Relating Changes in Freshwater Inflow to Species 

Distributions in Rookery Bay, Florida, via Habitat Suita

Modeling and Mapping 

PETER J. RUBEC1

, JESSE M. LEWIS1, MICHAEL A. SHIRLEY

 PATRICK O’DONNELL2, and STANLEY D. LOCKER3

1

Florida Fish and Wildlife Conservation Commission 

Fish and Wildlife Research Institute 

100 Eighth Ave. S.E. 

St. Petersburg, Florida 33701 USA 2

Florida Department of Environmental Protection 

Rookery Bay National Estuarine Research Reserve 

300 Tower Road 

Naples, Florida 34113 USA 3

College Of Marine Science, University of South Florida 

140 7th Ave. S. 

St. Petersburg, Florida 33701 USA 

ABSTRACT 

We conducted this study to assess the influence of changes in fre

inflow on the distribution and relative abundance of estuarine sp

Rookery Bay, Florida. Originally, freshwater entered the bay via she

In the 1960s, the creation of a canal system, which funnels water th

weir situated on Henderson Creek, altered inflows. To assess the e

these changes, we initiated monitoring in Rookery Bay and Fakahatch

The latter estuary served as a control, because it still has natural sheet-f

Bottom types and bathymetry in Rookery Bay were mapped usin

scan and QTC View sonar systems. Bottom types were verified via a

of bottom-grab and core samples. Salinity, temperature, and dissolved 

data collected seasonally in the two estuaries were interpolated to map 

column habitats. 

When this study was initiated, no long-term fisheries-inde

monitoring (FIM) had been conducted in Rookery Bay. Consequen

analyzed FIM data collected in Charlotte Harbor to determine habitat a

for 22 life stages of 11 species of fish and macroinvertebrates. Su

functions were derived by fitting splines to catch rates (CPUEs) 

environmental gradients and by calculating mean CPUEs within bott

categories. Abundance indices transferred from Charlotte Harbor were 

to Rookery Bay habitat layers so that we could conduct raster-based 

suitability modeling (HSM) for a dry season (spring) and a wet 

(summer) in Rookery Bay with differing freshwater inflows. Predicte

maps depict suitability zones (low to optimum) across the estuary. The 

were validated by calculating mean observed CPUEs (from month

sampling) within the predicted zones. Increasing mean observed 

across the zones indicated that the models adequately predicted the 

distributions of the species’ life stages. 
KEY WORDS: Fish habitat, GIS modeling, mapping, Rookery Bay 

Modela y Traza la Relaciona de los Cambios 

an la Afluencia de Agua Dulce a Distribuciones de 

Especias en Rookery Bay, Florida 

La Oportunidad del habitat que Modela y Traza la Relaciona 

Cambios En la Afluencia de Agua Dulce A Distribuciones de Espe

Rookery Bay, Florida. Realizamos este estudio para valorar la influe

cambios en la afluencia de agua dulce en distribuciones y abundancia 

de especias estuarinas en la Bahía de Rookery, Florida. Originalmen

dulce entró la bahía vía el sheet-flow. En la década de los 60, la creació

sistema de canales, que encauza riega por un vertedero situado en He

Creek, y altero afluencias. Para valorar el impacto de estos cambios, n

iniciamos un muestreo en Rookery y Fakahatchee Bay, Florida. Faka

Bay sirvió como un control, porque todavía tiene el sheet-flow natural. 

Tipos de fondo y bathymetry en Rookery Bay fueron trazado ut

side-scan y QTC View sistemas de sonar. Tipos de fondo fueron ver

por análisis de muestras inferioras de agarro y centro. Datos de sa

temperatura, y niveles disueltos de oxígeno se collecionaron durante d

tes temporadas en los dos esteros y fueron interpolados para trazar los h

de las columnas de agua. 

Porque no hay muestro consistente de pescados en Rookery Bay 

plazo, nosotros analizamos los datos de pescados colleccionados en C

Harbor para determinar las afinidades del habitat para 22 etapas de vid

especies de pescado y macro-invertibrados. Las funciones de la opo

fueron derivadas por tiras para agarrar los datos de la tasa (CPUE) a tr

declives ambientales, y calculando las unidades de procesamiento c

malas dentro de categorías de tipo fondo. Los índices de la abu

transferidos de Charlotte Harbor fueron aplicados a capas de ha

Rookery Bay para realizar la oportunidad trama-basado del habitat mo

(HSM) durante una temporada (primavera) seca y una temporada (

mojada en Rookery Bay. Los mapas predichos de HSM represe

oportunidad las zonas (bajo a óptimo) a través del estero. Los modelo

verificados calculando medio las unidades de procesamiento c

observadas (de rastreo mensual que prueba) dentro de las zonas pr

Creciente significa observó que las unidades de procesamiento cen

través de las zonas indicaron los modelos predijeron correctame

distribuciones espaciales de la especie’ las etapas de la vida. 

PALABRAS CLAVES: Habitat modelando, distribuciones espaciales, 

predichos Rookery Bay 
INTRODUCTION 

Watersheds in South Florida have been extensively altered 

canalization of streams and by water diversions through canals. The e

these changes on aquatic communities are not well understood (Sk

Browder 1998). A number of studies in Florida clearly demonstrate t

to manage freshwater inflow into estuaries in order to protect marine re

(Browder and Moore 1981, Browder 1985 1991, Livingston et al. 199

Browder et al. 2002). 

Starting in the 1920s, the Big Cypress Swamp near Naples was 

with the creation of U.S. Highway 41 (Gardner 1988). The creation 

Southern Golden Gate Estates Canal system and the Faka Union-

Ranch Canal system, to drain agricultural and residential areas dur

1960s, and the construction of major highways have altered the q

quality, and timing of freshwater entering the Rookery Bay system an

estuaries in the Ten Thousand Islands region. The canal systems, co

with deforestation and increasing urbanization, have reduced the am

upland swamps, lowered the water table, and reduced regional rainfal

in turn affected freshwater inflows to the estuaries (Carter et al. 1973, B

and Moore 1981, Colby et al. 1985). Consequently, the Big Cypres

Board of the South Florida Water Management District (SFWMD) fun

present study to provide information to help manage freshwater inflo

Rookery Bay in order to protect the integrity of estuarine habitats 

conserve estuarine fish and macro-invertebrate species present in the es

The Florida Fish and Wildlife Conservation Commission’s (FW

and Wildlife Research Institute (FWRI) has developed habitat su

models (HSM) using geographic information systems (GIS) to predic

distributions and relative abundance of estuarine species (Rubec et a

1999, 2001, 2003a,b). One of the main strengths of using GIS is its a

integrate data from a wide variety of sources. By transferring abu

relationships from estuaries with fisheries-independent monitoring 

programs, the HSM can allow the prediction of species distribut

estuaries that lack long-term FIM programs. 

The FWRI, Florida Department of Environmental Protection (FD

the University of South Florida (USF) College of Marine Science colla

to map habitats and model species distributions in relation to cha

environmental conditions in the Rookery Bay system. Data were c

across Rookery Bay and Fakahatchee Bay (control estuary). The e

mental data points were interpolated to create habitat layers for use w

HSM model. Habitat affinities for key species were derived from F

previously gathered by FWRI in Charlotte Harbor. The predicted HS

determined changes in habitat suitability associated with salinity 

related to different freshwater inflows. The study was conducted to 

water managers with information to help manage water flow through 

situated at the head of Henderson Creek, which regulates inflow f

Henderson Creek canal to the Rookery Bay system. It demonstrates th

HSM to assess the effects of changes in freshwater inflow on estuarine 
METHODS 

Study Area 

The Rookery Bay National Estuarine Research Reserve (RB

situated south of Naples, encompasses an area of 445 km2. It inclu

Rookery Bay system (424.4 hectares) and estuaries in the Ten Th

Islands. Rookery Bay is surrounded by mangroves and has islands w

rookeries, sand and mud substrates, oyster beds, and some areas w

merged aquatic vegetation (SAV). Most of Rookery Bay is quite shall

m). The bay’s high turbidity prevented us from using aerial photogr

map SAV distributions in Rookery Bay. 

Gear Standardization 

One of the main goals of the present study was to map geo

distributions of marine fish and macro-invertebrate species by young

(YOY), juvenile (Juv), and adult life stages during spring and summer 

in Rookery Bay. The HSM requires as input indices of relative abu

across environmental gradients for each species’ life stage. Ideall

indices would be obtained from FIM in Rookery Bay. Althoug

sampling (4 - 5 samples per month) has been conducted since 2000, th

insufficient long-term FIM sampling in the bay. Consequently, we u

larger FIM datasets (600 to 1500 samples per season) obtained in C

Harbor from 1989 to 1997 to create suitability functions (Rubec et al. 2

To use all survey data in a comprehensive analysis, sample CPU

standardized across gear types to create gear-correction factors by spec

stages by using a modification of Robson's (1966) "fishing power" est

method (Ault and Smith 2000). Gear-corrected CPUE data sets for C

Harbor were created for the following species life stages: YOY (10 - 

standard length-SL), Juv (120 - 199 mm SL), and adult (3 200 mm SL) 

seatrout (Cynoscion nebulosus); Juv (10 - 99 mm SL) and adult (3 100 

pinfish (Lagodon rhomboides); Juv (15 - 29 mm SL) and adult (3 30 m

bay anchovy (Anchoa mitchilli); YOY (10 - 139 mm SL) Juv (140-2

SL) and adult (3 240 mm SL) sheepshead (Archosargus probatocephalu

duorarum); and Juv (10 - 299 mm SL) red drum (Sciaenops ocellatus)

110 mm SL) hardhead catfish (Arius felis); Juv (150 - 279 mm SL) and 

280 mm SL) common snook (Centropomis undecimalis); Juv (10-149 m

and adult (3 150 mm SL) sand seatrout (Cynoscion arenarius); YOY (

mm SL) and Juv (150 - 199 mm SL) spot (Leiostomus xanthurus); 

YOY (10 - 119 mm SL) and adult (3 180 mm SL) southern 

(Menticirrhus americanus); Juv (5 - 17 mm carapace length-CL) and ad

mm CL) pink shrimp (Farfantepenaeus 

Suitability Functions 

Habitat affinities for 11 species of fish and macroinvertebrat

determined from 8.5 years of FIM data gathered in Charlotte Harbor fro

to mid-1997. The analyses involved development of suitability func

fitting splines across environmental gradients to mean gear-correcte
rates (CPUEs) for each species’ life stage (Rubec et al. 2003b). Firs

CPUEs were computed within each season for each environmental v

Then, splines (variable lambda) were fitted to mean CPUEs across grad

salinity, temperature, dissolved oxygen, and depth using JMP softwa

2002). Mean CPUEs were computed by 1 g/L (‰) salinity, 1oC temp

1-mg/L dissolved oxygen (DO), and 1 meter depth intervals. Season

CPUEs were also computed by Sand, Mud, and SAV bottom-type class

mean CPUE values across each gradient were placed in look-up tables 

GIS to facilitate HSM analyses. We then transferred the suitability fu

derived from Charlotte Harbor monitoring to Rookery Bay. 

Habitat Mapping 

The mapping of water-column and benthic habitats in Rooke

required data collection, data integration, and the use of GIS-based sof

interpolate raw data points. Bottom type and bathymetry were det

from data gathered by USF using sidescan and Quester Tangent QT

sonar systems (Locker and Wright 2003). Salinity, temperature, and d

oxygen data were gathered seasonally in the two estuaries using a H

MiniSonde Model 4a data logger. 

A skiff with the data logger mounted to the boat’s gunnel, a dif

global positioning system (DGPS), and a Furuno LS-6000 depth 

linked to a Furuno 520ST–PWD transducer were wired to a rugged A

laptop computer to gather environmental data. The data were merged 

computer using software developed for the project (Rubec et al. 2003b)

The boat cris-crossed Rookery and Fakahatchee bays during separ

to gather data believed to be representative of five seasonal time perio

to August 2002, September to November 2002, December 2002 to F

2003, March to May 2003, and June to August 2003). The data log

used to collect salinity, temperature, and dissolved oxygen data in R

Bay on August 22, 2002; October 30, 2002; February 20, 2003; May 2

and July 10, 2003. Data were collected in Fakahatchee Bay on Au

2003; October 31, 2003; February 21, 2003; May 1, 2003; and July 11, 

The GeoStatistical Analyst module associated with ArcGIS 8.3 w

to interpolate the environmental data points in an iterative manner using 

punctual kriging (Johnston et al. 2001). Semivariograms were used to 

the most optimal interpolation for each environmental variable. Raste

grids were created representing seasonal habitat layers for salinity, t

ture, and dissolved oxygen in the two estuaries, as well as grids for bath

(depth) and bottom type in Rookery Bay derived from data gathered by 

Habitat Suitability Modeling 

We used the Spatial Analyst extension in ArcMap associated with 

8.3 to relate abundance indices from Charlotte Harbor, for the spring 

May) and summer (June - August) seasons, with the habitat layers in R

Bay to conduct HSM analyses for Rookery Bay. The HSM analys

conducted to spatially compare the effects of several inflow condit

species’ life stages at two time periods during the summer and at one 

during the spring. 
The geometric mean algorithm was used to compute composite su

values in order to create predicted seasonal HSM maps for Rooke

Composite HSM values within each 18.5 m2

 cell were computed 

geometric mean of the suitability values associated with the habitat lay

environmental factors. Predicted HSM values were derived from abu

indices associated with five habitat layers, as follows: 

 

 HSM= ( Π CPUEi)

1/n . 

Separate HSM analyses were conducted for each time period to 

species distributions by each species’ life stage in Rookery Bay. The 

in predicted HSM grids were scaled from 0 to 10. The predicted HS

were classified into equal CPUE ranges to create four suitability zone

Moderate, High, and Optimum). This allowed us to compare the ef

changes in freshwater inflow into Rookery Bay. Percent changes in to

of Rookery Bay for the four HSM zones were used to determine whe

changes in salinity were beneficial or not for various estuarine spec

stages. 

Three tables were associated with each HSM map depicted on t

ROM (Rubec et al. 2003b). The first table presented the observed d

(no./m2

) within predicted HSM zones and minimum and maximum CPU

the standard deviation for each zone. Provided there were observed da

first table, a histogram was created as part of the validation analys

second table presented predicted densities (no./m2

) for the four HSM 

The third table presented the areas, expressed in hectares, for each 

predicted HSM zones and percentages of the total area for each of the 

ity zones in the estuary. Hence, the predicted suitability zones were 

rized both in terms of their area and by the proportion of the total ar

zone occupied in the Rookery Bay system. 

The HSM analyses were conducted for two time periods with d

inflow conditions (August 2002, July 2003) during the summer 

Changes in percentages of the total area with High plus Optimal suita

the estuary were computed to determine whether changes in salinity d

tions, associated with changes in freshwater inflow, were “suitable” for 

life stages of estuarine species. 

Model Validation 

The models presented are heuristic and qualitative in nature, 

precluding any formal statistical testing of model efficacy (Rubec et al

A simple test was developed to assess the adequacy of the HSM a

(Rubec et al. 2001, 2003a,b). If histograms of mean CPUE values 

within the predicted zones increased from “Low” to “Optimum”, then 

performance was judged to be adequate. 

CPUE data obtained by RBNERR staff from trawling on a month

in Rookery Bay (from 2000 to 2003) were used to validate the predicte

maps (Rubec et al 2003b). The observed CPUE data (74 samples fo

and 65 samples for summer) were overlaid onto the predicted season

maps. Then, mean CPUEs were calculated within the low to o
suitability zones. Increasing mean observed CPUEs across the HSM 

indicate whether the models adequately predicted habitat suitability f

species’ life stage. 

 RESULTS AND DISCUSSION 

Habitat Mapping 

The full results of the study are presented on a CD-ROM that ac

nied a report to the SFWMD (Rubec et al. 2003b). There were 24 s

habitat maps created for salinity, temperature, and dissolved oxy

Rookery Bay and Fakahatchee Bay, and one map each for bottom t

bathymetry in Rookery Bay. 

Water Quality 

In the bays proper (excluding tributaries), the ranges in water temp

between the two estuaries were similar during the spring (26 - 28 

during the summer (29 - 32oC). Dissolved oxygen values ranged from 

mg/L in Rookery Bay and 4 to 6 mg/L in Fakahatchee Bay during May 

to 7 mg/L in Rookery Bay and 3 to 6 mg/L in Fakahatchee Bay during 

2002, and 1 to 6 mg/L in Rookery Bay and 2 to 5 mg/L in Fakahatch

during July 2003. Low DO values (1 to 2 mg/L) extended out f

Fakahatchee River into the eastern part of Fakahatchee Bay during 

2002. Salinities were similar (30 - 33 g/L) in both estuaries during M

(the dry season). Marked differences in salinity were found betwee

hatchee Bay (8 - 16 g/L) and Rookery Bay (30 - 31 g/L) during Augu

Inflow data obtained from SFWMD indicates that the higher salin

Rookery Bay during August 2002 were related to the fact that the weir 

at the head of Henderson Creek kept freshwater from entering Rooke

There was heavy rainfall at the end of June, which lowered salinities 

estuaries during July 2003. Salinities ranged from 26 to 29 g/L in R

Bay and 16 to 19 g/L in Fakahatchee Bay during July 2003. 

Affinities for Salinity 

The ranges of salinities within which various species’ life stages 

highest affinity (top 25% of each suitability function) in Charlotte 

during the spring are depicted in Figure 1. The following species’ lif

had affinities for low salinity (< 10 g/L): YOY spot, Juv sheepshead, J

seatrout, Juv red drum, Juv spotted seatrout, and Juv bay anchovy. 

species’ life stages were found to have an affinity for moderate saliniti

and < 25 g/L): YOY and adult kingfish, YOY spotted seatrout, and a

anchovy. Other species had an affinity for high salinities (≥ 25 g/L): J

YOY and adult sheepshead, Juv spotted seatrout, Juv and adult pink 

adult hardhead catfish, Juv and adult snook, YOY and adult spotted s

and Juv and adult pinfish. The predominate salinity range (30 - 33 

Rookery Bay proper and the available salinity range (18 - 33 g/L

Rookery Bay system (including both the bay and Henderson Cree

unsuitable for the species with affinities for low salinity. Those spec
moderate salinity affinity were restricted to a relatively small area in 

son Creek. Only species whose life stages had affinities for higher s

had ranges that overlapped with the predominate salinity range (30 - 

available in Rookery Bay during the spring. 

 Figure 1. Salinity ranges over which various species’ life stages had 

densities (CPUEs) during spring in Charlotte Harbor and the predomin

proper) and total salinity ranges (bay plus Henderson Creek) available i

ery Bay during May 2003. 

During the summer, YOY kingfish, Juv sand seatrout, Juv red dr

and adult pink shrimp, and adult hardhead catfish in Charlotte Harbor 

finities for low salinity (Figure 2). Juvenile spot, adult kingfish, ad

seatrout, Juv pink shrimp, Juv and adult spotted seatrout, Juv and ad

anchovy had affinities for moderate salinity. Species with affinities

salinity included YOY, Juv, and adult sheepshead; Juv and adult sno

Juv and adult pinfish. Examining the predominate salinity range (30 - 

and total salinity range (18 - 33 g/L) available during August 2002, it i

ent that salinities in most of Rookery Bay did not match the salinities p

by the low or moderate salinity species’ life stages. 

With increasing rainfall during June and July 2003, the predomina
ity range available (26-29 g/L) matched the ranges preferred by the hig

ity species (Figure 2). However, the expansion of the total range of s

(2 - 29 g/L) indicated that there was more area available in Henderso

with a salinity range preferred by species’ life stages having affinities 

to moderate salinities.

Figure 2. Salinity ranges over which various species’ life stages o

macroinvertebrates had higher densities (CPUEs) during summer in C

Harbor and with predominate (bay proper) and total salinity ranges (b

Henderson Creek) respectively available in Rookery Bay during Augu

and July 2003. 

Percentage of Total Area Suitable for Species’ Life Stages 

To simplify the interpretation, we summed the areas determine

High and Optimum from the HSM analyses to determine the proportion

total areain Rookery Bay that were “suitable” for each species’ li

during the three time periods (Table 1). Although all environmental 

played a role in determining suitability, it is evident that salinity 

between time periods were important in influencing the total area of R

Bay predicted to be suitable for various species’ life stages. Differe
both water temperature and salinity appear to have been important in in

ing the differences in predicted suitability found between the spr

summer time periods. 

We consider the two summer time periods (August 2002 and July 2

be the most comparable because the same suitability functions were u

the HSM modeling for both time periods. There was little differenc

temperature and dissolved oxygen levels monitored and mapped betw

two summer time periods. Hence, we believe that changes in salinity 

most important in explaining the differences in computed habitat su

between these two periods. 

Heavy rainfall that occurred at the end of June 2003 increased the 

lower salinity found on July 10, 2003 in Rookery Bay. The increase in 

predicted to be suitable (Table 1) for Juv bay anchovy (1.61% in Augu

to 38.42% in July 2003) appears to be related to the reduction in salinit

Table 1. Percentage of the total area determined to be “suitable” for 

species’ life stages associated with increasing freshwater inflows duri

time periods in Rookery Bay.

Species’ Life Stage Percentage Percentage Perc

High + High + H

Optimum Optimum Op

May-03 Aug-02 J

Juvenile Bay Anchovy 21.03 1.61 

Adult Bay Anchovy 99.7 43.37 

Juvenile Pinfish 96.4 99.00 

Adult Pinfish 98.9 98.40 

YOY Spotted Seatrout 97 99.80 

Juvenile Spotted Seatrout 46.3 53.41 

Adult Spotted Seatrout 97.3 44.64 

Juvenile Common Snook 85.1 37.57 

Adult Common Snook 99.7 95.30 

Adult Hardhead Catfish 99.61 18.53 

Juvenile Pink Shrimp 99.8 62.83 

Adult Pink Shrimp 99.9 13.16 

Juvenile Red Drum 58.9 5.46 

Juvenile Sand Seatrout 1.1 6.54 

Adult Sand Seatrout 23.33 39.87 

YOY Sheepshead 99.4 97.60 

Juvenile Sheepshead 92.3 8.77 

Adult Sheepshead 46.4 12.44 

YOY Kingfish 5.17 0.37 

Adult Kingfish 3.19 1.52 

YOY Spot 99.8 95.80 

Juvenile Spot 63.06 3.78 
estuary. In contrast, the percentage of the area determined to be suit

adult bay anchovy decreased (43.37% to 10.28%). Some species’ lif

with affinities for higher salinity, such as Juv and adult pinfish, adult c

snook, and YOY sheepshead did not show marked percent changes 

estimated to be suitable over the three time periods (the higher s

present for all time periods were highly suitable). Other species with a

for higher salinity (Juv and adult spotted seatrout, Juv common sno

sheepshead, and YOY spot) were found to have decreases in th

predicted to be suitable, associated with the reduction in salinity dur

2003. The HSM analyses predicted increases in areas with suitable 

during July 2003 for species’ life stages (Juv spot, adult hardhead catf

and adult pink shrimp, Juv sand seatrout, and adult sheepshead) with a

for low or moderate salinities. 

Low percentages of suitable habitat during both summer time perio

predicted for some species such as Juv red drum, Juv sheepshead, an

and adult kingfish. The low suitability of the bay during the two summ

periods predicted for Juv and adult kingfish appears to be related to the 

these fish have for low salinity (lower than what was generally avai

Rookery Bay). The low suitability of Rookery Bay predicted for Juv r

and Juv sheepshead may be related to their high affinity for SAV (the 

short-bladed beds of SAV present in Rookery Bay may not provide su

cover for larger fish). 

Model Validation 

We produced 66 HSM maps to predict species distributions in R

Bay during the spring (May 2003) and summer (August 2002, Jul

seasons (Rubec et al. 2003b). Because, the trawl used for monthly sam

Rookery bay caught only juvenile fish (exceptions were adult bay anch

adult hardhead catfish), the validation test was conducted using those 

life stages. The histograms, created by overlaying the observed data f

species caught in Rookery Bay onto the predicted HSM zones, were f

have increasing relations across the zones in 14 of 23 (60.87%) of th

tested. These results confirmed our ability to adequately predict 

suitability in Rookery Bay using suitability values transferred from C

Harbor. 

CONCLUSIONS 

Large differences in salinity were found between Rookery an

hatchee bays during the summer and fall wet-seasons (Rubec et al. 

This may be partly related to natural and hydrological differences in 

canal runoff, and the size of the drainage basins for the two estuarie

was less monthly rainfall recorded near Rookery Bay (Naples) th

Fakahatchee Bay (Copeland) from 1990 to 2003. Based on data publish

Carter et al. (1973), the average total annual rainfall at Copeland from 1

1972 was 206.13 cm (n = 3) and the average annual rainfall recorded at 

over the same time period was 134.53 cm (n = 3). By comparison, the a

annual rainfall near Fakahatchee Bay at Copeland from 1990 to 2003 (n 
was 155.30 cm (SFWMD reports), and the average annual rainfall at N

near Rookery Bay over the same time period was 138.38 cm (n = 14) (N

National Weather Service on-line data (http://www.dnr.state.sc.us/ w

climate/sercc/index.html). 

Another factor influencing the lower salinities monitored in Faka

Bay in the present study appears to be the high flows of freshwater com

of the Faka Union Canal system. Salinities lower than those in Rook

were mapped in the northwestern part of Fakahatchee Bay, which adjoi

Union Bay, during August 2002, October 2002, and July 2003 (Rub

2003b). 

Differences in the ratios of drainage area to bay area may also 

explain the observed differences in salinity patterns between Rook

Fakahatchee bays during the wet seasons. Historically, the Belle 

watershed feeding water to Henderson Creek was similar in size and 

composition as the Fakahatchee Strand watershed feeding water t

hatchee Bay. The creation of the canal system during the 1960s 

freshwater from the upper part of the Belle Meade watershed thro

Golden Gate Canal to Naples Bay (Yokel 1979, Browder and Moore 1

Yokel (1979) concluded that excessive freshwater discharges f

Golden Gate Canal through the Gordon River into Naples Bay had c

rapid decline in salinities to near freshwater conditions from June 

September. In the lower part of Naples Bay, the freshwater discharge f

Golden Gate Canal suppressed plankton development, which in turn res

a low relative abundance of midwater fish. 

In the present study, we conducted HSM modeling to predict 

distributions and relative abundances of estuarine species’ life st

Rookery Bay over three time periods ordered as they relate to progr

decreasing salinity in the estuary (Rubec et al. 2003b). The modelin

that most of the 22 life stages of the 11 species modeled responded to 

in salinity, related to changes in freshwater inflow. The results demo

our ability to predict habitat suitability associated with the changes in 

in Rookery Bay. It appears that a number of estuarine species’ lif

would benefit if the Rookery Bay system received more freshwater 

during both the dry (winter and spring) and wet seasons (summer an

Further research is needed to define the salinity conditions that m

achieved in the Rookery Bay system by water diversions through th

system in the Belle Meade watershed and by fine-tuning the weir on 

son Creek. 

Based on the large differences in salinity ranges observed b

Rookery Bay and Fakahatchee Bay during the wet seasons, it is prob

feasible to augment freshwater inflows to Rookery Bay to exactly m

salinity ranges observed in Fakahatchee Bay. A more realistic mana

goal would be to use Fakahatchee Bay as a reference site, to help acc

the hydrological differences between the two systems, and then set fre

inflow targets for each season in Rookery Bay. This should broaden th

of salinities, and provide a more natural timing and variation in pat

freshwater inflow into Henderson Creek, thereby creating more 

habitats for various species’ life stages. 
Further studies are needed to develop a circulation model that ta

account monthly freshwater inflows and tidal variation in each estua

linking the HSM to both the circulation model and to stream gaugin

upstream weir, it will become possible to predict habitat suitability 

from inflow patterns. We recognize that seasonal patterns of salinity v

(measured by stationary data loggers) are also important (Shirley et al

Protecting biodiversity in the estuary should also become a manageme

through spatial evaluation of diversity-related indices such as species 

and evenness (Drake et al. 2002). We plan to conduct biodiversity-bas

analyses to help predict the volumes and timing of freshwater inflows 

in Rookery Bay to mimic freshwater inflow patterns found in Fakahatc

associated with natural sheet-flow. 

ACKNOWLEDGMENTS 

The participants are grateful for the funding provided to FWC

though a grant (No C-13253) from the Big Cypress Basin Board of th

Florida Water Management District. Comments by Dr. Joan Brow

NOAA/NMFS in Miami and by two anonymous reviewers, and 

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tract to FWC-FWRI. Software for the capture of field data was de

under subcontract from FWC-FWRI to Sasco Inc., Tampa, Florida. 

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