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## CALOOSAHATCHEE ESTUARY AND CHARLOTTE HARBOR CONCEPTUAL MODEL

A: Model Leads

Tomma B a rnes, South Florida Water Manage m e nt Di strict

Darren Ru m b old, So uth Fl orida Water Managem e nt District
Mark Salvato, U.S. Fish & Wildlife Service


## B: Introduction

The Caloosah atchee Estuar y and Charlotte H a r bor are located on th e lower we st coast of Florida. The Caloosahatch ee Rive r w a s originally a shallow, m e andering river with headwaters in the proxim i t y of Lake H i cpochee and tidal influence al m o st t o La Belle. To acco mm o d ate navigation, fl ood co ntrol, and land recl am ation needs, the freshwater portion of the river was reconfigured into a canal known as C- 43. Man y can als were co nstructed alo ng t h e banks of the river in support of the m a ny ag ricultural co mm unities asso ciated with the river. In addition, thre e lock-and-dam structures (S-77, S-78 , and S-79) were added to cont rol flow and stage height. The Caloosahatch ee River wat e rshed includes the ad jacent basins drained by the river from the Charlotte Ha rbor estuarine sy ste m whi c h includes San Carlos B a y , Matlacha Pas s , Pine I s land Sound and t h e estuaries and nearshor e waters asso ciated with Sanibel Island, Captiva, North Captiva and the I m m okale e Rise ar eas
Toda y , the Caloosahatchee River exten d s 105 km from L a ke Ok eechobee to San Carlos Bay

. The freshwater portion ranges from 50 m to 130 m in width and 6 m to 9 m in depth. Man y of the original bends remain as oxbows along both si d es of the canal. The wi dth of the estuarine portion is irregular, fro m 160 m in the upper porti o n to 2,500 m downstream at San Carlos Bay (Scarlatos 1988). The narrow section extends from Fr anklin Loc k and Dam t o Beautiful I s land. 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 dem a n d (Drew and Schomer 1984).

The tidal Ca loosahatchee basin includes por tions of Lee and Charlotte Counties. The estuary between Franklin Lock and Sh ell Point is 42 km long and is bordered b y Fort M y e r s on the southern shore and Cape Coral on the northern shore. Water disc harges fro m the Caloosahatch ee pas s Shell Point and enter the Gulf of Mexico at S a n Carlos B a y. Because of the long and narrow configuration of the estuary
, cha nge s in wind, tide, runoff, or precipitation can have effe cts o n estuarine fe atures such as flow, wa t e r d e pth, salinity, and turbidit y. Therefore, d u e to the dynam i c nature of the estuary , characteriz ation of the s y ste m is difficult. Major changes in the h ydrolog y of t h e Ca loosahatchee w a ter s hed are the result of significant modifications i n land and c a nal deve lopment, as well as water m a nagem e nt pol icy

. Adverse ecological im pacts in the estuary have o ccurred as a re sult of hy drologic a l changes in the tim ing, distribution, quality, and vol ume of fresh water released into t h e estuary fr om th e watershed an d Lake Okeechobee (SFWMD 1999). Despite these im pacts, the Caloosahat chee Estuary conti nues to be an im portant en vir onm ental and econom ic res ource. Understanding how this sy stem responds to stre ssors will provide a basis for well-informed m a nagement decisions.

Charlotte Harbor is Am erica’s 17 th largest and Florida’ s second largest open water estuary . It has a broad barrier island chain, la rge parts of which are in public ownership: its mangrove shoreline is largely i n tact and in pu b lic manage ment. The Harbo r is do m i nate d by

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rivers that flow into the coastal are as. Unlike other estuaries in Southwest Florida that are m o st influenced by the Gulf of Mexico, Charlotte Har bor’s speci al char acteristi cs a r e creat ed by la rg e rivers, such as the Caloosahatchee. Large fluctu ations of seasons strongl y affect the salinity and water char act eristics in Charlotte Harbor. Geographically, the watershed stretches from th e he a d waters of the Peac e Rive r in Polk Count y t o the southern end of Estero Bay in Lee Cou n t y , a distanc e of m o re than 10 0 m iles.

The m odel boundar y for t h e Caloosahatchee Es tuary and Charlott e Harbor Co nceptual Model extends east to the S-79 structure. This is th e final downstrea m struct ure and m a rk s the beginnin g of the Caloosahatchee Estuary. Also known as the W.P. Franklin Lock and Dam
, this
structure mai ntains specif i ed wate r le vels upstr ea m , regulate s freshw a ter discharge into the estuary , and acts a s an im p e di m e nt t o saltwater i n trusion to the river. From ther e, the m odel extends south w est to the n o rthern bou n d ary of Es ter o Bay and in to the Gulf of Mexico through Big Carlos P ass and includes a freshw a ter plu m e that extends ap proxim a tely 3 m iles offshore

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

m odel's western boun dar y extends 3 m i les offshore of Sanibel and Captiva Islan d s, making a turn through Captiva Pass. 

## C: External Drivers and Ecological Stressors

External Drivers
Water Management Water Managem e nt practices have result ed in drastic hy drol ogic and habitat alterations to the Caloosahatchee Estuary and Charlo tte Harbor systems in ord e r to conve y m o re watershed runoff and in clude regulator y releases from La ke Ok eechobee. Th ese changes have caus e d l a rge fluctuations i n the volum e, tim ing, and frequency of freshwater inflow to the estuary and h a ve had an overwhelm ing impact on th e ecolog y of the estuarine sy stems through the alteration of salinity zonation.

Natural Phenomenon

Sea level rise is an im portant natural phe nom enon that is causing th e inland m ovem e nt o f marine conditions int o the estuary transi tion z one (Ta m p a Bay Regional Planni n g Council, 19 93, Wanless et al . 1994, Meeder et al. 1996,). Sea level h as been rising along Florida's west coast and is projected to rise at an accele r ated rate becaus e of global war m ing (Ta m pa Bay Regional Planning Council, 1993). The inland m ove ment of m a rine con d itions due to sea level r i se is happening independent from so cietal-dri ven stressors.

Growth & D e velopment Changes in land use of a result of incr eased growth and development along with agricultural dem a nds have led to loss and frag m en tation of coastal and shoreline habitat, and changes in water use and an increase i n wate r dem a nds. Decreased water quality, resulting from an increased input of nutri ents and dissolved organi c s into the s y stem , has al so had an effect on this urban and agriculture pressure.
An additiona l ecological stressor is tha t placed on the natural syste ms by boa ting and fishing pressures. The need for navi gati on from the east coast through Lake Okeechobee to the
west coast h as re sulted in the dredging and the channelization of the original Caloosahatchee River to the current C-43 canal. The continue d cha nnelization o f the C-43 has had a profound i m pact in decreasing the am ount of submerged aqua t i c vegetation within the est uary . Further m or e increases in manatee m o rt ality and decr eases in na tive 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 Flo w Altered hydrology and fre shwater flow is one of the predom inate stressors of t h e sy stem and takes th e for m of ex cessive w a ter withdrawals (de m and) a nd over drainage. This c a uses changes in the tim i ng and qualit y of the watershe d runoff to the estuary and harbor, which n o w includes regulatory releases fro m Lake Okeechobee. These alterati ons result from providing f l ood protection and water supply to a growin g agriculture and urban po pulation. The altered hy dr o l og y is facilitated by the phy s ic al changes made in th e watershed, which include t h e developm ent of a

co m p lex network of secondar y canal s, enlargem en t of C-4 3 t o conve y more water, and the addition of th ree water con t rol structures on C-43, which connect the canal to Lake Okee chobee. Acco m p any i ng these hy drologic changes is a de cr e ase in wat e r quality
, m a rk ed by increases in turbidity and nutrient loading, cha nges in water residence ti m e in the estuary , and alteration in the natural salinity regim e

. Altered estu a rine and harbor salinity has resulted from man-m a de hydrological

m odifications that have dramatic ally altered the natural quantit y , quality , tim ing, and distributi o n of flows to the estuary , o f ten without proper rega rd to the biol ogical integrity of the estuary (Haunert et al., 2000) . During the wet season, rainfa ll runoff that was historically retained within the undeveloped watershe d now reaches the river in greater volume and less time (USC OE, 1957). Addi tionall y , t h e constructio n of S- 79 has confined the estuary b y restricting freshwat e r/low salinity waters fro m the upper r eaches of the estuary duri n g the dry season. Alte ra tions in the de live r y of fre s h wa te r a t S-79 c a u s e s a linity to va ry wide l y i n tim e a nd s p ace (USCOE, 1957). Rapid a nd u nnatural fluctuations i n salinit y hav e contributed to m a jor impacts on subm erged plant abun dance and distribution, in cluding a loss of the natural gradient of grass species bet w e e n Downtown Fort My ers and the m outh of the Caloosahatchee Ri ver.
The estuarine flora and fa una are sensi tive to fresh water rele ase s and disruption of the volum e, distributio n, circulation, and t e m poral patterns of fresh water discharges could place
severe stress on the entir e ecosy stem . "Such sa lini t y patterns a ffect product i vit y , pop ulat ion distributio n, co mm unity c o m position, predator-pre y interactions, and foo d web structure in the inshore mari n e habitat. In many wa ys, salinity is a m a ster e c o logical variable that controls i m portant aspects of co mm unity structure and food web organization in coastal sy stems" (My e rs and Ewel, 19 90).

Habitat Alteration and Loss

Habitat alter a tions to the estuary and harbor have also i m p a cted the pre sence and abundance of species historically found within the s y stem . These alterations include conver s ion of wetlands, dredging of channels and spoil disposal, changes in s horeline, snagging of navi gatio n hazards, and decrease in spatial extent of the estuari es 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). Chang es in the ph y s ical dimension of the estuary , whi c h resulted from the ad dition of S-79, reduced (or eli m ina t ed) the upstrea m oligohali ne portion of the estuary , especially duri n g the dr y season (Cham b erlain and Doering 1998a). Th is salinity zo n e is an im portant nurser y area, feeding area, and refugia for ju venile stages of desi rable sport an d co mmercial fishes. Construction and operation of the w a ter control
structures m a y interfere with m i grations pattern s of many estuarine species, by acting as a barrie r between the freshwat e r and saline water habitats a nd have hist orically resul t ed in deaths of
manate es atte m p ting to pass through the se structures.

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Changes in Water Quali t y & Increa s e d Sediment Contaminants Nutrients and dissolved organics enter t h e sy stem as a result of an thropogenic activities in the watershed. The greatest loadin gs co m e fro m agricultural runoff facilitated by water management practices, urb a n runoff, and poi nt s our ce discharges to the estuary fr om sewage treat ment pla n ts (Post, Bu ckley
, Schuh, and Jernigan and W. D e xter B e nder an d Associ ates, Inc 1999, Drew and Schom er 1984). I n a ddition, atm o spheric deposition contri butes to nitr ogen loading (Squires et al. 1998). These constituents lead to incr eased phy t oplankt on production and interact with altered salinity patterns, increased w a ter color, and se diment loading to reduce li ght penetration. This can lead to declines in sub merged plant abund ance. Increases in areas of lo w dissolved oxygen and shifts in species com position of benthic invertebrates to m o re pollution tolerant organism s are linked to increased nutrient level s (Barbour et al. 19 96). Toxins which include pesticides, fungicides, herbicides, coliform s from sewage treatment plants, oils, grease s, m e r c u r y , and other heavy m e ta ls such as copper and zinc can be introduced into the sy ste m fro m urban developm ent, agricultu r a l practices, and boating. Direct toxic effects have been docu m ented in other south Florida sy stems on zooplankton and fish. Indirect effect s can occur through the pr ocess of bioaccu m ulati on or biom agnification through the food w e b, increasing the toxic load to top predators (Day et al. 1989) . Studies in the Caloosahatchee Watershed have been unab l e to detect serious c ontamination of sedim ents with toxi ns (La Rose and McPherson 1 983, Fernandez. et al. 1999). It is reco mmended that m onitoring be continued. Boating and Fishing Pres sure Boating pressure is a str essor to the estuary through direct impacts such a s seagra s s scarring, sedi ment re suspe n sion, wake e r osion, a nd construction o f boating channels. In addition, boat collisions are the l ead ing cause of hum an-rel a ted m a natee mortalit y (W. Dexter Bender and Associat es 1 995). Fishi n g pressure fro m sport and co mmercial fisheries has i m p acted st anding stocks of man y species (Post, Buckley, Schuh, an d Jernigan, Inc. 1999) an d in turn impacted those species that depend on fish as their primar y food source. Recent resource trends for local fisheries sho w so m e incr ease as a re s u lt of cha nges in the m a n a ge m e nt proc ess (Muller e t al. 1996 , McMichael 1997).



## D: Ecological Attributes
Eight attribut es have been identified in t h e Caloosaha t chee Estuary and Charlotte Harbor as the biological or ecological indicators of environmental stress. Submerged Aquatic Veg e tation Community Structure, and Function

Subm erged Aquatic Vegetation (SAV), for the pur pose of this conceptual m odel, include onl y t h e vascular underwater plants that live thro ughout the estuary and i n near-coast waters. SAV play several roles in m a intaining an estua r y ' s health. The y pro v ide habitat and nur sery grounds for many fish and invertebrate co mm uniti es and are e s pecially im p o rtant in benthic based pri m ary productivit y. SAV and the organisms that live on t h em are i m portant food sources in the estuarine sy stem . M a natees, wate rfowl and wa ding birds rely heavily on seagra ss sy ste m s as forage areas. SAV help m a intain water clarity b y trapping fin e sediments and the y im p r ove water quality by taking up large quantities of nutr i ents that would otherwise accelerate th e eutrophicatio n of the estuarine sy stem

. Tape grass ( Vallisneria americana) is the dom inant subm erged aquatic vegetation i n the upper Caloos ahatchee Estuary and occ u rs in well-d e fined beds in shallow water. Vallisneria americana is an im portant habitat for a variety of freshwater and estuarine invertebrate and

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vertebrate species, including som e co mmerci ally a nd recreationall y im portant fishes (Bortone and Turpin 1999) . Additionall y, it can serve as a food source for the Florida manatee ( Trichechus

manatus ). Shoal grass ( Halodule wright ii), turtle grass (Thalassia t estudinum) , a nd m a natee grass (Syringodium filiforme) are the m o st c o mmon higher salinity grasse s in the Caloosahatch e e Estuary and Charlotte Harbor. Argopectin sp., the ba y scallop, prefers shoal an d turtle grass beds. Increasing sc allop populations to resem bl e histor ic distributions is currently a goal of the Charlotte Harbor Estuarine Program (CHNEP 1999). All species of SAV hav e a preferred a nd 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 Intracoa s ta l Water w ay have also shown negative im p acts to the se agrass es. The result h as be en a regional decrea se of seagra ss cove rage (Cham b erlain and Doerin g 19 98a). Th is decline negatively im pacts the fish and invertebrate

co mm unities. It also cau ses destabilization of sedim ents and a shift in primary productivi t y f r o m benthic m a croph y t es t o p h y toplan kto n , bot h of wh i c h provi de n e gative biofeedback to fu rther affect s eagras s beds. Oyster Ba r Community Structure, a nd Function Oy sters are sensitive to salinit y and siltation. The y require salinit y levels above 4-5 ppt (Loosanoff 1932) with an optim al salinity range between 14 and 28 ppt (Chanley 1 958, Galtsoff 1964) var y i n g with geogr aphical region. Higher sal init y levels increase negative effects fro m saltwat er predators such as oy ster drills (Hof stetter 197 7, W h it e and Wilso n 19 96) and the protozoan parasite P erkins us marinus (Derm o ) (Volety 19 95), th e prim ary oy s t er pathogen in the Gulf of Mexi co (Soniat 1 996). Derm o is estim ated to have kill ed 80% of th e oy sters in a bed under opt imal salinity a nd tem p erature with in Chesapeak e Bay (Andrews 1988). Presentl y , increased oli gohaline conditions have lim it ed dist ribution of oy sters in the Caloosahat chee estuarine sy ste m s. Oy ster bars provide several im portant func tions, i n cluding hab itat and food for other species. Wells (1961) lists 303 species that depend on o y ster bars either directly or indirec tly. Individual oysters filter 4 to34 liters of wate r per hour, rem o v i ng phy toplankton, particulate organic carbon, sedim ents, pollutants, and m i croor ganism s fro m the water colum n (Volety p e rs.

co m

. ). This process resul t s in greater light pe netration and prom ot es the growth of submerge d aquatic vegetation immediately do wnstrea m of the oyster bars. The epidem i o logy of Derm o disease coupled with phy s iological responses of oy sters in relations to environm ental and anthropogenic st ress will y i eld critical infor m ati on on conditions
necessary for healthy oy ster reefs. Sali nity a nd water quality conditions that y i eld enhanced distributio n of healthy o y ster reefs can be used as hy drol ogi cal targets for restoring and maintaining suitable salinity and water qualit y i n the Caloosahatchee Estua r y and Charlotte Harbor.

Mesohaline Benthic Co mmunity Structure and Function Open bottoms in the Cal oosah atchee Estuary and Charlotte Ha rbor are co mposed of mixtures of sand, m ud, shell, and bedro c k. M acroinvertebrates, in cluding m o llusks, are dominant ele ments of both the estuarine and tidal river Caloosahatchee and C h arlotte Harbor ecosy stems.
The num ber, diversity, dis p ersion, and conditio n of macroinvertebrates have been studied for decades, form ing a larg e and robust body of in f o r

mation on adaptations of numerous phy l a to the ph y s ical and chem ical conditions u n ique to estuaries. Nu mer ous studies have de m onstr ated that spatial and tem poral trends in m a croinverteb rate attributes vary in consistent form with variations in river flow, current speed, salin ity
, dissolved ox ygen, and f oodstuffs such as particulate organic carbon, phy t oplankt on, m a crophy t es, and prey. In recent y ears, a variety of

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studies have been published which indicate the ex te nt to which macroinverte b rate attributes c a n be related specifically to i n dependent va riables su ch as freshwat e r i n flow and salinit y alterations.

The m esoha line cla ms Rangia cu neata, (Bivalvia: Mactrida e), and Polymesoda carolineata (Bivalvia: Corbiculidae), are co mm onl y found associated with m ud and sandy bottom s in the Caloosahat chee Estu ary

. Both of thes e m o llusks re quire lower salinities and can be used as indicators of estuarine condition. Furthe rm or e, because mollusks leave behind their shells upon death, it is possible t o look at the death assem b lage to constr uct historical salinity regimes. Shell charact eristics such as si ze, shape
, and orn ame ntation vary according to salinity and can be used to const r uct historical salinity regi mes. The death assem b lag e , which is sam p l e d along with live co mm un ity, can be utilized as an indicator of conditions prior to recent alterations to the
sy stem and provide a useful target when co m p ared wit h 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 (Harri s et al. 1983, Estevez 1998, Lindall 1973). Within the estuary , seagrass

co mm unities provide critic al refugia for juvenile fi sh such as redfish, gro uper, snook, and spot ted seatrout. The decline in juvenile abunda nce and di stri bution of these and other s p ecies, along wit h the overall de cline in speci es richne ss m a y be related to a decline in this seagr a s s habitat and/ or a result of alterations in the s a linit y regim e and the tim ing of the freshwater dischar ges.
Co mmercial and recreational fishing pr essure has al so increased along t h e west coast of Florida. With this increase , ther e has been a decline in reported la ndings (Post, Buckley, Sc huh, and Jernigan and W. Dexter Bender an d Associat es, Inc 1999). In Lee County clear evidence for this decrea se can be s een with the spotted seatr out where ther e has been a de cline on catc h -perunit-effort fro m 1986 to 19 95 (Borto ne and Wilzbach, 1997).

The blue crab fishery is the largest, y ear-round fisher y in the upper and m i ddle portion of the Caloosahatchee River 

### and Charlo tte Harb or

. This commer cial fisher y is intensely fished virtuall y ever y da y of the y ear by several hundred cr ab traps and will be able to provide fishery landings data that can be correlated to other estuarine co m ponents to provide evidence of the overall productivity of the sy stem . Blue crabs a l so m ove fre ely about the sy stem ar e good

m onitors of localized changes in conditions re lative to tem p erature, salinity and other water quality parameters.

Manatee De mographics

Manatees are a very visible and publicly appreciated feature of the Caloosahatche e Estuary 

### and Charlotte H a rbor . The y have been listed by the st ate and federal governm e nt as an endangered species and are protected throug hout t h eir range. In the stud y area, the largest concentration of m a natees is found in t h e upper tid al reaches of the Caloosahat chee Estuary
, near the Orange River and the warm water outflow of the Florida Po wer and Light power generating plant (USFWS, 199 5).

The Florida manatee is an opp ortunist ic herb ivore, feeding on a wide variety of plants. Seagrass es, e s pecially V. Americana, can be an im portant food resource for manate es in the Caloosahatch ee Estuary

. Other critical require m e nt s for the m a natee ar e wa r m wat e r in winter

m onths and access to fresh water. Th ey prefer waters with sali n ities less th an 25 ppt, but can

m ove fr eely between fre sh and salt water (USFWS, 1999) Lee County l eads the west coast of Florida in the tot a l num ber of manatee deaths. Some of these deaths can be attributed to watercraft s, entanglement with crab lines, rope, or gill nets, and ingestion of m onofilament line or pieces of plas tic. Lee County also leads all other west coast

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counties in the num ber o f deaths in t h e categor ies of dependent calves, na tural cause s, and undeterm ined

. Shoreline Community Structure and Function

In 198 2 appr oxim a tely 6 7 4 ,26 0 acres o f m a ngrove forests occurred in Florida (Lewis et al ., 198 5). Approxim a tely 2,995 acres of mangrov es are found in the Lower Caloosahatchee River Subbasin (Post, Buckley, Schuh, and Jerni gan and W. Dexter Bender an d Associates, Inc 1999). In the Caloosahatchee Estuary and Charlo tte Harbor, m a n g roves support fish and macroinvertebrate co mm unities by providing protect ed nursery areas for fish es, crustaceans, and shellfish, and food f o r a multitude of important commerci al and recreational marine species such as snook, snapper, tarpon, jack, sheepshead , red drum , oy ster, and shrim p (Harris et al . 1983
, Lindall 1973) . Mangrove roots act to trap sediments and prevent shoreline ero s ion and provide attach ment surface s for various marine organis m s. Ad ditionall y , m a ngrove forest s provide hab itat for a highl y d i verse population of birds ( O dum et al. 1 982). Mangrove shoreline habitats have decre ased in spatia l extent and in function. Large area s of m a ngroves have been lost or frag mented th rough dredge-and-fill activ ities (National Safety Council 1998, Estevez 1998). In addition, m a ngr oves are sensitive to alte rations in upland drainage. In so m e are as, drainage for agricu ltural and ur ban dev e lopment has reduced ove rland flows of freshwater to the mangroves. This results in an increased am ount of concentrated runoff, which in turn changes the salinity balan ce, reduces the flushing of detritus, and washes nutrients directly i n to t h e estuary wi thout t h e benefit of filtration by the m a ngrove s y stem (E stevez, 1998). Algal Blooms Community Structure & Function

Periodic bloo ms of algae, including true algae, dinoflagellates, and cy ano b acteria or bluegreen algae have been reported within the marin e and freshwater portions of the Caloosahat chee Estuary and Charlotte Ha rbor. In m a n y inst ances these algal bloom s ar e me rely an aesthetic nuisance, however certain species producing toxi ns that kill fish, invertebrates, birds and mammal s (USGS 1988). Pigmented al gal bloom s t h at are toxic to the m a rin e environment are referred to a s “red tides” , while those produced by c y anobacteria in fresh water a r e ter m e d
cy ano b acterial bloom s (USGS 1988). Florida red tid e bloom s typically begi n in the Gul f of Mexico 40-80 m ile s offs hore and move slowly with the prevailing ocean currents toward southwest Florida. As the bloom progresses, the d e ns ity of red tide organisms in creas e to sev eral million cells in each liter of sea w a ter, an d the effected area expands to m a ny squa re m iles.

Red tides wi thin Charlotte Harbor can and have presented to marine ani m al s

. Marine algal toxins, such as brevetoxin, bioaccu m u late and are thereby magnified in the food chain, while anatoxins from fre shwater cy anobacteria af f ect the nerv ous sy stem

. There have been several documented ca ses in the field where bloom s of Karenia brevis , a brevetoxin that pr o duces neurotoxins and the m a jor species of ha r m ful alga l bloom in Gulf waters which causes red ti des, have killed both vertebrate and invertebrate species. At least 17 invertebrate species normally present in Tam p a Bay
, Florida, have been record ed absent immedi a tely after a red tide incidents (FMRI 2000) . Various species of bivalve shellfish, especially o y sters, clams and coquinas can

accu m u lat e s o m u ch toxin that they beco m e toxic t o both m a rin e ani mals and hum ans as well (MML 2002)

. During two of the largest recorded red tid e out bre a ks (1946– 19 47 and 1 953 –195 5) in southwest Florida catastrophic m o rtalities of marine anim als were recorded (FMRI 2000). Am ong the affected organism s during these periods were reports of dead bottl enose dolphi ns ( Tursiops truncatus ), sea turtles, and num erous fis h species. B ecause fish die quickly fro m exposure and contact with red tides the t oxins d o n o t have time to build up in t h eir tissue. Those fish exposes t o lower and hence sub leth al concen trati ons of red tide may accu mulate these toxins

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in their body. Such bioaccu m u lation of toxins in fish eaten that then eaten b y dolphins may a major fa ctor in the m a rine m a mma ls m o rtality in the study area. The largest r e d tide-associ ated dolphi n m o rtality i n volve d m o re than 740 bottlenos e dolphi n strandings along the Atlantic coast from June 1987 t o Ma y 1988. Although other i n fections were present in e x am ined dol phin carcasses, brevetoxin was suspected as the proxim a te cause of t h e m o rtality during t h is mass stranding. Along with toxin effects, algal blo o ms ne gatively influence aquatic organism s by depleting dis s olved oxygen concentrations in the water through their proliferation, death, decay and night l y r espiration (USGS 1988). Although coa s tal pollution has enhanced red tide bloo ms in other areas of the world, the Florida red tid es represent a natural phenom en on not caused by pollution. These bloo m s s e rve a purpose in the eco logy of Florida Gulf coast al regions (MML 2000).

Wading Birds Community Structure & Function

A num be r of ecological f actors ar e ne gativel y i n flu e ncing wading bird species in the Caloosahatch ee Estuary and Charlotte Harbor, ch ief am ong these are loss of shoreline habitat, decreased av ailability of SAV and fish with in the m a ngroves and littoral zones as well as potential infl uence fro m increased nutrients and conta m inant runoff

. Environm ental conta m ina n ts, such as pestic ides and heavy m e ta ls, used for a g ricultural and urban needs througho ut m u ch of South Flori d a pose a variety of p o tential threats to fauna, as they can be concentrated in organism s throug h food webs in the Caloosahat chee Estuary and Charlotte Har bor regions. These bioacc um ulat ed t oxins can have s i gnificant effects on the health of populations of m a croinvertebrates and fish, a nd ultim ately on the survival of wading bird species. Contam inants can also significantly aff ect aquatic fauna without being bioaccu m u lated, particularly f o r those species with gills or permeable surfaces exposed to water.
Many bird s p ecies can be affected by al gal to xi ns (USGS 1988). Most r e ports of

m o rt ality are from die-offs that occur in conjunc tion with a bloom that had wor k ed its way i n to that specie’s food chain

. D u ring a lon g duration out b r eak of K. br evis red tide on the Florid a west coast between October 19 73 to Ma y 1 974, large nu m b ers of aquatic birds, pa rticularly doublecrested cor m orants, Phalacrocorax auritus , red-breasted m e rgans e rs, M ergus merganser , and lesser scaup, Aythya affini s , were found m o ribund or dead in red t i de areas. Ov er an eight-week period several thousand lesser sc aup died (FMRI 2000). 

## E: Ecological Effects

Loss of Shoreline Habitat and Function Relationship of loss of sho reline habitat and functi on and shorelin e community structure and fu nction. The ecological functionality of shoreline habitat in the Caloosahatchee Estuary and Charlotte Ha rbor sy stem s is predom in antly co m posed of m a ngrove habitat. Urbanization and shoreline developm ent have resulted in the extensive loss of m a ngrove habitat along the Caloosahatch ee Estuary an d within Charlotte Harbor. Am ong the e c ological fun c tions carried out by m a ngroves are land formation (Warming, 1925; Davis, 1940), sedim ent stabilization, pri mary productivi t y , filtration of l a nd runoff, a b sorption and recharge floodwaters. The m a ngroves also serve as habitats and nurseries providing food and c over for a m u ltitude of native fish and wildl i fe (MacNae, 1968, Odum et al ., 198 2; Harris et al ., 1983; Dawes 1998). T h ese functions help to maintain wat e r quality , re cy cle nutrients, and control erosion (Harris et al ., 1983). In s outh Florida, m a n g roves have been destroyed by dred ge-fill operations to create real estat e, and port and industrial facilities. M a ngrove destruction results in a chain of reactions that affect estuarine

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and off shore production. In the Tampa Bay estua rine sy stem , one sim ilar in structure and function t o t h e Caloosahatchee, 44% of the m a ngr ove and salt marsh land has been lost due to construction and resultant turbidit y fro m runoff a nd polluti on (Le w is and Estevez 1988). Thi s loss in the Tam p a Bay Estuary has been linked to declines in fin fish and commer cial shri m p ing in the region (Dawes 1998). Relationship of loss of shoreline habitat a nd fu nction an d wading b i rd community structure and function. Mangroves, the dom inant shoreline hab itat for the lowe r Caloosahatc h ee Estuary and Charlotte Ha rbor, carry out a num ber of ecologic a l functions; in particular this
ecosy stem serves as prim ary habitat an d nurser y gro unds for bot h wading bir d s species and their various prey organism s such as estuarine invert ebrates and fish . Productivit y in the shor eline
mangrove sy s t e m s ar e also depressed as a result of diminished upland flows of freshwat e r to the mangroves. It is these lo w salinity mangrove for ests have been recognized as critical n u rsery habitat for sp ecies such as blue crab, snook, tarp on, and lad y fish (Odum et al. 1982 , Gilm ore et al. 19 83, Lewis et al. 1985) . Much of thi s habitat has been lost or highl y m odified. In m a ny areas, freshwat e r upland flows to these mangrove sy stem s have been decre ased or d e pleted due to a rerouting of the water through canals. Changes in freshwater discharge have also altered the structure of mangrove forests. The red u ction and modification of this habitat type may represent a lim iting facto r in total population sizes of some estuarine-dependent species (Lewis 1990).

Altered Sali nity Regime Relationship of altered salinity regime and fisheries. Alterations in the salinit y regime places undo stress on the sensitive life histor y stages of m a ny estuarine species (E mery 1957, Odum 1970, Lindall 1973
, Perry and McIlwain 1986, Cham berlain and Doering 1998b). Wit h in the Caloosah atchee E s tuar y and Charlotte Harbor al tered s a linity regi m e s hav e i m pa cts on the

co mm unity s t ructure and function of fisheries, oy ster bars, SAV and benth o s. While estuarine species are g e nerally well adapted to cope with vary i ng salinit y conditions, larger shifts th ese conditions can be a proble m

. Such chan ges in the natural salinity r e gi m e and timing of freshwater discharges have resulted in a decline in juven ile fish abunda nce, distribut ion, and spe c ies richness. For exam ple, the egg stage of spotted seat rout. Trout eggs are neutrall y buoy ant at about 20-22 ppt (Pattillo et al. 1997). The y spawn during the warmer m o nths of t h e y ear (Lassay 1983). If large and protracted reductions in salinit y we re to occur durin g the su mmer m onths, it coul d lead to the reduction or elimination of an entire y ear-class of spotted seatrout. Relationship of altered sal i nity regime and oysters

. Alterations in freshwater fl ow have lead to dry s eason salinity increase s in the estuary a nd harbor. Salinity is an im portant fa ctor in determ ining the distributio n of coastal and estuarine bivalves. Adult oy sters in the Gulf of M e xico

norm a lly occur at salinities between 10 and 30 ppt but they tolerate a salinity range of 2 to 40 ppt (Gunter and Gey e r 1955). Short pulses of freshwater inflow can greatly benefit oy ster populations by killing predators, such as the southern oy ster drill a nd the welk that cannot tolerate low salinit y water (Owen 1953, Marshall 1954)
, while excessive freshwater inflows m a y kill entire populati ons of oy sters (Gunter 1953, Sc hlessel man 1955, MacKenzie, 1977). Relationship of altered sali nity regimes and SAV . Different species of SAV have different desirable sali n ity ranges. When salinity falls outside of these ranges the SAV is negati vely i m pacted and may result in a reduction in dens ities and distributi on (Cham b erlain and Doering 1998b). Increases or decreases in salinity m a y gi ve one species a co m p etitive advantage over another (Livi ngston 1 987)

. Tabb et al (1962) stat ed: “Most of the effects of man-m ade changes on plant and an im al populati ons in Flori d a estuari es are a result of alterations in salinit y and turbidit y ”

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

co mm unity st ructure and function br ou ght b y cha nges in the natural salinity regime has resulted

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in substantial losses of mesohaline benthic speci es, such as m o llusks and blue crabs along wi th a decrea se in larval and adult fish recr uitment into t h e estuary an d har bor. Relationship of altered salinity regime and algal blooms. Rese arc h has found that high

m o rt alities in estuary and harbor organi sm s such as t h e m a nat ee appear related to concentration and geograp hic distributi on of the red tide outbr eaks, in relati on to salinity, as well as th e persistence of the bloom in relation to the dist ributio n and exposu r e time by of the organisms to the bloom (Landsberg, J.H. and K. A. S t eidinge r, 19 98). An u nus ual num ber of manatee deaths were docu m e n ted in 1996 (U.S. Marine Ma mmal Commis s ion, 1996). The beginning and ending of this event coincided with an inshor e bloom of Karenia brev is in southwest Florida (B aden, 1996).Eight y one of 149 manatee deat hs associ ated with this bloom of red tide occurred in Lee Count y , primarily i n the Caloosahatchee Estuary (Dryden pers. com

. ). Fish m o rtalities associated with K. brevis events are very comm on, widespread, and im pact hundreds of sp ecies and various life history st ages. Brevetoxin is absorbed direc tly across the gill mem b ranes o f fish or through ingestion of K. brevis cells. Relationship of altered sal i nity regime t o manatee demographics. Algal blooms, such as red tides, present a m a jor threat towards m a natee populations is r e d tide which historicall y been responsible for an increase in m a natee m o rt ality . Alt hough m a rin e m ammal mortalit y associated with red tide is poorly known several m o rtalities h a ve been recorded in this region fro m this toxin. Red tide was linked to the deaths of seven manatees in 1963 near Fort My ers (La y ne 1965, Bossart et al 1998). More recently
, duri ng a 1996 die off of m a nat ees, a large num ber of m a natees aggregated in war m w a ters near the For t My er s power plant in the Caloosahat chee River. F i nal reports conclude that brev etoxins from a bloom of red tide were responsible for the death of t hose manatees. Toxins were found in the m a natee carca sses in the liver, kidne y, and lung tissues, and also in stomach contents (USFWS 1999). Manat ee deaths are often attri buted t o red tide. However, in 1996 their increased vulnerability w as due to t h eir congregating near this war m water refuge and circu m sta n ces of the es tuary when the tide occurred.

Increas e d M a natee Mortality Relationship of increased manatee mortality and manatee demographic s

. Manatee populati ons and their habitats in the Caloosahatch ee Estuary and Charlotte Harbor are continually threatened by hum an activi t y. The greatest present threat to manat ees in southwest Florida is the high rate of m o rality caused by watercraft collisions . Boat channels are often used by m a nat e es to travel fro m o n e region to another (Curran 1989, Sirenia 1993). Manatees do not alway s m ove out of the way of boats using these ch annels which mak e the m vulnerable to colli sions. Waterc rafts using shallow coastal areas for fishing and s ite seei ng also increase the likeli hood of a m a natee injury or death if the boat passe s over them

. The second m o st significant threat to manatees is the loss and d e gradation of habitat, d u e primarily to direct da m a g e by aquatic recre a tional and comme rcial boating activities, c o astal construction, and poll u tion from sewage dischar ge and storm water runoff (M MC 1992, S m ith 1993). The seagrass beds t h at m a natees rely on fo r foraging, m a tin g, calving inc u r direct damage from boat propellers (Zieman 1982). Propeller dredgi ng of b o tt om habitat by b o ats, prop eller wash, and wave wake disturbance cause boat i nduced turbidit y. Sediments around seagrasses beco m e unconsolidated and suspended. This delay s recolonization of the grasse s for two to five
y ears or lo ng er, depending on the species type.

Decr ease of SAV Relationship of decreased SAV and manatee demographics. Manatees depen d on the submerged aquatic vegetation for f ood and habitat i n the Caloos ahatchee Est u ary and Cha r lotte Harbor. Seag rass b e ds an d m a ngroves provide im p o rtant areas f o r m a nate e f o raging, calving,

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resting, and mating. Preferred manatee habitat in south Florida is characterized by the availabilit y of subm erged aquatic vegetation (Sm ith 1993).
Manatees are opportu nistic herbivores and f eed on a variety of submergent, em ergent, and floating vegetation with seagrasses com p rising t h e largest com ponent of their diet in s outh Florida (Hartman 1979, Ziem an 1982, Sm ith 1993). Manatees usually forage in shallow grass beds that are adjacent to deeper channels (Hart man 1979, Powell and Rathbun 1984). Some
manate es hav e been observed to return to the sa m e seagra ss beds y ear after y e ar and m a y show preference fo r certain areas (USFWS 1999). Relationship of decreased SAV and wading bird c o mmunity structure and function. Negative cha nges, na m e ly decre ase s, in SAV co mm unity structure and function has re sulte d in reduced nutrients and nurseries for w a ding birds or their prey . Substantial losses in m o l l usk populati ons and a decrease in larval and adult fish recruitm ent into the estua ry are a direct result of declining SAV populati ons in the est uary an d harb or. Fish densities are ty pically greater in grass bed ha bitat within south Florida’s estuarie s and coastal lagoons t h an in adjacent habitats (R eid 1954, Tabb et al. 1962, Roes sler 1965, Yokel 1975, Weinstein et al. 1977). The grass beds provi de protection from predation for animals living in it. The dense se agrass blades and rhizomes a sso ciated with t h e grasse s provide cover for invertebrates and small fis h es while als o interfering with the feeding efficien cy of their potential predators (Ziem a n 1982). Reduction i n size and h ealth of S AV beds ef fects 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 colum n is often blam ed for the disappearance and dim i nishing of previousl y healthy seagrass meadows (US EPA 1983). Because seagrasses are rooted pl ants attached to t h e bottom
, reduced light reduces photosynthesis, growth, and reproduction. This condition is cited as a major source of seagrass de cline in Florida estuarine sy stems. (Du r ako 1988). Increased nutrients, such as nitrogen and phosph oro u s, can lead to light depri v ation b y sti m ulating the growth of phy t oplankt on. Th ese bloom s cloud the water and severely di minish sunlight penetration (Livingston 1987). This turbidity can increas e to such a level that seagra sses persist only i n patches (Ziem a n 1982). Nutrients can also trigger a thick growth of epiph y t e s which can also block the sunlight before it can reach the surface of th e seagrass (Murray et al. 1999). In fact , nutrient input has such a n effect that relatively m i nor changes in water quality can lead to sharp reductions in the productivity of seagrasses which can lead to broad habitat changes (Livingsto n 1 984). Relationship of decreased SAV and fi sh eries community structure and function . A decline in the am ount of seagrass habitat/covera ge has occurred in th e Ca loosahatchee and Charlotte Har bor drainage. The consequences of this d ecline is a red u ction in pote n tial habitat for

a nu m b er of seagra ss depe ndent species , and espe c ial l y the juvenile life stage s of m o st estua rine dependent species (Virnstein 1987, Stoner 1984
, Zieman 1982). Specifically , larval gag ( Myct eroper c a microlepis ) use sea grass beds a settlement substrate after having hatched offs hore on natural ha rd bottom structures. The larvae settl e i n the higher salinity areas of San Carlos Bay and Pine Isla nd Sound in the spring of each y ear. Af ter attaining a siz e of abo u t 60 - 80 mm T L they m i grate offshore to ta ke up residen ce on offshor e reefs (Jory and Iverson 1989). Juveni le spotted seatro ut ( Cynoscion nebulosus ) use gras s bed s for protecti on from predation while adults feed on m a ny of the seagrass a ssociated species such as shrim p an d sm aller fish es (Pearson 1929
, Miles 1950, Perret et al. 1980).

Increas e d N u trients & C o ntaminants

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Relationship of increased nutrients and c ont aminants and al gal bl ooms community structure and function . Th e am ount of nutrients entering the Calo osahatchee River and Charlotte Harbor has im portant effe cts on the water qualit y of the s y stem

. Organis m s us e these nutrients, but excessive am ounts may have negati ve im pact s (Neilson and Cronin 1981) . Algal blooms and epiphy te growth may cause decre ased water clarity and block sunlight for aquatic plants (Day 1989). As algae die, organic deco m p osition de ple t es the oxy gen in the water (LaRose and McPherson 1983, Drew and Schom er 1984, Da y 198 9). Low levels of dissolved ox y g en can have negative effects on fish an d ot her aquat i c organism s (Hey l 1 998)

. Eutrophicatio n m a y also result in an increase in red tide bl oom s (Gore 1992). Relationship of increased nutrients and co ntami nants and w ading birds community structure and function . Natural communities in Sout h Florida are adapted to surfa ce wat e rs wit h a che m ic al co m position that contains l o w concentr ations of dissolved m i nerals and nutrients. Changes in s u rface wate r quality t ypically involve increas ed nutrien t and m i neral concentrations

co m i ng from ditch and canal outflows into na tural wetlands (Drew and Scho mer 1984). T h ese increased con centrations can produce dramatic shifts i n the am ounts of nutrients within the water colum n , increasing turbidit y and havi ng detrim enta l e ffects on SA V spe c ies wh ich are adapt e d to specific nutrient and dissolved m i ner a l concen trations. Any detri m ental influence to SAV populati ons i s immediat e l y conferred t o wading bir d comm unity structure and function i n the form of lost productive n u rsery and prey habitat. Changes in Sediment Relationship of changes in sediment and SAV community structure and func tion . The submerged aquatic vegetation in the Caloosahatch ee Estuary and Charlotte Harbor will i n crease

as estuarine conditions im prove. The extent of th is increase depends on available area with suitable salinity, substrate, water cl arity
, and tem p e r at ure. Seagrasses require light f o r phot os y n t h esis. A num b e r of factors can influence water clarity and light penetration. These include colo r and suspended solids. The different speci es of SAV have distinct requirements for light. Num e rous resear ch indicates that Th allassia testudium, Halodule wrightii, and Syringodium fil iforme require levels of at least 10-15% of surface irradiance, w h ile Halophil a decipiens, Halophila en glemannii, H a lophi la jo hn sonii, and R uppia maritima appear to have so m e what l o wer require ments, perha p s as low as 2-3% of surfac e irradiance (URS Greiner Woodward Clyde 19 99).
Most seagrasses appear to tolerate a w i de range of substrate co nditions. Virtually all
seagrasses seem to grow on sandy or silty m uds and on sands with some mud contents (Reid 1954, Voss and Voss 1955, Phillips 1960) and requi re a sufficient depth of sediment for proper developm ent. Substrates m o st also contain nutrie n ts, especially n itrogen a nd phosp hor ous, available for SAV growth (Duarte 1991). The m i cr obially m e diated chem ical processes in m a rine sedi m ents provide a major source of th ese nutrients (Capone and Ta y l or 1980). Each specie s of SAV has their own tem p erat ure an d salinity tolerance r a nges and their tolerance to s a linity variation is si m ilar to their te m p erature tolera nces. Halodule wrightii is the

m o st broadly eury haline, Thallassia testudium is interm ediat e , and Syringodi um filiforme and Halophila ha ve the narrowest tolerance ranges (McMillian 1979, Ziem an 1 982). Vallisneria americana is generally a freshwat e r grass but can tole rate salinities of near 10 ppt. Therefore, Vallisneria is also an im portant com ponent of t h e oli gohaline estuarine SAV community (Tw illey and Barko 1990, Adair et al. 1994, Kraemer et al. 1999).

Decr ease of Fish Populations Relationship of decreased fish populat ions and wading bird community stru cture and function. A direct consequence from t h e decline in shoreline ha bitat and decreased SAV is a

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

co mm unities on which wading birds are dependant. Acco m p any i ng this reduction in habita t for specific lif e histories of various fishes, the reduction in grass be ds also has l e d to an ove rall reduction in wading bird s p ecies diversity within t h e sy stem

. Relationship of decreased fish popul ations and fisheries community structure and function. Caloosahatchee Estuary and Charlotte Har bor provi de habitat and nursery groun ds for a variety of estuarine fish communities. These fish es are an integral co m ponent of the estuarine food web and have a significant societal value for sport and co mmercial harvesting. Fish

co mm unity measures are sensitive to both short and long ter m changes to the overall biotic integrit y of estuarine sy stem s. Regard ing these regions, with their history of anthropogenic manipulation, inform ation th at would per m it the assess ment of overall changes (replace ment, additions an d subtractions) of its nati v e fish comm unity relative to environm ental change is lacking.


## F: Research Questions
Relationship of water management practi ces to estuarine protection and restoration.

How can estuaries of national im por ta nce, including the Caloosah atchee River; and the pristine

resources of the Charlot t e Ha rbor A quatic Preserve be protected or recover fro m water manage ment practices as s o ciated with freshwat e r pulsing, alternation in tim ing and durati on of base and sea s onal flows, contam inan ts, overnutrificati on and red tide? Relationship of Manatee Mortality to Red Tide Will changes in salinity, nutrient load, and water residence ti me due to the restoration of the

reco mmended estuarine salinit y envel ope reduce th e occurrence of red tide in inland waters a t times coincid e nt to when manate es m o ve be tween inland waters a nd estuarine waters? Relationship of Blue Crab Fishery to Temp erature, Salinity and Other Water Quality Parameters

How does CPUE of the blu e crab fishery respond to th e co m b ined effects of temperature, salinit y and other water qualit y par a m e ters in the Caloosah at chee estuary ? Can blue crab CPUE be used as an indicator of estuarine health in the estuary ? Relationship of Mollusk Populati ons and Fish Recruitment to Submerged Aquatic Vegetation a n d Sali n ity Will changing the salinity regi m e to a m o re na tural condition and increasing the coverag e of submerged aquatic vegetation in the Caloosahatch ee estuary provide a m o r e sui t able environment for estuarine m o llusks an d fishes? Will this lead to an increase in population density and

co mm unity diversity? Relationship of Current and Historic al S ubmerged Aquatic Vegetation Coverage to Potential Distribution

What area s i n the estuary potentially provide op tim al conditions for seagra ss reest ablish ment? Will we see t h is reestablishment with changing conditions?



## G: Hy drological Performance Measures

See addendum titled Southwest Florida Feasibility Study – Caloosahatch ee Estuary Hy drologic Evaluation Performance Me asures.

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## H: Ecological Performance Measures
Submerged Aquatic Veg e tation Community Structure & Function The performance m e asure s for subm er ged aqua tic vegetation community structure and function are SAV distribution, densit y / abundance, and comm unity com position. Seagrass beds

m u st be ree s t a blished in the Caloosahatc h ee Estu ary and Charlotte Harbor to increase biodiversity within the s y stem and enhance habit a t value for fish, caridean shrim p , wading birds
, and
manate es. The coverage of seagras s e s m u st increa s e in areas th at are indicat ed to be suitable habitat. To achieve these ta rgets, flows needed to achieve the pr oper salinity range for SAV m u st be maintained. Oyster Ba r, Community Structure an d Function The performance m e asure s for oy ster bar comm uni ty structure a nd function are oy ster growth, disease, m o rtality and recruit ment. The ta rgets ar e to increase the abu ndance and health of oy sters, restore oy ster beds in suitable habita t, and maintain hab itat function of o y ster bed s for fish, crabs an d birds. To a c hieve thes e t a rgets, flows needed to ac hieve the proper salinity range for oy sters must be maintained (see Sali nit y Envelope under H y drologic Performance Measures).

Mesohaline Benthic Co mmunity Structure and Function The perfor mance me asure s for s a nd/ mud bottom co mmunity structure and function are mesohaline clam abundan ce, growth a nd recruitm ent. The targ et is to obtai n targeted n o r mal distribution, populati on si ze, and condition acro ss optim al salinity rang es for these freshwater species of cla m

. Shoreline Community Structure and Function The perfor m a n ce measur e for shoreline mangrove habitat is shorel ine m a ngrove percen t cover. The targets are to restore and maintain shoreline m a ngrove habitat and to increas e or maintain functionality of the m a ngrove s y stem . To ac hieve these ta rgets, further loss of m a ngr ove habitat m u st be elim inat ed; mangrove habitat m u st b e restored when possible. The mangrove tree crab will be u sed an indicat or species to measure incr ease or loss o f functionality in the mangrove
sy stem

. Fisheries Community Structure and Function The performance m e asure for estuarine fish comm u n ity structure and function are fish

co mm unity s t ructure and diversit y

. The targ et is to restore assemblages with abunda nce, taxonom ic com position, diversity and representati on of life stages ch aracteristic of targeted salinity regim es for each es tuary

. Manatee De mographics The performa n ce m e asures for m a nat ee de m ogra phics are manatee birth, death, survival, distribution and abundanc e. Re storation and preservation of the manatee p opulation in the Caloosahatch ee Estuary and Charlotte Harbor w ill be achieved by m a intaini ng and enha ncing current habitat and foraging areas for manate es in t h e estuarie s and canals to prom ote spe c ies
recovery , especially near the Florida Power and Li ght war m wate r refugia. Also, manate e ha bitat values in can als should be m a intained or enhan ced, as reflected b y con tinued use of canals by manatees. Manatee deaths i n categories "undete rm ined " and "calves" need to decr ease. Algal Blooms Community Structure & Function

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The perfor m a n ce measur e s for algal blooms co mmun ity structure and function are algal bloom frequency
, duratio n, identit y , concentration and negative effects.

Wading Bird Community Structure & Function The performance measur es for wading bird co mmunity and structure are w a ding bird foraging and nesting surve y s.



## H: Baseline Conditions and Drivers for Water Quality in the Caloosahatchee Estuary and Lower Charlotte Harbor
Anthropogenic changes in water quality can act as str essors in estu a rine sy stem s. Driver s and pathways of water qualit y problems may in cl ude, am ong others, urban stormwater runoff (e.g., lawns, golf course s, "street dust"), ag ricultural runoff, surface mining runoff, s e ptic
sy stems, discharges fro m Publicly Owned Treat m e nt Works (POTW s ), direct industrial discharges (e.g., citrus pr ocessing plants, power plants), landfill runoff, as well as at m o spheri c deposition of conta m inants fro m varied sources (for a review of d r ivers in southern Florida, see USGS 1998). Although m u ch of the focus (and cont ro l) has been on poi nt sources, considerable evidence has been am assed to suggest nonpoint so urces, such as urban stormwater runoff, and diffuse pathway s , such as atm o spheric deposition, can play very significant roles in local W Q problem s. At m o spheric de position of contam inants f r om varied s ources (both local and dist ant) can be an important dri v er in estuarine WQ in one of two way s . D i rect atm o sph e ric deposition of
a conta m inant to the estuary includes loading from dr y depositi o n and wet deposition. Indi rect deposition fr om the at mosphere to the estuary o ccurs when the contam inant is initiall y depos ited to the watershed and then transported to the estua ry throug h runo ff and tributaries and, hence, a function of water managem ent. Along with the gr o w ing appreciation of pote n tial im pacts fro m atm o spheric transport and deposition al so co m e s a realization that we can no longer rely on the “dilutive effects of the ocean environm e n t” to so lve coastal pollution. Evidence has accu m u l a ted that anthropogenic contaminants, as wel l as natural occurring mate r ials, in riverine discharges can be transported and have biological effe cts far re m o v e d fro m their discharge sit e (Rabal ais e t al. 1996; Goolsb y, 19 94, Ru d n ick et al., 1 999). As one exam ple, algal bloom s in western Florida Bay have been linked to n u trient transport along the southwest sh elf of Florida (Rudnick et al., 1999).

A nu m b er 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 i n clude the federal Clean Water Act, Clean Air Act, Coastal Zone Act Reauthorization Amend m ents along, Fl orida’s Wa tershed Restoration Act and Water Resources Act that address i m ple men tation of the National Po llutant Discharge Elim inatio n Sy stem per m its, Total Maxim u m D a ily Load requirements, Surfa ce Wat e r I m prove ment and Manage m e nt (SWIM) program s , as well as both agricultural and ur ban nonpoi nt source m a nag e m e nt programs. Any recommendations related to water qualit y for alternatives analy s is will f i rst evaluate the efficacy of remedies brought about by t h ese outsi de program s. However, as will become evident from the current conditions discu ssed below, these program s ar e rarely 100 percent effec tive. Further, several exam ples will be presented to show that local WQ problems may have drivers outside of the stud y area and, thus, m a y not be rem e died throu gh local or state program s. During these a sse ss ments and d u ring any s ubsequent alternatives an aly s is the following baseline conditions and drivers should be considered when identify i ng m a j o r stressors i n estuarine water qualit y :
Results of a num ber of recent water quality assess ments of the Caloosahatch ee Estuary and Lower Charlotte Harbor show rem a rkable agreem ent (T able 1). In their prelim i n ary

15FINAL - Caloosahatchee & Charlotte Harbor CEM 22 Ma y 2006

assessment, FDEP classified thr ee waterbodies in the Caloosah atchee E s tuary as potenti all y im paired based on chloro ph y ll-a, disso lved ox yge n (DO), fe cal coliform
, cop p er, lead and or biology (for methodology and legislative authorit y , see Impaired Surface W a ters Rule [ I WR]
, Chapter 62-303 F.A.C.). I n a separate assessment, U.S. EPA (2000) also found that parts of the tidal Caloosahatchee and its tributaries had de graded water quality based on values of ke y para m e t e rs. These findings have added significance given the presen ce of the following Outstanding Florida Waters (OFWs) within the Caloosahatche e Estuary and Lower Charlotte Harbor: Caloosahatchee National Wildl i fe Refuge (40 acres locat ed in the Caloosahatchee nea r Interstate 75), J.N. “Ding” Darling NW R, Ma tlacha Pass NWR, P i ne Island Sound NWR, Estero Bay State Buffer Preserve, Matlach a Pass Aqua tic Preserve, Pine Island Sound State Aquatic Preserve. Although t h e state’s IWR focuses on chlorophyll-a rather than absolute concentrations of nutrients (i.e., because there are no numerical w a t e r quality standard [WQ S ] for nutrients), Doering and Cham berlain (199 8) an d Janicki En vironm ental Inc., (200 2) both f oun d t o tal nitrogen (TN ) and total p hosphor us (TP) to be elevated in the Caloosahatchee co m p ared to statewide me dian concentrations, refere nce site c onc entrations and com p ar ed to historical data (for TP). Doering and Cham berlain (1998) also report TP and TN exceeded targets that FDEP (Degrove, 1981) had set for the Caloosahatchee. Mo st of these assessments also found a sag in DO (Table 1), especially in bottom w a ter in th e upper Caloosahatchee (i.e., adjacent to S79). Color was an other param e ter not consid ered under th e IWR assessments but that was found to be unusuall y hi gh (Doering and Cham berlain, 19 98; ERD 2003). Accel erat ed deco m position of organic m a tter in the historic peat d e posits in the no rthern Everglades (due to land-use change) has been sho w n 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 reache d 67 Pt-Co units and 164 Pt-Co units in the dry and wet season, res p ectively (sta tewide m e dia n for estuaries is 22.5 Pt-Co; Friedem a nn and Hand, 1989). Color in the Caloosahatchee may have greater significance given the opt ical m odel developed b y Dixon and Kirkpatrick (19 99) for upper and lower Charlotte Harbor. Th ey fou nd that color acc ounted for 66% of light attenuation in the water colum n ; whe r eas, chlorophy ll, a nd turbidity accounted for only 4% and 31% , respectively

. A finding that c o lor accounts for m u ch of the water colum n light attenuation in Charlotte Harbor is also consiste nt with a report from Mc Pherson et al. (1996). Humic materials , which m a k e up

m u ch of the color, m a y also be im plicated in reports of a dark flocculant material settling on grassbeds in San Carlos B a y (G. Rom e is, FDEP, pers. co mm .). This could represent a “salting out” of DOM. Besides shading, DOM has si gnificance both as a pri mary nutrient and as a micronutrient and, consequentl y , m a y lead to in creased biological oxy g en demand (BOD). It is im portant to note that Dix on and Kirkp a trick ( 1999) found li ght w as further attenuated, from 21% to 44% (annual average s ), at the surfac e of seagra s s blades by epiphy tic growth, which is also a fam iliar result of nutrification. Despite all this, grassbeds are currently foun d in deep water (2.43 m) near the m outh of the Caloosahatc h ee relativ e t o other areas within Charlotte Harbor and elsewhere (Dixon and Kirkpatrick, 199 9; Crean et al., in review), suggesting adequate ligh t penetration. Not surprisingly , a recent asse ss ment by Janicki Environm en tal, Inc., (2003b) found water quality has declined in the Caloosahatchee ov er tim e . They found statistically signific a nt te m poral trends over the last 10 – 15 years with inc r ease s in BO D, increas es i n total suspended solids (TSS) and t u rbidit y, increases in fecal coliform bact eria, increases in many species of nutrients, and decreas es in DO levels.

In term s of spatial variation, Doering and Cham b e rlain (1998) and ERD (2002) b o th report a stro ng longitudi nal gradient with m o st constituents decreasing in concentration with increasing distance fro m t h e S79 structure. Based on this, both asses s ments c onclude freshwater

16FINAL - Caloosahatchee & Charlotte Harbor CEM 22 Ma y 2006

discharge fro m S79 play s a crucial ro le on wate r qualit y withi n the Caloosahatchee. Eq ually i m portant, because of the steepness in th e gradie nts, both assessments f ound relativel y good water quality downstrea m in San Carlos Bay
, as eviden ced by relatively low ch lorophyll-a and high DO (Table 1). Likewise, Pine Island Sound and Matl acha Pass also exhibited l o w chloroph yll-a and high DO (Table 1, Doering and Cham b e rlain, 1998). This is consiste nt with FDEP’s (2003) finding that t h ese three waterbodies met uses excep t fo r bacteria in shellfish (Table 1; note
, San Carlos Bay is classified as a Class II waterbody
, i. e., for shellfish propagatio n or harvesti ng). FDEP’s IWR assessment is consistent with the Ja nicki Environ mental, Inc. (2003 b) evaluation that found water qualit y i n Pine Island Sound and Ma tlacha Pass a cceptable based on an inform al application o f the IWR. However, it should be noted that the y also fou nd statistically sign ifi cant increases over ti m e in nutrients, TSS, and BOD. Fur t her, they also reported that so me st ations in this basin had frequent exceedance s of DO and a m m onia.

As m e ntioned above, Doering and Cham b e rlain (1998) and ERD (200 2) b o th identifie d freshwat e r discharge from S79 as play i ng a cr ucial role in water quality within the Caloosahatch ee. ERD (2003) reports that, depe nding on the seaso n (i.e., wet or dry ) , discharge from the S79 structure contributes fro m 90% to 95% of the m e an d a ily m a ss of TN and TP to the Caloosahatch ee Estuary ( up t o 1 1 ,0 51 kg of TN p e r day and 1 040 kg TP p e r day )

. The next largest contributor to the Caloosahatch ee Estuary was the Orang e River with 1.1%to 3.8% of the daily m ass of TN and TP . Nevertheless, for a co mplete understanding of water quality dr ivers within the re gion, especially localized effects withi n Matlacha Pass and Pine Island, loa d ings from Ft. My ers, Cape Coral, Pine Is land and Sanibel cannot be ig no red. These findings are consis tent with other loading as sess ments in southwest Fl orida that find the greatest nutrient loadings co m e from agricu ltural runoff and urban runof f (Post, Buckley, Schuh, and J e rnigan Inc., 1999; Post, Buckley
, Sc h uh, and Jerni gan Inc. and W. Dexter Bender and Associates, Inc., 1999; Drew and Schomer 1984) . South Flori d a' s high level of agricultural productivi t y can be a significant driver in WQ pr oble ms as a result of various activities including the substantial usage of soil amendments, includi ng m i neral fertilizers and biosolids (fertilizer usage estimated at 1.6 m illion tons in the y ear ending June 30, 1996; USEPA 1999), or simpl y due to soil di sturbance and deco m position of orga nic peat (esti mat es as high as 2 billion g-N per
y ear to the northern Everglades; Wang et al., 2002). Nitrogen rel ease fro m disturbance and peat deco m position in the Ever glades Agric u ltural Area h as been spec ulated to be a possible driver of outbreaks of “blackwater” in southwest Flor ida coastal waters (Zollo, 2002). However,
storm w ater runoff is not t h e onl y m ean s b y whic h 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, potentiall y even

m o r e significant than agricultural activities. Pros pero et al. (1996) esti m ated that present day deposition on nitrogen (inc luding amm o n ia) to the Nort h Atlantic Ocean to be f i ve ti m es gre a te r than pre-industrial ti m es, primarily due to fo ssil fue l com bustion and bi om ass burni ng. Gi ven this, it is not surprising tha t atm o spheric depositi on of nitrogen (pot entially from a distant source) could be a driver (external to the study area) contributing to WQ problem s in southwest Florida (Squires et al. 1998). At m o spheric deposition of ni trogen has be en estim ated to be respons ible for 21% of e x ternal nitrogen loading to Tam p a Ba y

. Nonetheless, we cannot lose site of the fact that urban a nd agricultur a l runoff re main the greatest source of no npoi nt nitrogen l o ad ing to Tam p a Bay (Pribble et al. 2001), and li k e ly t o Charlot t e Harbor, as well. Unlike nitrogen, phosphor us has no sta b le gas phase in t h e atm o sphere and is t r ansported only as particulates, thus limiting its atmospheric residence ti m e

. Based on the inform ation presented above, Janic ki Environm ental, Inc. (2003a), under contract to FDEP, developed a regress ion-based m o del between chlorophyll-a concentration in the Caloosahatchee and T N loads acro ss S79. U se of TN in the m odel rather than TP was

17FINAL - Caloosahatchee & Charlotte Harbor CEM 22 Ma y 2006

consistent with Doering and Ch am berlain (1998) th at found that ratio of dissolved inorga nic nitrogen to dissolved inor ganic phosphorus (i.e., DI N:DIP) to be less than 16, suggesting the
sy stem is nitrogen lim ited. Janicki Envi ronm enta l, In c. (2003a), developed regressions for both the dry and wet season and found greater sensitivity t o nutrient loading during the former (i.e., greater slope or greater i n creas e in c h lorophy ll- a per unit increase in TN l o ad). However, it should be not e d that the dr y season regression ha d a l o wer coeffici ent of determination (R 2 = 0.4). Other factors, including ammonia from the sewage treatment plants discharging to the Caloosahatch ee (see ERD, 2003), could account so m e of t h e unexplained variability in chloroph yll-a. As previously m e ntion e d, FD EP has set nu me rical nutrient targets for the Caloosahatch ee (Degrove, 1981); the y have also established water quality ba sed effluent lim its (WQBELs) for these facili ties (Baker, 1 990). The increased sensitivity to nutrients in th e dry season could be relat e d to i n creased residence ti m e in the Calo osahatchee (P . Doering, pers. co mm unication). Alternatively, Doering and Cham berlain (1998) a nd Janicki Environm ental, Inc. (2003b) both report i n stances of “wash out” under hi gh flow conditions (i .e., low chlorophy l l-a under unusu ally hi gh l o ading and, m o re im portantl y high flows: >150 m 3 /s). A study in the Potom a c estuary dem o nstrated a si milar interaction between load and hy drology. USEP A (2 001) summarized data attri buted to Boynton (1997) showi ng peak chlo roph y ll-co ncentrations in t h e estuary (also regressed against TN load) occurred under average flow cond itions. Bloo ms d i d not form in the Potomac estuary dur ing maxi m u m freshwater inflows because of a strong vertical density stratification and, m o re i m portantly
, because nutrients were a dvected downstrea m into the lower Chesapeake Bay

. Sim i l a rly
, it i s likely that, during high f l ow ev ents across S79, im pacts fro m nutrient loads could be further downstream (i.e., coastal nutrificati on). Residence ti me and “wash out” will li kely have significant i m plicati ons for altern atives anal y s is for CE RP both as they are influence d by CERP-co m ponents, such C43 BSR, whose goal is to pro v ide minim u m flows during t h e dr y season (i.e., p o tential for longer residence ti m e ) a nd from both a redirection of Lake Okeechobee water south and with-in ba sin storage facilities th at should reduce high flow e v ents (and, t hus, likely reduce frequency of “wash outs”).
From the discussion above, it is clear that a strong case can be m a de to consider TN loading at S79 as a means of reduc ing chlorophyll-a in the Calo osahatchee. H o wever, it should also be cl ear that water col u m n chlorophy ll-a is only one of several water quality concerns, some of which are not assess ed by the IWR (e.g., color, DOM, BOD, “ w ash outs”), and that discharge from S79 is onl y one of many proxim at e sources. Alt hough any re medial action to reduce TN at S79 would li kely have col a teral benefit s (both in terms of reduc ing other constituents and i m pact s to other resources) and would, in of itself, be an am b itious first step, it shoul d be recognized that it would not be a cure-all.
In this context, red ti des are a prefect illu stration of the potential significance of ot her nutrient sources on other resources, a s well as th e potential significance of “w ash outs”. Blooms of Karenia brevis , i.e., red tides, have been linked t o direct atm o spheric deposition of ammonia (Steidinger et al., 1998). Alternatively
, Lenes et al. (2001) m a ke a co m p elling argum ent that red tide outbreak s m a y be link e d to lon g -range atm o spheric transport of iron (a k n o w n growth fa ctor) and bloom stim ulation of the nitrogen fixing Trichodesmium , which, through the release of nitrogen cont aining exuda tes, could fertilize Kareni a brevis . Hence, this im portant south w est Florida issue may have e x ternal drive r s not u nder local contro l. Not surpri singl y , m odelers

rem a in " s ty mied by the chaos of unknown initial c onditions" that stim ulate 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 manage ment” (Geesey and Tester 1993) and will likel y continue despite out best efforts. Consequentl y , occurrence of re d tides will not be a perform ance m e asure (ei t her evaluation or assessment) for the SWFFS. Nonethel ess, it is con ceivable that so m e reducti on i n

18FINAL - Caloosahatchee & Charlotte Harbor CEM 22 Ma y 2006

red tide magnitude, d u ration, or freque ncy is ach ievable if coastal nutrification were reduced (especially as a result “wa s h outs”). As a result of productivity level, crop va riety, m u ltiple planting seasons, and cli m ate, Florida agriculture requires the usage of a wide va riet y of pesticide s , i.e., insecti c ides, herbici d es, and fungicide s. Residues o f so m e of these pestic ides (i.e., both or ganics and metals) have b een detected in s e di m e nts and surfac e w a ter at District structures at various ti mes (Pfeuff e r and Matson, 2002). As m e nti oned above, fertilizers are also extens ively used in Florida. Several studies have measured m e tals (e.g., cadmiu m , lead
, nickel and copper; USEPA 1999) in m i neral ores and resulting fertili zers. Organic and bios olid fertilizers m a y also have m e asurable concentrations of metals. However, agriculture m a y no longer be the prim ary source of pesticides to the envir o nment. Contr a ry t o pu blic percep tion, USGS reports that pesticides occur mor e frequentl y in urban stream s than in m o st agricultural strea ms (USGS
, 1999).

As m e ntioned previo usl y , FDEP has li sted two waterbodies (WBID 3240B a nd 3 240A) within this region as pote n tiall y im paired for coppe r and lead. Althoug h the f o cus of the IWR

asse ss ment is on water col u m n concentrations, m e ta l i m pair ment i s consistent with a survey of sedim ents in the Caloosahatchee by Fernandez et al. (1999). T h ey fo und le vels of cad m ium, copper, lead, and zinc ab ove “natural backgroun d” concentrations. At certain stations, one or

m o r e of thes e metals exc eeded either the thres hold effects lev e l or, worse, the probable effects level (Fernandez et al., 1999). The y f u rther re ported that imm u noassay s were positive for th e organochlorine pesticides DDT and cy clodienes (as chlordane), with levels exceedin g the probable effects level at several sites (F ernand ez et al., 1999) . These findings are consistent with results of the District’ s m onitoring of sedi m en t just upstream of S79 that foun d DDT, DDE and PCB-1245, with levels occasionally exceeding the th reshold effects level (for det a il, see quarterly reports by P f euffer and Matson, 200 2). Since 1992, the District’s surface water m onitoring
program at S79 has detected low levels of the herb icides a metry n, atrazine, b r omacil, diuron, hexazinone, norflurazon, and sim a zine at relativ e high frequenc y (frequency of detection >20%). The following pesticides and degr adates: atrazine desethy l, atr azine desisopropy l endosul fan sulfate, m e t a l a xy l
, ethopr op, and m e trib uzin were detected less frequentl y . However, based on various criteria, the concen trations of de tected pesticides should no t pose a signi ficant risk to fish or aquatic invertebrates (Pf e uffer and Matson, 200 2 a nd references therein).

At m o spheric loading is also the dom i n ant proxim a te source of inorganic mercury to many water bodies, with the ultimate prim ary drivers being coal-fired u tilit y boilers and

m unicipal and medical waste incinerato rs (USEPA 1 997a). However, the co m p lication lies in the relationship between influx of in o r ganic mer cu ry and the a m ount that is m e thy l ated post deposition by sulfate-reducing bacteria. The la tter process is of fundam e ntal concern because methy lm ercury (MeHg) is the m o re toxic and bio accum u l a tive form that can build up in the f ood chain to leve ls harm ful to hum ans and other fish -eating anim als. Rarely is the state WQS for
mercury , which is based on total m e r c ury rather th an MeHg, exce eded in south Florida; however,
many south Florida waterbodies are co nsidered i m p a ired by FDEP based on fish consu m ption advisories for m e rcury

. T h e principal pathway for mercury exposure to humans is through the

consum ption of m a rine fish a nd fish products. Stu d ies of south Florida estuaries have fo und elevated level s of mercury (both the inorganic and m e thy l form ) in surface w a ter discharges a nd,

m o re im portantl y , in fish (Adam s and McMi chael, 2003; Rum bold et al. 2003). FDEP lists the entire southwest coastal area as pote n tially im pa i r ed for m e r c ury based on fish consu m ption advisories (Table 1). Currentl y , limited consum ption adviso ries have been issued for the following coastal fish bas e d on their mercury content: King Mackerel, Spanish Mackerel , all sharks, spotted seatrout, Little Tunny
, Cobia, Gr eater A m berj ack, Bluefish and Crevalle Jack. (Florida Departm e nt of Health 20 03).

19FINAL - Caloosahatchee & Charlotte Harbor CEM 22 Ma y 2006

Table 1. Summary of findings of water quality as sessments in the Caloosahatchee Estu ary , Sa n Carlos Bay
, P i ne Island So und and Matlacha Pass.

W a ter body Doer ing and Cham ber l ain, 1998 a Janicki E nvir on. I n c. , 2002 b FDE P , 2002; 2003 c E R D, 2003 d Janicki E nvir on I n c. , 2003 e Tetra Tech, Inc.
, 2003 f

Upper Caloosahatchee ( W B I D 3240C) Chl a>11 ug/L

TP>state

me d i a n

TN>state

me d i a n

DO< WQS

Color r e l. high Chl a>ref

. site, IWR

TN>ref. site
TP>historic, ref

. site
DO<historic, ref. site, I W R
Turbidity>historic Im pa i r e d for : Chl a,
DO, coliform Str ong gr adient with decreasing

conc. of m o st constituents with increasing dist. fr o m S79;
Chl a>11 ug/L

DO< WQS Unaccept. based on i n f o rm a l IW R:
Chl a,
DO, coliform ; tr end of declining WQ in

BOD, TSS, nutrients, secchi depth

Middle Caloosahatchee ( W B I D 3240B) Chl a>11 ug/L

TN > state

me d i a n Chl a>ref

. site, IWR

TN>ref. site

TP>ref . sit e

DO<ref. sit e , IWR
Turbidity>ref . sit e Im pa i r e d for : Chl a,

DO,

copper , colif or m Spike in downstr eam gr adient in

am m onia, TKN, TN and Chl a.
Chl a>11 ug/L Unaccept. based on i n f o rm a l IW R:
Chl a,
DO, coliform ; tr end of declining WQ in

BOD, TSS, nutrients, secchi depth

Lo wer Caloosahatchee ( W B I D 3240A) TN>state

me d i a n Chl a>ref

. site, IWR

TN>ref. site
TP>historic, ref

. site
DO<historic, ref. site, I W R
Turbidity>historic Im pa i r e d for : Chl a,

DO,

copper , lead,
biology Mean DO> WQS Unaccept. based on i n f o rm a l IW R:
Chl a,
DO, coliform ; trend of declining WQ in

BOD, TS S, nutrients, secchi depth

San Car l os B a y ( W B I D 2065H) Chl a rel. low

TN>state

me d i a n

DO r e l. high
Turbidity r e l. low

TSS>state

me d i a n not assessed N o l i s t e d im

pa i r m e nt Concentr ation of m o st constituents substantially reduced
Chl a<11 ug/L

Mean DO> WQS Assessed un der Matlacha P a ss

Pine I s land Sound ( W B I D 2065E and G) Chl a rel. low

TN>state wide

me d i a n

DO r e l. high

TSS>state

me d i a n not assessed Im pa i r e d for : bacteria (in shellf ish) not assessed Accept. based on i n form a l IW R; exceedances in

am m onia and DO
at so m e stat ions

20FINAL - Caloosahatchee & Charlotte Harbor CEM 22 Ma y 2006

Matlacha Pa s s ( W B I D 2065F) Chl a rel. low

TN>state

me d i a n

DO r e l. high not assessed N o l i s t e d im

pa i r m e nt not assessed Accept. based on i n form a l IW R; im

p r oving tr ends in secchi depth and T N

SW coast not assessed not a ssessed Mercury not assessed

a. Doer ing and Ch am ber l ain 1998, based on SFWMD data collected fr om 1985 – 1995.
b. Janicki Report (2002): report to FDEP on current co nditions in t h e Caloos ahatchee co m p aring it to historical data, referenc e si tes and the Im pair ed W a ter Rule ( C hapter 62- 303 F. A. C. ); data sour ces included SFWMD, L e e County
, ST OR E T ( L egacy and Moder n )
, USGS.

c. FDE P

. 2002. B a sin Status Repor t Dr aft: Caloosahat chee, 12/02; FDE P

. 2003. Basin Status Repor t Dr aft: Char lotte Har bor . 9/03: potential im pair m e nt based on Im p a ir ed W a ter Rule ( I WR, Chapter 62- 303 F. A. C.) on data fr o m ST ORET

. d. E nvir o n m ental Resear ch and Design, I n c. 200 3: asse ss m e nt ba sed on i n tense data collection d u r i ng two m o nths o f the y ear ( w et and dr

y season collections) for 200 0- 200 2.
e. Janicki Report (2003b): draft re p o rt to the CHNEP on water quality based o n st atus an d trends, an d IWR assess m e nt of p e riod of

r ecor d data ( a ll av ailable data)

. Mar c h 2003.

f. Tetra Tech, Inc., (2003): water quality assess m e nt of the SWFFS area based on u n o ffici al assess m e nt using IWR and status and tr ends of data fr o m per i od-of- r ecor d ( a ll available data)



## I: Linkages Between Water Quality and Attributes
This section provides specific exam p l es of critical linkages between wat e r quality stressors and valued ecosystem co m ponents. This list should not be consid ered exhaustive. This section will exam ine how deviations, from a defin e d baseline, in the chem i cal and phy s i cal
param e t e rs measuring water quality, stress the ecol ogical s y stem by affecting the health and distribution of the indicators that describe the s y stem’ s attributes. The SWFFS differs fro m other si m ilar feasib ilit y studies, i n particular IRL-South and Florida Ba y / Flori d a Key s , in that c a useand-effect research within the stud y b o undar y has b een lim ited and technical-polic y docum ents are few in num b er. In the absence of local in form at ion, WQ data will be assessed for potential linkage based on benchm ar ks established in surrogate studies.



###  Phy t opla n kt on and SA V

i. Ph y t op lankto n and SAV species have a preferred and t o lerable range of sal inity

. When salinity falls outside of these r a nges the SA V is negatively i m p acted and may result i n a reduction in densities and distribu ti on (Cham b erlain and Doering 1998). Increases or decreases in salinity may give one species a co mpetitive advantage over another (Livingston 1987; Zi em an 1982).



###  Be nthi c C o mm unities a n d Fi sh P o pul ations

i. Salinity is a "mast er ecological variable" controlling co mm unity structure and food web or g a nization in c o astal sy stems (My e rs and Ewel, 1990). Negative i m p acts to oy sters can lead to shellfish closures.

ii. Alterations in the salinit y re gime places stress on the sensitive life history stages of man y estuarine species (Odum 1970, Cham berlain and Doering 199 8 b ).

▪ Mangroves

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### i. Mangrove communitie s are sensitive to sa linity leve ls. Where freshwater flow has been insignificant over a long period of time, and salinity levels incr ease above historic leve ls, m a ngroves displace cypress and wetland plant comm unit i es.


## DO

 Phy t opla n kt on and SA V

i. As a result of primary p r oduction
, day l i ght levels of DO can actually reac h supersatura tion levels in the presenc e of phy t oplankton bloom s or thick stands of m acrophy te s. However, both phy t opla nkton and SAV utilize DO and, in the dark, are a net sink for DO, this can re sult in hy poxic and someti m e s anoxic condit i ons (Mitchell-Tapping et al., 199 8)



###  Be nthi c C o mm unities a n d Fi sh P o pul ations

i. Hy p oxia (low dissolved ox ygen) can be a significant problem in certain estuar i es, especi ally those recei ving excessive nutrient loa d s, im pacting the health of f i sh and shellfish pop ulatio ns (EPA 200 0b).

ii. The response of benthic communiti es to alterations in sedim ent and water quality is relatively well under stood and i s often expressed as chang e s in co mm unity structure, d e nsity , and di versity (for r e view, see Mitchell-Tapping et al., 1998; E P A 1999).



### • Se dime nt che m istr y

i. Increas ed nutrient loading, su spended solids and dissolved organic m a terial from the watershed can result in hi gher BOD, higher sediment

ox y g en demand (SOD) or both and, con sequently, h y po xia or even anoxia, especially when freshwat e r flows produce a density stratification (CDM, 1998; Turner, 20 01; cf. Doering and Cham berlain, 199 7).

ii. Anoxic conditions can result in altered redox conditions and altered che m i s try in the sedi m ent 

## Total Suspended Soli ds and Wa ter Clarity (e.g., Turbidity, TSS, Col o r)

 Phy t opla n kt on and SA V

i. Inorganic suspended sediments, organic nonchl orophy ll-based detritus, and
, of particul ar im portan ce in south Florida, humic material s (McPherson et al. 1996) m a y reduce wa ter clarity and shade out SAV. A statistically significant inve rse correl a tion has been re ported between the depth of the deep edge of a s eagra ss bed and co lor and turbid ity i n souther n Indian River Lagoon; preli m inary targe t s have been established based on WQ observed at these deep se agrass beds ( C rean et. al., in review).

ii. Becaus e s e a g rasses are r ooted pl ants attached to the bottom
, reduced light reduces photosynthesis, grow th, and reproduction. This condition i s

22FINAL - Caloosahatchee & Charlotte Harbor CEM 22 Ma y 2006

cited as a ma jor source of seagra ss decl ine in Florida estuarine sy ste m s ( D urako 1988).

iii. Under certai n circu m stan ces, dissolve d organics (e.g., hum ics, etc.) and attendant water color and cl arity have been thoug ht to reduce undesirable algal growth u n d er high nutri ent conditio n s (McPherson et al. 199 6).

iv. SAV need suitable substrate for successful rec r uitment and establish ment. Deposits of silt / m u ck can displace or m odify normal substrate in the estuary and contribute to the decreas e in extent of SAV beds.



###  Be nthi c C o mm unities a n d Fi sh P o pul ations

i. Suspended solids m a y clog gills and int e rfere with filtering and respiration of o y sters (Cake 1983).

ii. Hu m i c mat erials can influence the che m ic al speciation, bioavailabilit y and, in some cases, t oxi cit y of certain metals and organi cs (McCarthy et al. 1994).



###  Shoreline Habitat functionality

i. Sedim e nt load caused by dredge and fill operations and in runoff from shoreline construction has been id entified as a cause of mangrove loss and salt m a r s h destruction. 

## Nutrients (macro- and micronutrients)

 Phy t opla n kt on and SA V

i. Nuisance alg a l bloom s: Ta m p a Bay National Estuary Program produced an e m piric a l regression-ba sed WQ model that s howed strong relationship between TN load and Chl- a (as a m e asure of ph y t oplan kt on abundance; Janicki and W a de 1996). A si m ilar relationship has been established for the C43 B asin / Calooshatchee Rive r (Janicki Envi ronm ental, In c. 2003).

ii. Nutrification can l ead to subtle re sponses such as changes in

co mm unities at the spe c ies level, alter e d rates of biogeoche m i c a l p r ocess es ( e .g., nutrient recy c ling, sedim en t oxy g en demand, etc.), and shifts in sea sonal patterns (i.e., spring versus su mmer prim ary pr oduc tion) or magnitude of variabilit y (f or review, see Cloern, 20 01; EPA, 2001).

iii. Resource co m p etition, not just in terms of N or P, but also their specific for m (e.g., concentration of a mm oniu m to nitrate) can also result in species shift s . Many organic N mol ecules are not readily available to ph y t o p lankt o n , while m a n y organic P m o lecules are, due to the activity of phosphatase enzy m es (Vito usek and Howarth, 1991).

iv. Nutrients can trigger a thick growth of epiph y tes which can reduce the am ount of light that can reach the surface of the seagrass blad e (Murray et al. 199 9).

v. Relatively minor changes in nutrient input can lead to sharp reductions in the productiv ity of seagrasse s, which can lead to broad habitat changes (Livingston 198 4). Encourages growth of m o re nutrient tol e rant species

23FINAL - Caloosahatchee & Charlotte Harbor CEM 22 Ma y 2006

that cause un desirable effects such as mono specific communities which decrease the value for fisheries and benthic invertebrate speci es

. vi. Unnaturally l o w ratios of silicon (Si) to P or Si :N (due to increases in P or N) are thought t o favor the selection and possible ascendancy of lightl y -silicifi e d diatom s and non- diatoms (Dortch & Whitledge 1992).



###  Se dime nt Chemistr y

i. Nutrification can lead to altered rates of biogeochem i cal processes (e. g ., nutrient r ecy cling, sedi m ent oxygen demand, redox, etc. CDM, 1998 , Turner, 2001; for r e view, see Cloern 2001), which, in turn, can lead to further changes in water quality (e.g., sol ubilit y of m e t a ls).

ii. Nutrification can also lead to saturation of soils whe r e substrat e beco m es a source, and not a sink, for ad ditional n u tri e nts (internal loading).



## Toxicants

 Be nthi c C o mm unities a n d Fi sh P o pul ations

i. Both acute and chronic effects have been reported for both organic and inorganic toxi cants to a wide variety of aquatic spec ies (N ational Toxics Rule, 57 FR 60848, Decem b er 22, 1992; U SEPA 2002 and references therein, Wiener et al. 2002)

. ii. Many of these substance s are either ins o luble in water or tend to associat e wit h particulate m a tter that flocculates (i.e., “salti ng-out") often resulting in concentrations m u ch high er in the estuarine sedi ments than that observed within the overl y ing water colum n

.



###  Upper trophi c lev e l predat or s, incl udi ng list e d specie s

i. Persistent bioaccu m u lative toxicants (P BTs) c a n pose a risk to upper trophic level predators (USEPA, 1997b, Rum bold, 2000)



###  Human health

i. Persistent bioaccu m u lative toxicants (P BTs) c a n pose a risk to hum ans (EPA, 2002 an d r e ferences therein)

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## J: Model

25FINAL - Caloosahatchee & Charlotte Harbor CEM 22 Ma y 2006



## K: Literature Cited
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### Barbour, Michael et al. 1 996. The Developm ent of the Stream Condition Index for Florida. F l orida Department of Environ m ental Protection, Tallahassee, Florida. Bortone, S.A. and R.K. Turpin. 1999. Tape gras s life his t ory m e trics ass o ciated with environm ental variables in a controlled estuary. In Seagrasses: Monitoring, Ecology, Physiology, and Management, S.A. Bortone (ed.). CRC Press, Boca Raton, pp. 65-79. Bortone, S.A. and M.A. W ilzbach. 1997. St atus and Trends of the Co mm ercial and Recreational Landings of Spotted Seatrout (Cynoscion nebulosus): South F l orida. Florida Cen t er for Environm ental Studies Techn i cal Pub lication No. 2. Palm Beach Gard ens, FL. 47 pp. Bossart, G. D., D. G. Baden, R. Y. Ewing, B. Ro berts and S. D. W r ight. Brevitoxicosis in

m a natees (Trichechus manatus latirost ris) from the 1996 epizootic: gross, histologic and immunoh istochem ical f eatures. Toxicol. Pathol., 26: 276-282 (1998).

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Estuary and the resou r ce-based m e thod fo r evalu a tion. In Pro ceedings of the Charoltte Harbor Public Conference and T echnical Sym posium, S.F. Treat (ed.).

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### Charlotte Harbor Estu ary Program , Tech . Rep. No. 98-02, North Fort Myers, Florida, pp. 88-91.

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### Drew, R.D. and N.S. Scho m e r 1984. An Ecological Characterization of the Caloosahatchee River/Big Cypress Watershe d. U.S. Fish and W ildlif e Servic e. FW S/OBS-82/58.2. 225 pp. Duarte, C.M. 1991. Seagrass depth lim its. Aquatic Botany. 40: 263-377. Durako, M.J. 1988. The seagrass bed: a comm uni ty under assault. Florida Naturalist F a ll 1988 pp. 6-8.

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### Meeder, J.F. , M.S. Ross, G. Telesnicki, P.L. Ruiz, and J.P. Sah. 1996. Vegetation analysis in the C-111/Taylor Slough Basi n. Docum e nt 1: The Southeast S a line Everglades revisited: a h a lf-centu ry of coastal vegetation change. Docu ment 2: Marine transgression in Southeast S a line Ev erglades, Florid a: rates, cau s es, and plant sedim e nt responses. Final Re port. Contract C-4244. Southeast Environm ental Rese arch Program . Florida In te rn ationa l Univ ersity, Miami, FL. Miles, D.W

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### Twilly, R.F. and J.W

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### U.S. Fish and W ildlife Service. 1999. Sout h Florida Multi-species Recovery Plan. Atlanta, Georgia. 2172 pp.

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. 1987. Seagrass -ass ociated i nvertebrate communities of the southeas tern U.S.A.: A review. In Pro ceedings of the Sym posium in Subtropical-tropical Seagrasses o f the Southeastern U.S., Pub lica tion 42, M.J. Durako, R.C. Phillips, and R.R. Lewis (eds.), 89-116. Bureau Ma rine Research, Florida Departm e nt of Natural Res ources, St.P etersbu r g. Volety, A.K. 1995. A study of the historic oys ter parasite, Perkinsus m a rinus : I) Disease
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. 1961. The fauna of oyster beds with special reference to the salinity factor. Ecological Monographs 31:239-266. Weinstein, M.P., C.M. Courtney, and J.C. Kinch. 1977. The Marco Island estuary: a summary of physiochem ical and biological param e ters. Fla. Sci. 40(2): 98-124. White, M.E. and E.A. Wilson. 1996. Predators, p e sts, and co mpetitors. In : The Eastern Oyster, Cras sostrea virg inica. V.S. Kennedy, R.I.E. Newell, and A.F. Abl e (eds.) Maryland S ea Grant College Publication (UM-S G -TS-96-01). 559-79 pp. Yokel, B.J. 1975. Rookery Bay land use studi es: environm ental planning strategies for developm ent of a m a ngr ove shoreline, No . 5. Estuarine Biology. Conservation Foundation, Washington, D.C.

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### Addendu m

SUMMARY FORM (3 PAGES)



## SOUTHWEST FLORIDA FEASI B ILITY STUDY – CALOOSAHATCH EE ESTUARY

HYDROLOGIC EVALUATI ON PERFORMANCE MEASURES

Name of Per f ormance M e asures Doc u ment : S-79, Shell Point, and San Carlos Bay Freshwate r I n flow

Status (date this 3 page s u mmary created/revised): 12 Ma y 20 0 5

For: 5/12/05 DRAFT of full Performance Me asures Docu ment (atta ched). Previous Draft 4/20/0 5

Category: Hydrolo g ic – ( W ater Levels, Flow Volu mes )

Justification: The Caloosahatchee Ri ver is the major source of freshwat e r for the Caloosahatch ee Estuary an d southern Charlotte Harb or aquatic en vironm ent. The river bisects its watershed and now functions as a primary canal (C-43) that conve y s both runoff from the Caloosahatch ee wat e rshed and regulat or y re leases from Lake Okeechobee. The C-43 has undergone numerous physical changes to fac ilitate increased freshwater discharge for flood protection and m e et water suppl y dem a nds. Together, these phy s i cal changes and alterations of the natural freshwater inflow to the Caloosahatchee Estuary ha ve caused unnatural large scale fluctuations i n the salinity an d water qualit y with in the area above Shell Point, as well as reduction in environm ental stability for the San Ca rlos Bay area. The area’ s bi otic richness and significant econom ic value are threatened b y l ong-ter m shifts in water quantit y and qualit y

.

Desc ription of Perfor mance Measu r e : Reduce the high variability i n freshwater inflow to the Caloosahatchee Estuary
, thereb y restoring the full range of salinity alo n g its longi tud i nal axis required to suppor t naturally occurring c onditions for estuarine b i ota. This can be

acco m p lished by : (1) reduc tion of wet se ason high fl ow fro m the w a tershed, c a pturing and storing this water, and then releasi ng it during the dr y season in a m o re environm entally sensitive and beneficial m a nner to estua rine resources; and (2) reducing discharges from Lak e Okeechobee to the Caloosahatchee Estuar y.

SWFFS/ C ERP Tar g ets & Current Condition: Ecological Pe rform a nce targe t s 1. (a) Maintai n a 30-da y m oving average salinity < 10 ppt during the dry season at the Ft. My ers contin uous salinit y sensor (near the surface at the Ft. My ers 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 ( v alues are provisional and may be adjusted after cur r ent

37FINAL - Caloosahatchee & Charlotte Harbor CEM 22 Ma y 2006

research (M ML 2004 and 2007 reports) are evaluated) ; (b) Daily average salinity shall not exceed 20 ppt at Ft. My ers m o re t h an once every two y ears, and neither shall the 30-da y m oving average salinity of 1 0 ppt (MFL Rule: SFWMD 2000); (c ) Lim it the occurrence of average m o nthl y salinity <15 ppt at t h e Cape Coral Bridge sensor, so salinity > 20 ppt is prom oted in I ona C ove, which is supportive of m i nim u m seagrass density (coverage > 3 0 % at 1 meter water depth and average blade length > 10 cm - value s ar e provisional and may be a d justed upon further resear ch); and (d) Maintain daily salinit y at Piney Point > 5 ppt, so that minim u m conditi ons are provided for the recruitment, survival, and growth of juve nile oysters upstream of Shell Point duri ng Ma rch – October (ju v enile oy ster growth > 2.5 mm a m onth; recruitment > 3 spat s per substrate sh ell a

m onth; and m o rt ality < 20% per m onth - values ar e based on information interpreted from Volety et al. 2003). 2) Maintain an average monthly salinity > 25 ppt, as m e asured at the Sanibel Causew ay Bridge near surface continuous sensor, so that hi stori cal seagrass density and coverage in the San Carlos B a y area (as dete r m ined fro m previous survey s, h ydro acoustic m o n itoring, and aerial photography ) is protected and restored to a prev i ous conditi on (at least circa Harris et al. 1983) that includes reestablish m e n t of continuous coverage at deeper depths in the San Carlos Bay area between Shel l Point and the Sanibel Causeway

.

Hy drologic perfor m anc e ta rgets to achieve the Ecological targets
1a). For each a lternative, c o mpare the num b er of tim es that m ean m onthly infl ows from the Caloosa h atc h ee

w a tersh e d fall b e low a l o w-fl o w li m it o f 450 cf s , m easured at S-79
, d u rin g O c t o b e r t o Ju ly . Th e alternativ e

w ith th e few e st nu m b er of times th at m o n t h l y av erag e flows fall b e l o w 450 cfs w ill b e con s id ered b e tter fo r p r o t ectin g aquatic v e g e tation
, o y sters, an d fi sh co mm u n itie s.

1b). For eac h a lternative, c o mpare the fre que n cy th at the m e an m o n t h l y low

- flow limit o f 45 0 cfs th r ough S-79 fr om t h e wat e rs hed wa s not m e t for just o n e m ont h ( n o t fol l o we d by a not her m o nt h b e l o w t h i s l o wflow limit), as w e ll as th e frequ e n c y fo r 2
, 3, 4

... etc. consec utive m onths

. T h e w a t e r ma n a g e me n t altern ativ e w ith th e few e st n u m b er o f con s ecu tiv e m o n t h s belo w 45 0 cfs will b e con s id ered b e tter for protecting estuarine a q uatic resources

. 1c). For each a lternative, c o mp are the fre que n cy that the m e an m onthly low-flow limit of 45 0 cfs th r o ugh S-79 fr om t h e wat e rs hed wa s not m e t for just o n e y ear ( n ot fol l o we d by an ot he r y ear wi t h m ont hs bel o w 45 0 c f s ) , as we ll as the fre que ncy for 2, 3, 4...etc. co n s ecutiv e years. Th e w a ter m a n a g e men t altern ative

w ith th e f e w e st nu m b er of year s an d con s ecutiv e years with avera g e m onthly flow occ u rre n ces below 450 cfs w ill b e co nsid ered b e tter fo r pr o t ecting estu arin e aqu a ti c reso urces 1d )

. Co upl e t h e hy d r ody nam i c m odel wi t h t h e Va llisn e ria m odel t o est i m a t e pl ant c o ver a ge a n d ot her metrics w ith in th e li m its o f the m o d e l. Th e altern ativ e th at p r ov id es t h e b e st Va llisn e ria m o d e l resu lts fo r th e reg i on up stream o f U.S. 41 Bri d g e s in Ft . Myers w ill b e con s id ered m o re d e sirab l e.

2a). For each managem e nt alternativ e, com p are the num b er of tim es th at m ean m onthly infl ow from the
waters hed exce eds 2,800 cfs at S-79 . Th e alt e rn ativ e w ith th e few e st nu mb er of tim es th at th is criterion is exceeded at any tim e of y ear will be considered better for protecting bot h SAV an d juvenile oysters at Shell Po in t and u p strea m . A d d itionally, a b e tter ran k i n g w ill b e giv e n t o th e altern ativ e w ith the least nu m b er o f d i sch a rg es ab ov e th ese limits du ri n g March th ro ugh O c tober, i n o r d e r to l i m i t critically l o w salin ity

co nd itio ns from o ccu rring both up stream and d o wn str eam o f Shell Po i n t, w h ich threatens estu arin e

reso u r ces, i n cl udi ng S A V an d ju ve ni l e oyst er rec r uitm ent and s u rvival 2b). For eac h a lternative, c o mpare the fre que n cy th at t h e m e an m ont hl y i n f l ow fr om t h e w a t e rshe d,

m easured at S-79 , e x ceeds 2,800 c f s for just one m onth (not followe d by a not her m onth a b ove t h is limit), as well as t h e freque ncy for 2, 3, 4... etc. c onsecutiv e m o n t hs. Th e altern ativ e w ith th e few e st co n s ecu tiv e

m o n t h s th at v i o l ate th is criterio n t h rou gho u t th e y ear w ill be con s id ered better for p r o t ectin g est u ari n e resources, i n clu d i n g juv e n ile o y ster recru itmen t and su rv i v al. Ad d ition a lly, a b e tter rank ing w ill b e g i v e n to th e altern ativ e w ith th e least nu m b er of d i scharg es abov e these li m its d u r i n g March throu g h O c tob e r, i n

38FINAL - Caloosahatchee & Charlotte Harbor CEM 22 Ma y 2006

o r d e r to lim it c r itically lo w salin ity co n d itions fro m o ccurri n g bo th up strea m an d do wn st ream o f Sh ell Po in t, wh ich threaten s estu ari n e re sources, i n cluding SAV and juvenile oyster recruitm e n t and survi v al

3a). For each a lternative, c o mpare the num b er of tim es that m ean m onthly and m ean wee k ly infl ows from the wate rshe d exceed 4,500 c f s at S-79 (w eek l y is im p o r tant for p r o t ectin g o y ster recru itmen t an d su rv iv al). Th e altern ativ e w ith t h e least n u m b e r o f times flow s ex ceed th ese limits w ill b e co nsid ered b e tter fo r protecting the estuarine res ources, i n cl u d i n g t hose d o w nst r e a m i n t h e S a n Carl os Bay reg i on. A d di t i onal l y , a b e tter ran k i ng w ill b e g i v e n to th e altern ati v e w ith th e least nu m b er of d i sch a rg es abov e th ese lim i t s d u ring March th rou g h O c tob e r, i n o r d e r to li mit critica lly l o w salin ity cond itio n s fro m o c cu rring b o t h

u p s t r eam an d do wn stream o f Sh ell Po in t, which threat en s estu arin e resou r ces, in cl u d i n g SAV an d juv e n ile oyster recruitment and survi v a l

. 3b). For eac h a lternative, c o mpare the fre que n cy that m ean m onthly a nd m ean weekly inflows from the
wat e rs hed
, m e asure d at S-79 , excee ds 4, 5 0 0 cfs f o r j u st on e m ont h an d 1 week ( n ot f

o l l o wed by a n ot he r

m ont h o r week ab ove t h i s l i m i t ) , as wel l as t h e fre que ncy f o r

2
, 3, 4...et c. co nsec ut i v e m ont hs a n d wee k s. Th e altern ativ e w ith t h e few e st n u m b e r o f con s ecu tiv e m o n t h s and week s th at v i o l ate th is criterio n w ill be

co nsid ered b e tt er for p r o t ecting aq u a tic resources, i n cl ud ing j u v e n ile o y sters. Add itio n a lly, a b e tter rank i n g

w ill b e g i v e n t o th e altern ative w ith t h e least nu m b er of co nsecu tiv e d i sch a rg e p e riod s abo v e th ese li m i t s d u ring March th rou g h O c tob e r, i n o r d e r to li mit critica lly l o w salin ity cond itio n s fro m o c cu rring b o t h

u p s t r eam an d do wn stream o f Sh ell Po in t, which threat en s estu arin e resou r ces, in cl u d i n g SAV an d juv e n ile oyster recruitment and survi v a l

. 4). For each alternative
, c o m p are the freque ncy di stribution of m onthly ave r age freshwate r inflows th ro ug h S-79 f o r t h e e n t i r e peri od o f r ecor d bei n g e v al uat e d. The al t e rnat i v e wi t h t h e fre que ncy d i st ri but i o n of in flow s t h at b e st app r o ach es t h e rang e (EST0 5 ) d e fi n e d in t h e m a in Performan ce Measures Do cu m e n t w ill be c o n s i d ere d bet t e r f o r pr ot e c t i ng est u ari n e reso u r ces, w h i l e f u rt he r pr om ot i n g bi ot i c di v e rsi t y

. Specifically, the alternative t h at m a xim i zes u p to 75 % of f l ow s f r o m S- 79 i n th e 450 t o 800 cf s an d a l mo s t all th e rem a in i n g fl o w s in t h e 80 0-2 800 cfs ran g e w ill b e con s id ered th e m o st d e sirab l e.
The preferred flow distributio n (EST05) may change as more in formation is provided regarding: predevelopment flow and salinit y conditions; nat u ral variation; what salinit y conditions were naturally (historically ) associat ed with droughts a nd flood events; and what flows are needed to protect and restore the biotic feat ures in the current and future devel oped s y stem

.

Rationale: The Caloosahatchee River is the major source of freshwate r for the Caloosahatch ee Estuary and southern Charlotte Ha rbor aquatic environm ent. The Caloosahatchee Estuary and d o wnstream region sup ports a wide di versity of estuarine or ganism of environm ental and commer cial value. A lteration to the natural freshwater inflow to the es tuary have caused unnatural large scal e fluct u ations in the salinity and water quali ty withi n the area above Shell Point, as well as reduction in environmental stab ility for the San Carlos Bay area. The resu lting i m pacts to seagrass, oy sters, benthic invertebrates, an d fishes can b e dramatic an d long lasting. It is the goal o f the Southwest Florida F easibility Study (SWFFS) and relevant CERP efforts to reduce the high variabilit y in freshwater inflow to th e Caloosahatchee Estuary
, so to restore a full range of salinit y alon g its longit udinal axis th at is supportive of naturall y oc curring estuarine biota. This go al can be accom p lished by reducing hig h flows durin g the wet s e a s on, capturing and storing this w a ter, then releasing it in a m o r e e nvironmentally sensitive manner that is beneficial to estuarine resources during the dry season.

Modeling Evaluatio n P r otocol: Regional and subregional models will be used to si m u late hist orical (base) and predicted flows to the estuary with and without SWFFS and CERP project features for each alternative considered. Natural sy stem flow s to the Caloosahatchee Estuary fr om its watershed and ti dal b asins m a y also be considered in order to com p are fl ows associat ed wi th the developed basins. Output (flow s) from the above m odel runs will be used to evaluate the level that hydrologic targets are achieved for each alternative and base condition.

39FINAL - Caloosahatchee & Charlotte Harbor CEM 22 Ma y 2006

Model output will be used as input for the estuari ne salinity m odel to further assess changes in salinity . To help evaluate if ecological goals w ill be met, the estimated salinit y will be used to assess the i m pact on ke y biota by em ploy ing ha bitat suitability indices rel a ted to salinity

. Monitoring Assessment Protocol: 1). Define and asses s appropriate attributes (s pecific species and/ or comm unit y values) to
ascert a in if this project’ s ecological goals are at t a ined and there is a discernable positive im p a ct on the estuary, specificall y including SAV, oy ster, and fish as follows: a). Routinely (at seasonall y im portant inte rvals) m o nitor SAV coverage, density , an d
canop y heigh t to at

least 1.5-2.0 m depth at key species locations. b). Routinely m onitor (at seasonally important in tervals) oy ster survival and recruitment at key locations. c). Routinely m onitor (seasona lly ) water quality, including temperature, D.O
., salinity , nutri ents, chlorophyll, suspended solids, and wa ter clarity along the l o ngitudinal axis of the estuary (S-79 -

Sanibel Causew ay and into lo wer Pine Island Sound and Matla cha Pass). d). Monitor r outinel y (at appropriate seasonal intervals) species a nd biotic groups of

concern as se parately defined in performance m e a s ure docu m ents and the CE conceptual m odel. At a

m i n i mu m, i n s u r e t h e Monitoring Asses s ment Plan (MAP) effort within RECOVE R is being fulfill ed. 2). Scientifically assess and publicly a g ree wh at co nstitutes desirable natural variability (predevelopment

condit i ons) related to salinit y an d cau sal freshwater inflow fro m S-79 and t h e tidal basin. 3). Install and m onitor flow gages in downstrea m ti dal tributaries to begin asse m b ling a long term data set to: verify m odel predictions of flo w s; determ in e actual am o unt and t i m i n g of tidal tributary flows relate d to MFL requirements for achieving the salinity c r iteria; and to help

asse ss flow i m p acts on biota being m onitored for CERP (RECO V ER). 4). Monit o rin g S-79 discharge adherence to the selecte d alternative flow distribution. 5). Continue to m a intain and m onitor exis ting 7 salinity recorders and other per m anent sensors in the Caloosahat chee Es tuary

. Install new sensors to monitor salinit y and other water qualit y parameters of concern at key loc a tions for VEC. Suggest additional sensors be located in western San Carlos Bay
, lower Pine Island Sound, a nd Matlacha Pass. 6). Assess limits of SAV m o rphology for pr oviding suitable habitat as a VEC and its relationship t o flow, salinit y, and water qualit y con d it ions. 7). Finish de velopm ent of the: tape gra ss m odel; C a l oosahatchee Hy drodynam i c/Salinity Model; a water qualit y m odel com ponent; habitat sui t abilit y m odels; and a seagrass m odel fo r the lower estuary

.

Comments:

40FINAL - Caloosahatchee & Charlotte Harbor CEM 22 Ma y 2006

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