves. It is these low salinity mangrove forests have been recognized as critical nursery 

habitat for species such as blue crab, snook, tarpon, and ladyfish (Odum et al. 1982, Gilmore et

al. 1983, Lewis et al. 1985). Much of this habitat has been lost or highly modified. In many areas, 

freshwater upland flows to these mangrove systems have been decreased or depleted due to a

rerouting of the water through canals. Changes in freshwater discharge have also altered the 

structure of mangrove forests. The reduction and modification of this habitat type may represent a 

limiting factor in total population sizes of some estuarine-dependent species (Lewis 1990).

Altered Salinity Regime

Relationship of altered salinity regime and fisheries. Alterations in the salinity regime 

places undo stress on the sensitive life history stages of many estuarine species (Emery 1957,

Odum 1970, Lindall 1973, Perry and McIlwain 1986, Chamberlain and Doering 1998b). Within 

the Caloosahatchee Estuary and Charlotte Harbor altered salinity regimes have impacts on the

community structure and function of fisheries, oyster bars, SAV and benthos. While estuarine 

species are generally well adapted to cope with varying salinity conditions, larger shifts these 

conditions can be a problem. Such changes in the natural salinity regime and timing of freshwater 

discharges have resulted in a decline in juvenile fish abundance, distribution, and species 

richness. For example, the egg stage of spotted seatrout. Trout eggs are neutrally buoyant at about 

20-22 ppt (Pattillo et al. 1997). They spawn during the warmer months of the year (Lassay 1983). 

If large and protracted reductions in salinity were to occur during the summer months, it could

lead to the reduction or elimination of an entire year-class of spotted seatrout. 

Relationship of altered salinity regime and oysters. Alterations in freshwater flow have 

lead to dry season salinity increases in the estuary and harbor. Salinity is an important factor in 

determining the distribution of coastal and estuarine bivalves. Adult oysters in the Gulf of Mexico 

normally occur at salinities between 10 and 30 ppt but they tolerate a salinity range of 2 to 40 ppt

(Gunter and Geyer 1955). Short pulses of freshwater inflow can greatly benefit oyster populations

by killing predators, such as the southern oyster drill and the welk that cannot tolerate low salinity 

water (Owen 1953, Marshall 1954), while excessive freshwater inflows may kill entire 

populations of oysters (Gunter 1953, Schlesselman 1955, MacKenzie, 1977). 

Relationship of altered salinity regimes and SAV. Different species of SAV have different 

desirable salinity ranges. When salinity falls outside of these ranges the SAV is negatively 

impacted and may result in a reduction in densities and distribution (Chamberlain and Doering 

1998b). Increases or decreases in salinity may give one species a competitive advantage over

another (Livingston 1987). Tabb et al (1962) stated: “Most of the effects of man-made changes on 

plant and animal populations in Florida estuaries are a result of alterations in salinity and 

turbidity”. 

Relationship of altered salinity regime and the benthic community. Alterations in SAV 

community structure and function brought by changes in the natural salinity regime has resulted 

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FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

in substantial losses of mesohaline benthic species, such as mollusks and blue crabs along with a 

decrease in larval and adult fish recruitment into the estuary and harbor. 

Relationship of altered salinity regime and algal blooms. Research has found that high 

mortalities in estuary and harbor organisms such as the manatee appear related to concentration 

and geographic distribution of the red tide outbreaks, in relation to salinity, as well as the 

persistence of the bloom in relation to the distribution and exposure time by of the organisms to

the bloom (Landsberg, J.H. and K. A. Steidinger, 1998). An unusual number of manatee deaths 

were documented in 1996 (U.S. Marine Mammal Commission, 1996). The beginning and ending 

of this event coincided with an inshore bloom of Karenia brevis in southwest Florida (Baden,

1996).Eighty one of 149 manatee deaths associated with this bloom of red tide occurred in Lee 

County, primarily in the Caloosahatchee Estuary (Dryden pers. com.). Fish mortalities associated 

with K. brevis events are very common, widespread, and impact hundreds of species and various 

life history stages. Brevetoxin is absorbed directly across the gill membranes of fish or through 

ingestion of K. brevis cells.

Relationship of altered salinity regime to manatee demographics. Algal blooms, such as 

red tides, present a major threat towards manatee populations is red tide which historically been 

responsible for an increase in manatee mortality. Although marine mammal mortality associated 

with red tide is poorly known several mortalities have been recorded in this region from this

toxin. Red tide was linked to the deaths of seven manatees in 1963 near Fort Myers (Layne 1965, 

Bossart et al 1998). More recently, during a 1996 die off of manatees, a large number of manatees 

aggregated in warm waters near the Fort Myers power plant in the Caloosahatchee River. Final

reports conclude that brevetoxins from a bloom of red tide were responsible for the death of those 

manatees. Toxins were found in the manatee carcasses in the liver, kidney, and lung tissues, and

also in stomach contents (USFWS 1999). Manatee deaths are often attributed to red tide.

However, in 1996 their increased vulnerability was due to their congregating near this warm

water refuge and circumstances of the estuary when the tide occurred. 

Increased Manatee Mortality 

Relationship of increased manatee mortality and manatee demographics. Manatee 

populations and their habitats in the Caloosahatchee Estuary and Charlotte Harbor are continually

threatened by human activity. The greatest present threat to manatees in southwest Florida is the 

high rate of morality caused by watercraft collisions. Boat channels are often used by manatees to 

travel from one region to another (Curran 1989, Sirenia 1993). Manatees do not always move out 

of the way of boats using these channels which make them vulnerable to collisions. Watercrafts

using shallow coastal areas for fishing and site seeing also increase the likelihood of a manatee 

injury or death if the boat passes over them. 

The second most significant threat to manatees is the loss and degradation of habitat, due 

primarily to direct damage by aquatic recreational and commercial boating activities, coastal

construction, and pollution from sewage discharge and storm water runoff (MMC 1992, Smith

1993). The seagrass beds that manatees rely on for foraging, mating, calving incur direct damage 

from boat propellers (Zieman 1982). Propeller dredging of bottom habitat by boats, propeller 

wash, and wave wake disturbance cause boat induced turbidity. Sediments around seagrasses 

become unconsolidated and suspended. This delays recolonization of the grasses for two to five 

years or longer, depending on the species type. 

Decrease of SAV 

Relationship of decreased SAV and manatee demographics. Manatees depend on the

submerged aquatic vegetation for food and habitat in the Caloosahatchee Estuary and Charlotte 

Harbor. Seagrass beds and mangroves provide important areas for manatee foraging, calving, 

10 
FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

resting, and mating. Preferred manatee habitat in south Florida is characterized by the availability

of submerged aquatic vegetation (Smith 1993). 

Manatees are opportunistic herbivores and feed on a variety of submergent, emergent, 

and floating vegetation with seagrasses comprising the largest component of their diet in south 

Florida (Hartman 1979, Zieman 1982, Smith 1993). Manatees usually forage in shallow grass 

beds that are adjacent to deeper channels (Hartman 1979, Powell and Rathbun 1984). Some 

manatees have been observed to return to the same seagrass beds year after year and may show 

preference for certain areas (USFWS 1999). 

Relationship of decreased SAV and wading bird community structure and function.

Negative changes, namely decreases, in SAV community structure and function has resulted in 

reduced nutrients and nurseries for wading birds or their prey. Substantial losses in mollusk 

populations and a decrease in larval and adult fish recruitment into the estuary are a direct result 

of declining SAV populations in the estuary and harbor. 

Fish densities are typically greater in grass bed habitat within south Florida’s estuaries

and coastal lagoons than in adjacent habitats (Reid 1954, Tabb et al. 1962, Roessler 1965, Yokel

1975, Weinstein et al. 1977). The grass beds provide protection from predation for animals living 

in it. The dense seagrass blades and rhizomes associated with the grasses provide cover for 

invertebrates and small fishes while also interfering with the feeding efficiency of their potential

predators (Zieman 1982). Reduction in size and health of SAV beds effects the location, 

abundance, and speciation of fisheries in the estuary. 

Relationship of decreased SAV and SAV community structure and function. Reduction in 

penetration of light into the water column is often blamed for the disappearance and diminishing 

of previously healthy seagrass meadows (US EPA 1983). Because seagrasses are rooted plants 

attached to the bottom, reduced light reduces photosynthesis, growth, and reproduction. This 

condition is cited as a major source of seagrass decline in Florida estuarine systems. (Durako

1988).

Increased nutrients, such as nitrogen and phosphorous, can lead to light deprivation by

stimulating the growth of phytoplankton. These blooms cloud the water and severely diminish 

sunlight penetration (Livingston 1987). This turbidity can increase to such a level that seagrasses

persist only in patches (Zieman 1982). Nutrients can also trigger a thick growth of epiphytes 

which can also block the sunlight before it can reach the surface of the seagrass (Murray et al. 

1999). In fact, nutrient input has such an effect that relatively minor changes in water quality can 

lead to sharp reductions in the productivity of seagrasses which can lead to broad habitat changes 

(Livingston 1984). 

Relationship of decreased SAV and fisheries community structure and function. A 

decline in the amount of seagrass habitat/coverage has occurred in the Caloosahatchee and 

Charlotte Harbor drainage. The consequences of this decline is a reduction in potential habitat for 

a number of seagrass dependent species, and especially the juvenile life stages of most estuarine 

dependent species (Virnstein 1987, Stoner 1984, Zieman 1982). Specifically, larval gag

(Mycteroperca microlepis) use sea grass beds a settlement substrate after having hatched offshore 

on natural hard bottom structures. The larvae settle in the higher salinity areas of San Carlos Bay

and Pine Island Sound in the spring of each year. After attaining a size of about 60 - 80 mm TL

they migrate offshore to take up residence on offshore reefs (Jory and Iverson 1989). Juvenile 

spotted seatrout (Cynoscion nebulosus) use grass beds for protection from predation while adults

feed on many of the seagrass associated species such as shrimp and smaller fishes (Pearson 1929,

Miles 1950, Perret et al. 1980). 

Increased Nutrients & Contaminants 

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Relationship of increased nutrients and contaminants and algal blooms community 

structure and function. The amount of nutrients entering the Caloosahatchee River and Charlotte 

Harbor has important effects on the water quality of the system. Organisms use these nutrients, 

but excessive amounts may have negative impacts (Neilson and Cronin 1981). Algal blooms and

epiphyte growth may cause decreased water clarity and block sunlight for aquatic plants (Day

1989). As algae die, organic decomposition depletes the oxygen in the water (LaRose and

McPherson 1983, Drew and Schomer 1984, Day 1989). Low levels of dissolved oxygen can have 

negative effects on fish and other aquatic organisms (Heyl 1998). Eutrophication may also result 

in an increase in red tide blooms (Gore 1992). 

Relationship of increased nutrients and contaminants and wading birds community 

structure and function. Natural communities in South Florida are adapted to surface waters with a 

chemical composition that contains low concentrations of dissolved minerals and nutrients. 

Changes in surface water quality typically involve increased nutrient and mineral concentrations

coming from ditch and canal outflows into natural wetlands (Drew and Schomer 1984). These 

increased concentrations can produce dramatic shifts in the amounts of nutrients within the water 

column, increasing turbidity and having detrimental effects on SAV species which are adapted to 

specific nutrient and dissolved mineral concentrations. Any detrimental influence to SAV 

populations is immediately conferred to wading bird community structure and function in the 

form of lost productive nursery and prey habitat. 

Changes in Sediment 

Relationship of changes in sediment and SAV community structure and function. The 

submerged aquatic vegetation in the Caloosahatchee Estuary and Charlotte Harbor will increase 

as estuarine conditions improve. The extent of this increase depends on available area with

suitable salinity, substrate, water clarity, and temperature. 

Seagrasses require light for photosynthesis. A number of factors can influence water 

clarity and light penetration. These include color and suspended solids. The different species of

SAV have distinct requirements for light. Numerous research indicates that Thallassia testudium,

Halodule wrightii, and Syringodium filiforme require levels of at least 10-15% of surface 

irradiance, while Halophila decipiens, Halophila englemannii, Halophila johnsonii, and Ruppia

maritima appear to have somewhat lower requirements, perhaps as low as 2-3% of surface

irradiance (URS Greiner Woodward Clyde 1999). 

Most seagrasses appear to tolerate a wide range of substrate conditions. Virtually all 

seagrasses seem to grow on sandy or silty muds and on sands with some mud contents (Reid

1954, Voss and Voss 1955, Phillips 1960) and require a sufficient depth of sediment for proper 

development. Substrates most also contain nutrients, especially nitrogen and phosphorous, 

available for SAV growth (Duarte 1991). The microbially mediated chemical processes in marine 

sediments provide a major source of these nutrients (Capone and Taylor 1980). 

Each species of SAV has their own temperature and salinity tolerance ranges and their 

tolerance to salinity variation is similar to their temperature tolerances. Halodule wrightii is the 

most broadly euryhaline, Thallassia testudium is intermediate, and Syringodium filiforme and

Halophila have the narrowest tolerance ranges (McMillian 1979, Zieman 1982). Vallisneria

americana is generally a freshwater grass but can tolerate salinities of near 10 ppt. Therefore, 

Vallisneria is also an important component of the oligohaline estuarine SAV community (Twilley 

and Barko 1990, Adair et al. 1994, Kraemer et al. 1999). 

Decrease of Fish Populations 

Relationship of decreased fish populations and wading bird community structure and

function. A direct consequence from the decline in shoreline habitat and decreased SAV is a

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FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

reduction in potential habitat for a numerous fish species found in the seagrass and littoral zone

communities on which wading birds are dependant. Accompanying this reduction in habitat for 

specific life histories of various fishes, the reduction in grass beds also has led to an overall

reduction in wading bird species diversity within the system. 

Relationship of decreased fish populations and fisheries community structure and 

function. Caloosahatchee Estuary and Charlotte Harbor provide habitat and nursery grounds for a 

variety of estuarine fish communities. These fishes are an integral component of the estuarine 

food web and have a significant societal value for sport and commercial harvesting. Fish

community measures are sensitive to both short and long term changes to the overall biotic

integrity of estuarine systems. Regarding these regions, with their history of anthropogenic 

manipulation, information that would permit the assessment of overall changes (replacement,

additions and subtractions) of its native fish community relative to environmental change is

lacking. 

F: Research Questions 

Relationship of water management practices to estuarine protection and restoration. 

How can estuaries of national importance, including the Caloosahatchee River; and the pristine

resources of the Charlotte Harbor Aquatic Preserve be protected or recover from water 

management practices associated with freshwater pulsing, alternation in timing and duration of

base and seasonal flows, contaminants, overnutrification and red tide?

Relationship of Manatee Mortality to Red Tide 

Will changes in salinity, nutrient load, and water residence time due to the restoration of the 

recommended estuarine salinity envelope reduce the occurrence of red tide in inland waters at

times coincident to when manatees move between inland waters and estuarine waters?

Relationship of Blue Crab Fishery to Temperature, Salinity and Other Water Quality 

Parameters 

How does CPUE of the blue crab fishery respond to the combined effects of temperature, salinity 

and other water quality parameters in the Caloosahatchee estuary? Can blue crab CPUE be used 

as an indicator of estuarine health in the estuary?

Relationship of Mollusk Populations and Fish Recruitment to Submerged Aquatic

Vegetation and Salinity 

Will changing the salinity regime to a more natural condition and increasing the coverage of 

submerged aquatic vegetation in the Caloosahatchee estuary provide a more suitable environment 

for estuarine mollusks and fishes? Will this lead to an increase in population density and 

community diversity? 

Relationship of Current and Historical Submerged Aquatic Vegetation Coverage to 

Potential Distribution 

What areas in the estuary potentially provide optimal conditions for seagrass reestablishment?

Will we see this reestablishment with changing conditions? 

G: Hydrological Performance Measures 

See addendum titled Southwest Florida Feasibility Study – Caloosahatchee Estuary

Hydrologic Evaluation Performance Measures. 

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H: Ecological Performance Measures 

Submerged Aquatic Vegetation Community Structure & Function 

The performance measures for submerged aquatic vegetation community structure and

function are SAV distribution, density/abundance, and community composition. Seagrass beds 

must be reestablished in the Caloosahatchee Estuary and Charlotte Harbor to increase biodiversity 

within the system and enhance habitat value for fish, caridean shrimp, wading birds, and 

manatees. The coverage of seagrasses must increase in areas that are indicated to be suitable

habitat. To achieve these targets, flows needed to achieve the proper salinity range for SAV must

be maintained. 

Oyster Bar, Community Structure and Function 

The performance measures for oyster bar community structure and function are oyster 

growth, disease, mortality and recruitment. The targets are to increase the abundance and health

of oysters, restore oyster beds in suitable habitat, and maintain habitat function of oyster beds for 

fish, crabs and birds. To achieve these targets, flows needed to achieve the proper salinity range 

for oysters must be maintained (see Salinity Envelope under Hydrologic Performance Measures). 

Mesohaline Benthic Community Structure and Function 

The performance measures for sand/mud bottom community structure and function are

mesohaline clam abundance, growth and recruitment. The target is to obtain targeted normal 

distribution, population size, and condition across optimal salinity ranges for these freshwater 

species of clam. 

Shoreline Community Structure and Function

The performance measure for shoreline mangrove habitat is shoreline mangrove percent

cover. The targets are to restore and maintain shoreline mangrove habitat and to increase or 

maintain functionality of the mangrove system. To achieve these targets, further loss of mangrove 

habitat must be eliminated; mangrove habitat must be restored when possible. The mangrove tree

crab will be used an indicator species to measure increase or loss of functionality in the mangrove 

system. 

Fisheries Community Structure and Function 

The performance measure for estuarine fish community structure and function are fish 

community structure and diversity. The target is to restore assemblages with abundance,

taxonomic composition, diversity and representation of life stages characteristic of targeted 

salinity regimes for each estuary.

Manatee Demographics 

The performance measures for manatee demographics are manatee birth, death, survival, 

distribution and abundance. Restoration and preservation of the manatee population in the 

Caloosahatchee Estuary and Charlotte Harbor will be achieved by maintaining and enhancing 

current habitat and foraging areas for manatees in the estuaries and canals to promote species 

recovery, especially near the Florida Power and Light warm water refugia. Also, manatee habitat 

values in canals should be maintained or enhanced, as reflected by continued use of canals by 

manatees. Manatee deaths in categories "undetermined" and "calves" need to decrease. 

Algal Blooms Community Structure & Function 

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The performance measures for algal blooms community structure and function are algal

bloom frequency, duration, identity, concentration and negative effects. 

Wading Bird Community Structure & Function 

The performance measures for wading bird community and structure are wading bird 

foraging and nesting surveys. 

H: Baseline Conditions and Drivers for Water Quality in the 

Caloosahatchee Estuary and Lower Charlotte Harbor 

Anthropogenic changes in water quality can act as stressors in estuarine systems. Drivers 

and pathways of water quality problems may include, among others, urban stormwater runoff

(e.g., lawns, golf courses, "street dust"), agricultural runoff, surface mining runoff, septic

systems, discharges from Publicly Owned Treatment Works (POTWs), direct industrial

discharges (e.g., citrus processing plants, power plants), landfill runoff, as well as atmospheric 

deposition of contaminants from varied sources (for a review of drivers in southern Florida, see

USGS 1998). Although much of the focus (and control) has been on point sources, considerable 

evidence has been amassed to suggest nonpoint sources, such as urban stormwater runoff, and 

diffuse pathways, such as atmospheric deposition, can play very significant roles in local WQ

problems. Atmospheric deposition of contaminants from varied sources (both local and distant) 

can be an important driver in estuarine WQ in one of two ways. Direct atmospheric deposition of

a contaminant to the estuary includes loading from dry deposition and wet deposition. Indirect 

deposition from the atmosphere to the estuary occurs when the contaminant is initially deposited 

to the watershed and then transported to the estuary through runoff and tributaries and, hence, a 

function of water management. Along with the growing appreciation of potential impacts from 

atmospheric transport and deposition also comes a realization that we can no longer rely on the 

“dilutive effects of the ocean environment” to solve coastal pollution. Evidence has accumulated 

that anthropogenic contaminants, as well as natural occurring materials, in riverine discharges can 

be transported and have biological effects far removed from their discharge site (Rabalais et al.

1996; Goolsby, 1994, Rudnick et al., 1999). As one example, algal blooms in western Florida 

Bay have been linked to nutrient transport along the southwest shelf of Florida (Rudnick et al., 

1999). 

A number of different federal, state and local government programs outside of CERP are 

in place or will be in place in the future to address WQ problems resulting from both point and

nonpoint sources. These include the federal Clean Water Act, Clean Air Act, Coastal Zone Act

Reauthorization Amendments along, Florida’s Watershed Restoration Act and Water Resources 

Act that address implementation of the National Pollutant Discharge Elimination System permits, 

Total Maximum Daily Load requirements, Surface Water Improvement and Management

(SWIM) programs, as well as both agricultural and urban nonpoint source management programs.

Any recommendations related to water quality for alternatives analysis will first evaluate the 

efficacy of remedies brought about by these outside programs. However, as will become evident 

from the current conditions discussed below, these programs are rarely 100 percent effective.

Further, several examples will be presented to show that local WQ problems may have drivers 

outside of the study area and, thus, may not be remedied through local or state programs. During 

these assessments and during any subsequent alternatives analysis the following baseline

conditions and drivers should be considered when identifying major stressors in estuarine water 

quality: 

Results of a number of recent water quality assessments of the Caloosahatchee Estuary

and Lower Charlotte Harbor show remarkable agreement (Table 1). In their preliminary 

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FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

assessment, FDEP classified three waterbodies in the Caloosahatchee Estuary as potentially

impaired based on chlorophyll-a, dissolved oxygen (DO), fecal coliform, copper, lead and or 

biology (for methodology and legislative authority, see Impaired Surface Waters Rule [IWR],

Chapter 62-303 F.A.C.). In a separate assessment, U.S. EPA (2000) also found that parts of the 

tidal Caloosahatchee and its tributaries had degraded water quality based on values of key 

parameters. These findings have added significance given the presence of the following

Outstanding Florida Waters (OFWs) within the Caloosahatchee Estuary and Lower Charlotte 

Harbor: Caloosahatchee National Wildlife Refuge (40 acres located in the Caloosahatchee near

Interstate 75), J.N. “Ding” Darling NWR, Matlacha Pass NWR, Pine Island Sound NWR, Estero 

Bay State Buffer Preserve, Matlacha Pass Aquatic Preserve, Pine Island Sound State Aquatic 

Preserve. 

Although the state’s IWR focuses on chlorophyll-a rather than absolute concentrations of 

nutrients (i.e., because there are no numerical water quality standard [WQS] for nutrients), 

Doering and Chamberlain (1998) and Janicki Environmental Inc., (2002) both found total 

nitrogen (TN) and total phosphorus (TP) to be elevated in the Caloosahatchee compared to

statewide median concentrations, reference site concentrations and compared to historical data

(for TP). Doering and Chamberlain (1998) also report TP and TN exceeded targets that FDEP

(Degrove, 1981) had set for the Caloosahatchee. Most of these assessments also found a sag in 

DO (Table 1), especially in bottom water in the upper Caloosahatchee (i.e., adjacent to S79). 

Color was another parameter not considered under the IWR assessments but that was found to be 

unusually high (Doering and Chamberlain, 1998; ERD 2003). Accelerated decomposition of 

organic matter in the historic peat deposits in the northern Everglades (due to land-use change) 

has been shown to provide a significant source of dissolved organic matter (DOM) and nutrients 

(Wang et al., 2003). ERD (2003) reports that color at the S79 structure reached 67 Pt-Co units

and 164 Pt-Co units in the dry and wet season, respectively (statewide median for estuaries is

22.5 Pt-Co; Friedemann and Hand, 1989). Color in the Caloosahatchee may have greater 

significance given the optical model developed by Dixon and Kirkpatrick (1999) for upper and

lower Charlotte Harbor. They found that color accounted for 66% of light attenuation in the water 

column; whereas, chlorophyll, and turbidity accounted for only 4% and 31%, respectively. A

finding that color accounts for much of the water column light attenuation in Charlotte Harbor is 

also consistent with a report from McPherson et al. (1996). Humic materials, which make up 

much of the color, may also be implicated in reports of a dark flocculant material settling on 

grassbeds in San Carlos Bay (G. Romeis, FDEP, pers. comm.). This could represent a “salting 

out” of DOM. Besides shading, DOM has significance both as a primary nutrient and as a

micronutrient and, consequently, may lead to increased biological oxygen demand (BOD). It is

important to note that Dixon and Kirkpatrick (1999) found light was further attenuated, from 21% 

to 44% (annual averages), at the surface of seagrass blades by epiphytic growth, which is also a 

familiar result of nutrification. Despite all this, grassbeds are currently found in deep water (2.43 

m) near the mouth of the Caloosahatchee relative to other areas within Charlotte Harbor and

elsewhere (Dixon and Kirkpatrick, 1999; Crean et al., in review), suggesting adequate light

penetration. 

Not surprisingly, a recent assessment by Janicki Environmental, Inc., (2003b) found 

water quality has declined in the Caloosahatchee over time. They found statistically significant 

temporal trends over the last 10 – 15 years with increases in BOD, increases in total suspended 

solids (TSS) and turbidity, increases in fecal coliform bacteria, increases in many species of 

nutrients, and decreases in DO levels. 

In terms of spatial variation, Doering and Chamberlain (1998) and ERD (2002) both 

report a strong longitudinal gradient with most constituents decreasing in concentration with

increasing distance from the S79 structure. Based on this, both assessments conclude freshwater 

16 
FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

discharge from S79 plays a crucial role on water quality within the Caloosahatchee. Equally 

important, because of the steepness in the gradients, both assessments found relatively good water 

quality downstream in San Carlos Bay, as evidenced by relatively low chlorophyll-a and high DO 

(Table 1). Likewise, Pine Island Sound and Matlacha Pass also exhibited low chlorophyll-a and 

high DO (Table 1, Doering and Chamberlain, 1998). This is consistent with FDEP’s (2003)

finding that these three waterbodies met uses except for bacteria in shellfish (Table 1; note, San 

Carlos Bay is classified as a Class II waterbody, i.e., for shellfish propagation or harvesting).

FDEP’s IWR assessment is consistent with the Janicki Environmental, Inc. (2003b) evaluation

that found water quality in Pine Island Sound and Matlacha Pass acceptable based on an informal

application of the IWR. However, it should be noted that they also found statistically significant 

increases over time in nutrients, TSS, and BOD. Further, they also reported that some stations in 

this basin had frequent exceedances of DO and ammonia. 

As mentioned above, Doering and Chamberlain (1998) and ERD (2002) both identified

freshwater discharge from S79 as playing a crucial role in water quality within the 

Caloosahatchee. ERD (2003) reports that, depending on the season (i.e., wet or dry), discharge 

from the S79 structure contributes from 90% to 95% of the mean daily mass of TN and TP to the 

Caloosahatchee Estuary (up to 11,051 kg of TN per day and 1040 kg TP per day). The next

largest contributor to the Caloosahatchee Estuary was the Orange River with 1.1%to 3.8% of the 

daily mass of TN and TP. Nevertheless, for a complete understanding of water quality drivers 

within the region, especially localized effects within Matlacha Pass and Pine Island, loadings

from Ft. Myers, Cape Coral, Pine Island and Sanibel cannot be ignored. 

These findings are consistent with other loading assessments in southwest Florida that 

find the greatest nutrient loadings come from agricultural runoff and urban runoff (Post, Buckley,

Schuh, and Jernigan Inc., 1999; Post, Buckley, Schuh, and Jernigan Inc. and W. Dexter Bender 

and Associates, Inc., 1999; Drew and Schomer 1984). South Florida's high level of agricultural

productivity can be a significant driver in WQ problems as a result of various activities including

the substantial usage of soil amendments, including mineral fertilizers and biosolids (fertilizer 

usage estimated at 1.6 million tons in the year ending June 30, 1996; USEPA 1999), or simply

due to soil disturbance and decomposition of organic peat (estimates as high as 2 billion g-N per 

year to the northern Everglades; Wang et al., 2002). Nitrogen release from disturbance and peat 

decomposition in the Everglades Agricultural Area has been speculated to be a possible driver of

outbreaks of “blackwater” in southwest Florida coastal waters (Zollo, 2002). However, 

stormwater runoff is not the only means by which agricultural activities may be a driver. Nitrogen

can volatilize directly from the surface of fields (dependent on application method) or animal 

waste lagoons, or can be blown off as particles. Yet, there are other sources, potentially even

more significant than agricultural activities. Prospero et al. (1996) estimated that present day

deposition on nitrogen (including ammonia) to the North Atlantic Ocean to be five times greater

than pre-industrial times, primarily due to fossil fuel combustion and biomass burning. Given 

this, it is not surprising that atmospheric deposition of nitrogen (potentially from a distant source) 

could be a driver (external to the study area) contributing to WQ problems in southwest Florida 

(Squires et al. 1998). Atmospheric deposition of nitrogen has been estimated to be responsible 

for 21% of external nitrogen loading to Tampa Bay. Nonetheless, we cannot lose site of the fact

that urban and agricultural runoff remain the greatest source of nonpoint nitrogen loading to 

Tampa Bay (Pribble et al. 2001), and likely to Charlotte Harbor, as well. 

Unlike nitrogen, phosphorus has no stable gas phase in the atmosphere and is transported 

only as particulates, thus limiting its atmospheric residence time. 

Based on the information presented above, Janicki Environmental, Inc. (2003a), under 

contract to FDEP, developed a regression-based model between chlorophyll-a concentration in 

the Caloosahatchee and TN loads across S79. Use of TN in the model rather than TP was 

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FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

consistent with Doering and Chamberlain (1998) that found that ratio of dissolved inorganic 

nitrogen to dissolved inorganic phosphorus (i.e., DIN:DIP) to be less than 16, suggesting the 

system is nitrogen limited. Janicki Environmental, Inc. (2003a), developed regressions for both 

the dry and wet season and found greater sensitivity to nutrient loading during the former (i.e., 

greater slope or greater increase in chlorophyll-a per unit increase in TN load). However, it 

should be noted that the dry season regression had a lower coefficient of determination (R2

 = 0.4). 

Other factors, including ammonia from the sewage treatment plants discharging to the 

Caloosahatchee (see ERD, 2003), could account some of the unexplained variability in 

chlorophyll-a. As previously mentioned, FDEP has set numerical nutrient targets for the 

Caloosahatchee (Degrove, 1981); they have also established water quality based effluent limits 

(WQBELs) for these facilities (Baker, 1990). 

The increased sensitivity to nutrients in the dry season could be related to increased 

residence time in the Caloosahatchee (P. Doering, pers. communication). Alternatively, Doering 

and Chamberlain (1998) and Janicki Environmental, Inc. (2003b) both report instances of “wash

out” under high flow conditions (i.e., low chlorophyll-a under unusually high loading and, more 

importantly high flows: >150 m3

/s). A study in the Potomac estuary demonstrated a similar

interaction between load and hydrology. USEPA (2001) summarized data attributed to Boynton 

(1997) showing peak chlorophyll-concentrations in the estuary (also regressed against TN load) 

occurred under average flow conditions. Blooms did not form in the Potomac estuary during 

maximum freshwater inflows because of a strong vertical density stratification and, more 

importantly, because nutrients were advected downstream into the lower Chesapeake Bay.

Similarly, it is likely that, during high flow events across S79, impacts from nutrient loads could 

be further downstream (i.e., coastal nutrification). Residence time and “wash out” will likely 

have significant implications for alternatives analysis for CERP both as they are influenced by

CERP-components, such C43 BSR, whose goal is to provide minimum flows during the dry 

season (i.e., potential for longer residence time) and from both a redirection of Lake Okeechobee 

water south and with-in basin storage facilities that should reduce high flow events (and, thus, 

likely reduce frequency of “wash outs”). 

From the discussion above, it is clear that a strong case can be made to consider TN 

loading at S79 as a means of reducing chlorophyll-a in the Caloosahatchee. However, it should 

also be clear that water column chlorophyll-a is only one of several water quality concerns, some 

of which are not assessed by the IWR (e.g., color, DOM, BOD, “wash outs”), and that discharge

from S79 is only one of many proximate sources. Although any remedial action to reduce TN at 

S79 would likely have colateral benefits (both in terms of reducing other constituents and impacts 

to other resources) and would, in of itself, be an ambitious first step, it should be recognized that

it would not be a cure-all. 

In this context, red tides are a prefect illustration of the potential significance of other

nutrient sources on other resources, as well as the potential significance of “wash outs”. Blooms

of Karenia brevis, i.e., red tides, have been linked to direct atmospheric deposition of ammonia 

(Steidinger et al., 1998). Alternatively, Lenes et al. (2001) make a compelling argument that red 

tide outbreaks may be linked to long-range atmospheric transport of iron (a known growth factor) 

and bloom stimulation of the nitrogen fixing Trichodesmium, which, through the release of

nitrogen containing exudates, could fertilize Karenia brevis. Hence, this important southwest 

Florida issue may have external drivers not under local control. Not surprisingly, modelers 

remain "stymied by the chaos of unknown initial conditions" that stimulate red tides in southwest 

Florida (Walsh et al. 2002). Red tides have been documented along the west coast of Florida well 

before the “age of water management” (Geesey and Tester 1993) and will likely continue despite 

out best efforts. Consequently, occurrence of red tides will not be a performance measure (either 

evaluation or assessment) for the SWFFS. Nonetheless, it is conceivable that some reduction in

18 
FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

red tide magnitude, duration, or frequency is achievable if coastal nutrification were reduced 

(especially as a result “wash outs”). 

As a result of productivity level, crop variety, multiple planting seasons, and climate,

Florida agriculture requires the usage of a wide variety of pesticides, i.e., insecticides, herbicides,

and fungicides. Residues of some of these pesticides (i.e., both organics and metals) have been 

detected in sediments and surface water at District structures at various times (Pfeuffer and 

Matson, 2002). As mentioned above, fertilizers are also extensively used in Florida. Several 

studies have measured metals (e.g., cadmium, lead, nickel and copper; USEPA 1999) in mineral 

ores and resulting fertilizers. Organic and biosolid fertilizers may also have measurable 

concentrations of metals. However, agriculture may no longer be the primary source of pesticides 

to the environment. Contrary to public perception, USGS reports that pesticides occur more

frequently in urban streams than in most agricultural streams (USGS, 1999). 

As mentioned previously, FDEP has listed two waterbodies (WBID 3240B and 3240A) 

within this region as potentially impaired for copper and lead. Although the focus of the IWR 

assessment is on water column concentrations, metal impairment is consistent with a survey of 

sediments in the Caloosahatchee by Fernandez et al. (1999). They found levels of cadmium, 

copper, lead, and zinc above “natural background” concentrations. At certain stations, one or

more of these metals exceeded either the threshold effects level or, worse, the probable effects 

level (Fernandez et al., 1999). They further reported that immunoassays were positive for the 

organochlorine pesticides DDT and cyclodienes (as chlordane), with levels exceeding the

probable effects level at several sites (Fernandez et al., 1999). These findings are consistent with 

results of the District’s monitoring of sediment just upstream of S79 that found DDT, DDE and 

PCB-1245, with levels occasionally exceeding the threshold effects level (for detail, see quarterly 

reports by Pfeuffer and Matson, 2002). Since 1992, the District’s surface water monitoring 

program at S79 has detected low levels of the herbicides ametryn, atrazine, bromacil, diuron, 

hexazinone, norflurazon, and simazine at relative high frequency (frequency of detection >20%). 

The following pesticides and degradates: atrazine desethyl, atrazine desisopropyl endosulfan

sulfate, metalaxyl, ethoprop, and metribuzin were detected less frequently. However, based on 

various criteria, the concentrations of detected pesticides should not pose a significant risk to fish 

or aquatic invertebrates (Pfeuffer and Matson, 2002 and references therein). 

Atmospheric loading is also the dominant proximate source of inorganic mercury to

many water bodies, with the ultimate primary drivers being coal-fired utility boilers and 

municipal and medical waste incinerators (USEPA 1997a). However, the complication lies in 

the relationship between influx of inorganic mercury and the amount that is methylated post

deposition by sulfate-reducing bacteria. The latter process is of fundamental concern because 

methylmercury (MeHg) is the more toxic and bioaccumulative form that can build up in the food 

chain to levels harmful to humans and other fish-eating animals. Rarely is the state WQS for 

mercury, which is based on total mercury rather than MeHg, exceeded in south Florida; however, 

many south Florida waterbodies are considered impaired by FDEP based on fish consumption 

advisories for mercury. The principal pathway for mercury exposure to humans is through the 

consumption of marine fish and fish products. Studies of south Florida estuaries have found

elevated levels of mercury (both the inorganic and methyl form) in surface water discharges and, 

more importantly, in fish (Adams and McMichael, 2003; Rumbold et al. 2003). FDEP lists the 

entire southwest coastal area as potentially impaired for mercury based on fish consumption 

advisories (Table 1). Currently, limited consumption advisories have been issued for the 

following coastal fish based on their mercury content: King Mackerel, Spanish Mackerel, all

sharks, spotted seatrout, Little Tunny, Cobia, Greater Amberjack, Bluefish and Crevalle Jack.

(Florida Department of Health 2003). 

19 
FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

Table 1. Summary of findings of water quality assessments in the Caloosahatchee Estuary, San 

Carlos Bay, Pine Island Sound and Matlacha Pass. 

Waterbody

Doering and 

Chamberlain,

1998a

Janicki Environ.

Inc., 2002b

FDEP, 2002; 

2003c ERD, 2003d Janicki Environ Inc., 2003e

Tetra Tech, Inc., 

2003f

Upper

Caloosahatchee 

(WBID 3240C)

Chl a>11 ug/L

TP>state 

median

TN>state

median

DO<WQS 

Color rel. high 

Chl a>ref. site,

IWR 

TN>ref. site 

TP>historic, ref.

site 

DO<historic, ref. 

site, IWR 

Turbidity>historic

Impaired for:

Chl a, 

DO, coliform

Strong gradient 

with decreasing 

conc. of most 

constituents 

with increasing 

dist. from S79; 

Chl a>11 ug/L

DO<WQS 

Unaccept. based 

on informal IWR:

Chl a, 

DO, coliform;

trend of declining 

WQ in

BOD, TSS,

nutrients, secchi 

depth 

Middle 

Caloosahatchee 

(WBID 3240B)

Chl a>11 ug/L

TN > state 

median

Chl a>ref. site,

IWR 

TN>ref. site 

TP>ref. site

DO<ref. site, IWR

Turbidity>ref. site

Impaired for:

Chl a, 

DO, 

copper,

coliform

Spike in 

downstream

gradient in 

ammonia, 

TKN, TN and 

Chl a. 

Chl a>11 ug/L

Unaccept. based 

on informal IWR:

Chl a, 

DO, coliform;

trend of declining 

WQ in

BOD, TSS,

nutrients, secchi 

depth 

Lower 

Caloosahatchee 

(WBID 3240A)

TN>state

median

Chl a>ref. site, 

IWR 

TN>ref. site 

TP>historic, ref.

site 

DO<historic, ref.

site, IWR 

Turbidity>historic

Impaired for:

Chl a, 

DO, 

copper,

lead, 

biology

Mean 

DO>WQS 

Unaccept. based 

on informal IWR:

Chl a, 

DO, coliform;

trend of declining 

WQ in

BOD, TSS,

nutrients, secchi 

depth 

San Carlos Bay 

(WBID 2065H)

Chl a rel. low 

TN>state

median

DO rel. high 

Turbidity rel.

low 

TSS>state

median

not assessed No listed

impairment

Concentration 

of most 

constituents 

substantially 

reduced 

Chl a<11 ug/L

Mean 

DO>WQS 

Assessed under 

Matlacha Pass 

Pine Island Sound

(WBID 2065E and

G) 

Chl a rel. low 

TN>statewide 

median

DO rel. high 

TSS>state

median

not assessed 

Impaired for:

bacteria (in

shellfish) 

not assessed

Accept. based on 

informal IWR; 

exceedances in 

ammonia and DO 

at some stations 

20 
FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

Matlacha Pass

(WBID 2065F)

Chl a rel. low 

TN>state

median

DO rel. high 

not assessed No listed

impairment not assessed

Accept. based on 

informal IWR; 

improving trends

in secchi depth 

and TN

SW coast not assessed not assessed Mercury not assessed

a. Doering and Chamberlain 1998, based on SFWMD data collected from 1985 – 1995.

b. Janicki Report (2002): report to FDEP on current conditions in the Caloosahatchee comparing it to historical data, reference sites and 

the Impaired Water Rule (Chapter 62-303 F.A.C.); data sources included SFWMD, Lee County, STORET (Legacy and Modern), USGS. 

c. FDEP. 2002. Basin Status Report Draft: Caloosahatchee, 12/02; FDEP. 2003. Basin Status Report Draft: Charlotte Harbor. 9/03:

potential impairment based on Impaired Water Rule (IWR, Chapter 62-303 F.A.C.) on data from STORET.

d. Environmental Research and Design, Inc. 2003: assessment based on intense data collection during two months of the year (wet and 

dry season collections) for 2000-2002.

e. Janicki Report (2003b): draft report to the CHNEP on water quality based on status and trends, and IWR assessment of period of

record data (all available data). March 2003.

f. Tetra Tech, Inc., (2003): water quality assessment of the SWFFS area based on unofficial assessment using IWR and

status and trends of data from period-of-record (all available data)

I: Linkages Between Water Quality and Attributes 

This section provides specific examples of critical linkages between water quality 

stressors and valued ecosystem components. This list should not be considered exhaustive. This 

section will examine how deviations, from a defined baseline, in the chemical and physical

parameters measuring water quality, stress the ecological system by affecting the health and 

distribution of the indicators that describe the system’s attributes. The SWFFS differs from other 

similar feasibility studies, in particular IRL-South and Florida Bay / Florida Keys, in that causeand-effect research within the study boundary has been limited and technical-policy documents 

are few in number. In the absence of local information, WQ data will be assessed for potential 

linkage based on benchmarks established in surrogate studies. 

 Phytoplankton and SAV

i. Phytoplankton and SAV species have a preferred and tolerable 

range of salinity. When salinity falls outside of these ranges the SAV is 

negatively impacted and may result in a reduction in densities and distribution 

(Chamberlain and Doering 1998). Increases or decreases in salinity may give one 

species a competitive advantage over another (Livingston 1987; Zieman 1982). 

 Benthic Communities and Fish Populations

i. Salinity is a "master ecological variable" controlling community

structure and food web organization in coastal systems (Myers and Ewel, 1990).

Negative impacts to oysters can lead to shellfish closures. 

ii. Alterations in the salinity regime places stress on the sensitive 

life history stages of many estuarine species (Odum 1970, Chamberlain and 

Doering 1998b). 

▪ Mangroves 

21 
FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

i. Mangrove communities are sensitive to salinity levels.

Where freshwater flow has been insignificant over a long period of time, 

and salinity levels increase above historic levels, mangroves displace 

cypress and wetland plant communities. 

DO

 Phytoplankton and SAV

i. As a result of primary production, daylight levels of DO can

actually reach supersaturation levels in the presence of phytoplankton blooms or 

thick stands of macrophytes. However, both phytoplankton and SAV utilize DO 

and, in the dark, are a net sink for DO, this can result in hypoxic and sometimes

anoxic conditions (Mitchell-Tapping et al., 1998) 

 Benthic Communities and Fish Populations

i. Hypoxia (low dissolved oxygen) can be a significant problem in

certain estuaries, especially those receiving excessive nutrient loads, impacting

the health of fish and shellfish populations (EPA 2000b). 

ii. The response of benthic communities to alterations in sediment 

and water quality is relatively well understood and is often expressed as changes

in community structure, density, and diversity (for review, see Mitchell-Tapping 

et al., 1998; EPA 1999). 

• Sediment chemistry

i. Increased nutrient loading, suspended solids and dissolved 

organic material from the watershed can result in higher BOD, higher sediment

oxygen demand (SOD) or both and, consequently, hypoxia or even anoxia, 

especially when freshwater flows produce a density stratification (CDM, 1998; 

Turner, 2001; cf. Doering and Chamberlain, 1997). 

ii. Anoxic conditions can result in altered redox conditions and 

altered chemistry in the sediment 

Total Suspended Solids and Water Clarity (e.g., Turbidity, 

TSS, Color)

 Phytoplankton and SAV

i. Inorganic suspended sediments, organic nonchlorophyll-based 

detritus, and, of particular importance in south Florida, humic materials

(McPherson et al. 1996) may reduce water clarity and shade out SAV. A

statistically significant inverse correlation has been reported between the depth of

the deep edge of a seagrass bed and color and turbidity in southern Indian River 

Lagoon; preliminary targets have been established based on WQ observed at

these deep seagrass beds (Crean et. al., in review). 

ii. Because seagrasses are rooted plants attached to the bottom,

reduced light reduces photosynthesis, growth, and reproduction. This condition is

22 
FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

cited as a major source of seagrass decline in Florida estuarine systems (Durako

1988). 

iii. Under certain circumstances, dissolved organics (e.g., humics,

etc.) and attendant water color and clarity have been thought to reduce

undesirable algal growth under high nutrient conditions (McPherson et al. 1996).

iv. SAV need suitable substrate for successful recruitment and

establishment. Deposits of silt / muck can displace or modify normal substrate in 

the estuary and contribute to the decrease in extent of SAV beds. 

 Benthic Communities and Fish Populations

i. Suspended solids may clog gills and interfere with filtering and 

respiration of oysters (Cake 1983). 

ii. Humic materials can influence the chemical speciation, 

bioavailability and, in some cases, toxicity of certain metals and organics 

(McCarthy et al. 1994). 

 Shoreline Habitat functionality

i. Sediment load caused by dredge and fill operations and in runoff

from shoreline construction has been identified as a cause of mangrove loss and 

salt marsh destruction. 

Nutrients (macro- and micronutrients)

 Phytoplankton and SAV

i. Nuisance algal blooms: Tampa Bay National Estuary Program 

produced an empirical regression-based WQ model that showed strong 

relationship between TN load and Chl-a (as a measure of phytoplankton

abundance; Janicki and Wade 1996). A similar relationship has been established

for the C43 Basin / Calooshatchee River (Janicki Environmental, Inc. 2003). 

ii. Nutrification can lead to subtle responses such as changes in

communities at the species level, altered rates of biogeochemical processes (e.g., 

nutrient recycling, sediment oxygen demand, etc.), and shifts in seasonal patterns

(i.e., spring versus summer primary production) or magnitude of variability (for 

review, see Cloern, 2001; EPA, 2001). 

iii. Resource competition, not just in terms of N or P, but also their 

specific form (e.g., concentration of ammonium to nitrate) can also result in

species shifts. Many organic N molecules are not readily available to 

phytoplankton, while many organic P molecules are, due to the activity of 

phosphatase enzymes (Vitousek and Howarth, 1991).

iv. Nutrients can trigger a thick growth of epiphytes which can

reduce the amount of light that can reach the surface of the seagrass blade 

(Murray et al. 1999). 

v. Relatively minor changes in nutrient input can lead to sharp 

reductions in the productivity of seagrasses, which can lead to broad habitat 

changes (Livingston 1984). Encourages growth of more nutrient tolerant species 

23 
FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

that cause undesirable effects such as mono specific communities which decrease 

the value for fisheries and benthic invertebrate species. 

vi. Unnaturally low ratios of silicon (Si) to P or Si:N (due to 

increases in P or N) are thought to favor the selection and possible ascendancy of 

lightly-silicified diatoms and non-diatoms (Dortch & Whitledge 1992). 

 Sediment Chemistry

i. Nutrification can lead to altered rates of biogeochemical 

processes (e.g., nutrient recycling, sediment oxygen demand, redox, etc. CDM, 

1998, Turner, 2001; for review, see Cloern 2001), which, in turn, can lead to 

further changes in water quality (e.g., solubility of metals). 

ii. Nutrification can also lead to saturation of soils where substrate

becomes a source, and not a sink, for additional nutrients (internal loading). 

Toxicants

 Benthic Communities and Fish Populations

i. Both acute and chronic effects have been reported for both

organic and inorganic toxicants to a wide variety of aquatic species (National 

Toxics Rule, 57 FR 60848, December 22, 1992; USEPA 2002 and references 

therein, Wiener et al. 2002). 

ii. Many of these substances are either insoluble in water or tend to 

associate with particulate matter that flocculates (i.e., “salting-out") often

resulting in concentrations much higher in the estuarine sediments than that 

observed within the overlying water column. 

 Upper trophic level predators, including listed species

i. Persistent bioaccumulative toxicants (PBTs) can pose a risk to

upper trophic level predators (USEPA, 1997b, Rumbold, 2000) 

 Human health

i. Persistent bioaccumulative toxicants (PBTs) can pose a risk to

humans (EPA, 2002 and references therein) 

24 
FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

J: Model 

25 
FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

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Addendum

SUMMARY FORM (3 PAGES)

SOUTHWEST FLORIDA FEASIBILITY STUDY – 

CALOOSAHATCHEE ESTUARY 

HYDROLOGIC EVALUATION PERFORMANCE MEASURES 

Name of Performance Measures Document : S-79, Shell Point, and San Carlos Bay 

Freshwater Inflow

Status (date this 3 page summary created/revised): 12 May 2005

For: 5/12/05 DRAFT of full Performance Measures Document (attached). Previous 

Draft 4/20/05

Category: Hydrologic – (Water Levels, Flow Volumes) 

Justification: The Caloosahatchee River is the major source of freshwater for the 

Caloosahatchee Estuary and southern Charlotte Harbor aquatic environment. The river bisects its 

watershed and now functions as a primary canal (C-43) that conveys both runoff from the 

Caloosahatchee watershed and regulatory releases from Lake Okeechobee. The C-43 has 

undergone numerous physical changes to facilitate increased freshwater discharge for flood 

protection and meet water supply demands. Together, these physical changes and alterations of

the natural freshwater inflow to the Caloosahatchee Estuary have caused unnatural large scale 

fluctuations in the salinity and water quality within the area above Shell Point, as well as 

reduction in environmental stability for the San Carlos Bay area. The area’s biotic richness and

significant economic value are threatened by long-term shifts in water quantity and quality.

Description of Performance Measure: Reduce the high variability in freshwater inflow 

to the Caloosahatchee Estuary, thereby restoring the full range of salinity along its longitudinal 

axis required to support naturally occurring conditions for estuarine biota. This can be

accomplished by: (1) reduction of wet season high flow from the watershed, capturing and storing 

this water, and then releasing it during the dry season in a more environmentally sensitive and 

beneficial manner to estuarine resources; and (2) reducing discharges from Lake Okeechobee to

the Caloosahatchee Estuary. 

SWFFS/CERP Targets & Current Condition: 

Ecological Performance targets 

1. (a) Maintain a 30-day moving average salinity < 10 ppt during the dry season at the Ft. 

Myers continuous salinity sensor (near the surface at the Ft. Myers Yacht Basin), such that 

Vallisneria americana (tape grass) in the Beautiful Island area does not decrease below 20%

coverage and blade length is > 10 cm (values are provisional and may be adjusted after current 

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research (MML 2004 and 2007 reports) are evaluated); (b) Daily average salinity shall not exceed

20 ppt at Ft. Myers more than once every two years, and neither shall the 30-day moving average

salinity of 10 ppt (MFL Rule: SFWMD 2000); (c) Limit the occurrence of average monthly 

salinity <15 ppt at the Cape Coral Bridge sensor, so salinity > 20 ppt is promoted in Iona Cove, 

which is supportive of minimum seagrass density (coverage > 30% at 1 meter water depth and 

average blade length > 10 cm - values are provisional and may be adjusted upon further research); 

and (d) Maintain daily salinity at Piney Point > 5 ppt, so that minimum conditions are provided

for the recruitment, survival, and growth of juvenile oysters upstream of Shell Point during March

– October (juvenile oyster growth > 2.5 mm a month; recruitment > 3 spats per substrate shell a

month; and mortality < 20% per month - values are based on information interpreted from Volety 

et al. 2003). 

2) Maintain an average monthly salinity > 25 ppt, as measured at the Sanibel Causeway 

Bridge near surface continuous sensor, so that historical seagrass density and coverage in the San 

Carlos Bay area (as determined from previous surveys, hydroacoustic monitoring, and aerial 

photography) is protected and restored to a previous condition (at least circa Harris et al. 1983) 

that includes reestablishment of continuous coverage at deeper depths in the San Carlos Bay area 

between Shell Point and the Sanibel Causeway. 

Hydrologic performance targets to achieve the Ecological targets

1a). For each alternative, compare the number of times that mean monthly inflows from the Caloosahatchee 

watershed fall below a low-flow limit of 450 cfs, measured at S-79, during October to July . The alternative 

with the fewest number of times that monthly average flows fall below 450 cfs will be considered better for 

protecting aquatic vegetation, oysters, and fish communities. 

1b). For each alternative, compare the frequency that the mean monthly low-flow limit of 450 cfs through

S-79 from the watershed was not met for just one month (not followed by another month below this lowflow limit), as well as the frequency for 2, 3, 4... etc. consecutive months. The water management

alternative with the fewest number of consecutive months below 450 cfs will be considered better for 

protecting estuarine aquatic resources. 

1c). For each alternative, compare the frequency that the mean monthly low-flow limit of 450 cfs through

S-79 from the watershed was not met for just one year (not followed by another year with months below 

450 cfs), as well as the frequency for 2, 3, 4...etc. consecutive years. The water management alternative 

with the fewest number of years and consecutive years with average monthly flow occurrences below 450

cfs will be considered better for protecting estuarine aquatic resources 

1d). Couple the hydrodynamic model with the Vallisneria model to estimate plant coverage and other

metrics within the limits of the model. The alternative that provides the best Vallisneria model results for 

the region upstream of U.S. 41 Bridges in Ft. Myers will be considered more desirable. 

2a). For each management alternative, compare the number of times that mean monthly inflow from the 

watershed exceeds 2,800 cfs at S-79. The alternative with the fewest number of times that this criterion is 

exceeded at any time of year will be considered better for protecting both SAV and juvenile oysters at Shell 

Point and upstream. Additionally, a better ranking will be given to the alternative with the least number of

discharges above these limits during March through October, in order to limit critically low salinity 

conditions from occurring both upstream and downstream of Shell Point, which threatens estuarine 

resources, including SAV and juvenile oyster recruitment and survival 

2b). For each alternative, compare the frequency that the mean monthly inflow from the watershed, 

measured at S-79, exceeds 2,800 cfs for just one month (not followed by another month above this limit), 

as well as the frequency for 2, 3, 4... etc. consecutive months. The alternative with the fewest consecutive 

months that violate this criterion throughout the year will be considered better for protecting estuarine 

resources, including juvenile oyster recruitment and survival. Additionally, a better ranking will be given to

the alternative with the least number of discharges above these limits during March through October, in

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order to limit critically low salinity conditions from occurring both upstream and downstream of Shell 

Point, which threatens estuarine resources, including SAV and juvenile oyster recruitment and survival 

3a). For each alternative, compare the number of times that mean monthly and mean weekly inflows from

the watershed exceed 4,500 cfs at S-79 (weekly is important for protecting oyster recruitment and survival). 

The alternative with the least number of times flows exceed these limits will be considered better for 

protecting the estuarine resources, including those downstream in the San Carlos Bay region. Additionally,

a better ranking will be given to the alternative with the least number of discharges above these limits 

during March through October, in order to limit critically low salinity conditions from occurring both

upstream and downstream of Shell Point, which threatens estuarine resources, including SAV and juvenile 

oyster recruitment and survival. 

3b). For each alternative, compare the frequency that mean monthly and mean weekly inflows from the 

watershed, measured at S-79, exceeds 4,500 cfs for just one month and 1 week (not followed by another 

month or week above this limit), as well as the frequency for 2, 3, 4...etc. consecutive months and weeks. 

The alternative with the fewest number of consecutive months and weeks that violate this criterion will be 

considered better for protecting aquatic resources, including juvenile oysters. Additionally, a better ranking 

will be given to the alternative with the least number of consecutive discharge periods above these limits

during March through October, in order to limit critically low salinity conditions from occurring both

upstream and downstream of Shell Point, which threatens estuarine resources, including SAV and juvenile 

oyster recruitment and survival. 

4). For each alternative, compare the frequency distribution of monthly average freshwater inflows through 

S-79 for the entire period of record being evaluated. The alternative with the frequency distribution of

inflows that best approaches the range (EST05) defined in the main Performance Measures Document will 

be considered better for protecting estuarine resources, while further promoting biotic diversity. 

Specifically, the alternative that maximizes up to 75% of flows from S-79 in the 450 to 800 cfs and almost

all the remaining flows in the 800-2800 cfs range will be considered the most desirable. 

 The preferred flow distribution (EST05) may change as more information is provided

regarding: predevelopment flow and salinity conditions; natural variation; what salinity 

conditions were naturally (historically) associated with droughts and flood events; and what flows 

are needed to protect and restore the biotic features in the current and future developed system. 

Rationale: The Caloosahatchee River is the major source of freshwater for the

Caloosahatchee Estuary and southern Charlotte Harbor aquatic environment. The Caloosahatchee

Estuary and downstream region supports a wide diversity of estuarine organism of environmental

and commercial value. Alteration to the natural freshwater inflow to the estuary have caused

unnatural large scale fluctuations in the salinity and water quality within the area above Shell 

Point, as well as reduction in environmental stability for the San Carlos Bay area. The resulting 

impacts to seagrass, oysters, benthic invertebrates, and fishes can be dramatic and long lasting. It

is the goal of the Southwest Florida Feasibility Study (SWFFS) and relevant CERP efforts to

reduce the high variability in freshwater inflow to the Caloosahatchee Estuary, so to restore a full

range of salinity along its longitudinal axis that is supportive of naturally occurring estuarine 

biota. This goal can be accomplished by reducing high flows during the wet season, capturing and

storing this water, then releasing it in a more environmentally sensitive manner that is beneficial

to estuarine resources during the dry season. 

Modeling Evaluation Protocol: Regional and subregional models will be used to 

simulate historical (base) and predicted flows to the estuary with and without SWFFS and CERP

project features for each alternative considered. Natural system flows to the Caloosahatchee

Estuary from its watershed and tidal basins may also be considered in order to compare flows

associated with the developed basins. Output (flows) from the above model runs will be used to 

evaluate the level that hydrologic targets are achieved for each alternative and base condition.

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FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

Model output will be used as input for the estuarine salinity model to further assess changes in 

salinity. To help evaluate if ecological goals will be met, the estimated salinity will be used to 

assess the impact on key biota by employing habitat suitability indices related to salinity. 

Monitoring Assessment Protocol:

1). Define and assess appropriate attributes (specific species and/or community values) to 

ascertain if this project’s ecological goals are attained and there is a discernable positive impact

on the estuary, specifically including SAV, oyster, and fish as follows: 

a). Routinely (at seasonally important intervals) monitor SAV coverage, density, and

canopy height to at 

 least 1.5-2.0 m depth at key species locations. 

b). Routinely monitor (at seasonally important intervals) oyster survival and recruitment 

at key locations. c). Routinely monitor (seasonally) water quality, including temperature, D.O., 

salinity, nutrients, 

 chlorophyll, suspended solids, and water clarity along the longitudinal axis of the 

estuary (S-79 - 

 Sanibel Causeway and into lower Pine Island Sound and Matlacha Pass). 

d). Monitor routinely (at appropriate seasonal intervals) species and biotic groups of 

concern as separately

defined in performance measure documents and the CE conceptual model. At a

minimum, insure the 

 Monitoring Assessment Plan (MAP) effort within RECOVER is being fulfilled. 

2). Scientifically assess and publicly agree what constitutes desirable natural variability

(predevelopment 

conditions) related to salinity and causal freshwater inflow from S-79 and the tidal

basin. 

3). Install and monitor flow gages in downstream tidal tributaries to begin assembling a

long term data set to: verify model predictions of flows; determine actual amount and timing of 

tidal tributary flows related to MFL requirements for achieving the salinity criteria; and to help 

assess flow impacts on biota being monitored for CERP (RECOVER). 

4). Monitoring S-79 discharge adherence to the selected alternative flow distribution. 

5). Continue to maintain and monitor existing 7 salinity recorders and other permanent

sensors in the Caloosahatchee Estuary. Install new sensors to monitor salinity and other water 

quality parameters of concern at key locations for VEC. Suggest additional sensors be located in 

western San Carlos Bay, lower Pine Island Sound, and Matlacha Pass. 

6). Assess limits of SAV morphology for providing suitable habitat as a VEC and its 

relationship to flow, salinity, and water quality conditions. 

7). Finish development of the: tape grass model; Caloosahatchee Hydrodynamic/Salinity 

Model; a water quality model component; habitat suitability models; and a seagrass model for the 

lower estuary. 

Comments: 

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FINAL - Caloosahatchee & Charlotte Harbor CEM 22 May 2006 

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