# Site

- Specific Information in Support of Establishing Numeric Nutrient Criteria

for the Southwest Coastal Estuaries
, Including Naples Bay, Rookery Bay, and
the Ten Thousand Islands

Division of Environmental Assessment and Restoration
Standards and Assessment Section Florida Department of Environmental Protection Tallahassee, FL 32399

in cooperation with



# Florida International University Rookery Bay Natio nal Estuary Research Reserve Collier County City of Naples

August 20, 2010Nutri ent Criteria Technical Support Document Southwest Coastal Estuaries

Draft ii August 2010 

### Table of Contents

Executive Summary

................................................................................................................ i Geographic Description and General Information

.................................................................. 1
Naples Bay

................................................................................................ ................................ .5 Rookery Bay and the Ten Thousand Islands

............................................................................... 10 

### Biological Summary

............................................................................................................. 14
General Community Types

........................................................................................................ 14 Natural Communities in Naples Bay

.......................................................................................... 18 Natural Communities in Rookery Bay/Ten Thousand Islands/Whitewater Bay

............................ 20 

### Water Quality Conditions

.................................................................................................... 28
Existing Water Quality Standards

.............................................................................................. 28
Designated Uses

....................................................................................................................... 28
Outstanding Flor ida Waters

...................................................................................................... 28 Summary of Existing Water Quality

........................................................................................... 29



### Sources of Nutrients

............................................................................................................ 42

Waters on the 303(d) List

..................................................................................................... 42 Criteria Development

.......................................................................................................... 44
Regionalization

......................................................................................................................... 44 

### Proposed Numeric Nutrient Targets

..................................................................................... 47
Methodology

............................................................................................................................ 47



### References

.......................................................................................................................... 53 Appendix A: Threaten ed and Endangered Species

............................................................. 57 Appendix B: Impaired Waters List

...................................................................................... 60 Appendix C: Summary of Regionalization Method

............................................................. 62Nutri ent Criteria Technical Support Document Southwest Coastal Estuaries

Draft iii August 2010 

### List of Tables

Table 1. Checklist of nutrient enrichment symptoms for the Southwest Coastal Estuaries.

........................ ii Table 2. Land use composition for the Southwest Coast Estuaries region in hectares (ha).

........................ 4

T

able 3. Percent of total area in conservation and urban land uses for the Southwest Coast Estuaries region.

............................................................................................................................ 4 Table 5. Acreage of natural community types within RBNERR.

................................................................ . 20 Table 6. Fish species showing significant differences between Faka Union Bay and Fakahatchee
and Pumpkin Bays, using the Kruskal

- Wallis one

- way ANOVA on ranks.

................................... 26 Table 7. Summary of sampling sites.

.......................................................................................................... 32 Table 8. List of facilities permitted for surface water discharge in the Southwest Coastal Estuaries region.

.......................................................................................................................... 42 Table 9a. Proposed regionalization for the Whitewater Bay to the Ten Thousand Islands area of
the Southwest Coastal Estuaries.

................................................................................................ 45 Table 9b. Proposed regionalization for the Pine Island Sound to Rookery Bay area of the
Southwest Coastal Estuaries.

...................................................................................................... 45 Table 10a. Proposed numeric TP criteria for sub

- basins within the Southwest Coastal Estuaries region.

................................................................................................ ......................................... 50 Table 10b. Proposed numeric TN criteria for sub

- basins within the Southwest Coastal Estuaries

area.

................................................................................................ ............................................ 51 Table 10c. Proposed numeric chlorophyll a criteria for sub

- basins within the Southwest Coastal
Estuaries area.

............................................................................................................................. 52



### List of Figures

Figure 1. Predevelopment vegetation (data source: South Florida Water Management District [SFWMD], southwest Florida predevelopment vegetation map, 2002).

....................................... 3 Figure 2. Land use and WBIDs for the Southwest Coastal Estuaries region.

............................................... 5 Figure 3. Bathymetry of Naples Bay and Dollar Bay (data source: SFWMD 2005).

..................................... 7 Figure 4. Historical changes in the Naples Bay shoreline since 1927 (after Schmid et al. 2006).

................ 8
Figure 5. Naples Bay and Gordon Pass in 1953 (left) and 1999 (right) (RBNERR from U.S. Geological Survey [USGS]).

............................................................................................................ 9
Figure 6. RBNERR boundary with major features.

..................................................................................... 12 Figure 7. Map of RBNERR showing reserve boundaries surrounding conservation lands.

........................ 13
Figure 8 . Coastal bay and barrier island conceptual model.

...................................................................... 17
Figure 9 . Shoreline mapping data collected by Taylor Engineering (2004).

............................................... 19
Figure 1 0 . Quadrate on the shoal of Cape Romano in 1998 (left); image of seagrass taken on the same shoal in 2009 (right).

.......................................................................................................... 23
Figure 1 1 . Map of the 2010 Cape Romano quadrate locations along a fixed transect.

............................ 23
Figure 1 2 . Species richness comparison between Fakahatchee, Faka Union, Pumpkin, and Rookery Bays.

.............................................................................................................................. 27Nutri ent Criteria Technical Support Document Southwest Coastal Estuaries

Draft ii August 2010 

### Table of Contents

Executive Summary

................................................................................................................ i Geographic Description and General Information

.................................................................. 1
Naples Bay

................................................................................................ ................................ .5 Rookery Bay and the Ten Thousand Islands

............................................................................... 10 

### Biological Summary

............................................................................................................. 14
General Community Types

........................................................................................................ 14 Natural Communities in Naples Bay

.......................................................................................... 18 Natural Communities in Rookery Bay/Ten Thousand Islands/Whitewater Bay

............................ 20 

### Water Quality Conditions

.................................................................................................... 28
Existing Water Quality Standards

.............................................................................................. 28
Designated Uses

....................................................................................................................... 28
Outstanding Flor ida Waters

...................................................................................................... 28 Summary of Existing Water Quality

........................................................................................... 29



### Sources of Nutrients

............................................................................................................ 42

Waters on the 303(d) List

..................................................................................................... 42 Criteria Development

.......................................................................................................... 44
Regionalization

......................................................................................................................... 44 

### Proposed Numeric Nutrient Targets

..................................................................................... 47
Methodology

............................................................................................................................ 47



### References

.......................................................................................................................... 53 Appendix A: Threaten ed and Endangered Species

............................................................. 57 Appendix B: Impaired Waters List

...................................................................................... 60 Appendix C: Summary of Regionalization Method

............................................................. 62Nutri ent Criteria Technical Support Document Southwest Coastal Estuaries

Draft iii August 2010 

### List of Tables

Table 1. Checklist of nutrient enrichment symptoms for the Southwest Coastal Estuaries.

........................ ii Table 2. Land use composition for the Southwest Coast Estuaries region in hectares (ha).

........................ 4

T

able 3. Percent of total area in conservation and urban land uses for the Southwest Coast Estuaries region.

............................................................................................................................ 4 Table 5. Acreage of natural community types within RBNERR.

................................................................ . 20 Table 6. Fish species showing significant differences between Faka Union Bay and Fakahatchee
and Pumpkin Bays, using the Kruskal

- Wallis one

- way ANOVA on ranks.

................................... 26 Table 7. Summary of sampling sites.

.......................................................................................................... 32 Table 8. List of facilities permitted for surface water discharge in the Southwest Coastal Estuaries region.

.......................................................................................................................... 42 Table 9a. Proposed regionalization for the Whitewater Bay to the Ten Thousand Islands area of
the Southwest Coastal Estuaries.

................................................................................................ 45 Table 9b. Proposed regionalization for the Pine Island Sound to Rookery Bay area of the
Southwest Coastal Estuaries.

...................................................................................................... 45 Table 10a. Proposed numeric TP criteria for sub

- basins within the Southwest Coastal Estuaries region.

................................................................................................ ......................................... 50 Table 10b. Proposed numeric TN criteria for sub

- basins within the Southwest Coastal Estuaries

area.

................................................................................................ ............................................ 51 Table 10c. Proposed numeric chlorophyll a criteria for sub

- basins within the Southwest Coastal
Estuaries area.

............................................................................................................................. 52



### List of Figures

Figure 1. Predevelopment vegetation (data source: South Florida Water Management District [SFWMD], southwest Florida predevelopment vegetation map, 2002).

....................................... 3 Figure 2. Land use and WBIDs for the Southwest Coastal Estuaries region.

............................................... 5 Figure 3. Bathymetry of Naples Bay and Dollar Bay (data source: SFWMD 2005).

..................................... 7 Figure 4. Historical changes in the Naples Bay shoreline since 1927 (after Schmid et al. 2006).

................ 8
Figure 5. Naples Bay and Gordon Pass in 1953 (left) and 1999 (right) (RBNERR from U.S. Geological Survey [USGS]).

............................................................................................................ 9
Figure 6. RBNERR boundary with major features.

..................................................................................... 12 Figure 7. Map of RBNERR showing reserve boundaries surrounding conservation lands.

........................ 13
Figure 8 . Coastal bay and barrier island conceptual model.

...................................................................... 17
Figure 9 . Shoreline mapping data collected by Taylor Engineering (2004).

............................................... 19
Figure 1 0 . Quadrate on the shoal of Cape Romano in 1998 (left); image of seagrass taken on the same shoal in 2009 (right).

.......................................................................................................... 23
Figure 1 1 . Map of the 2010 Cape Romano quadrate locations along a fixed transect.

............................ 23
Figure 1 2 . Species richness comparison between Fakahatchee, Faka Union, Pumpkin, and Rookery Bays.

.............................................................................................................................. 27Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 30 August 2010 collected monthly water quality data at 22 sites in Whitewater Bay and 2 6 sites in the Ten Th ousand Islands beginning in September 1992

, and 1 7 sites in the Naples Bay

- Cape Romano area starting in January 1999. All of the data collected as part of the FIU monitoring program for the period of record
are available at: http://serc.fiu.edu/wqmnetwork/SFWMD

- CD/index.htm . A summary of water quality in the southwest coastal region is provided in the 2007 Cumulative Annual Report for the Coastal Water Quality Monitoring Network (Boyer and Briceño 2008)

, which is also available at the website listed
above. Contour maps showing the spatial distributions of all measured variables (quarterly) are also
available

.

In an analysis of the monitoring data

, Boyer (2006) used a combination of principa l components analysis (PCA) and multivariate cluster analysis to spatially aggregate monitoring sites located along the southwest Florida coast based on similar water quality characteristics. One of the most interesting findings was that P dec reases, while N increases, from north to south in area.

The analysis also suggested that the nutrient gradients likely resulted from changes in coastal geomorphology

, geological setting

, and watershed characteristics over this gradient . In the southern region

, the sediments are composed of carbonates , but they change to siliceous quartz sand to the
north around Cape Romano (Gleason 1984). During the process of biogenic carbonate formation

, P is scavenged from the water column (Bosence 1989). Therefore, one would exp ect the southern estuaries of the region to be more P limited than those in the north.

Figure 14 summarizes TP, TN, and chlorophyll a concentrations for various estuaries within the area based on data collected from 1999 through 2008 by FIU

. B ased on the differences in geology, coastal geomorphology, and watershed characteristics, N and P concentrations within the region showed the expected north

- south gradients

, with TP concentrations being highest in the northern areas (Naples Bay and Rookery Bay) and considerably lower in the southern portion (Whitewater Bay)

. Annual geometric mean TP concentrations ranged from 13 to 30 μg/L in Whitewater Bay

, while the annual mean concentrations in Rookery Bay ranged from 28 to 48 μg/L.

In contrast to TP

, TN concentrations were highest in the southern portions of the region (Ten Thousand Islands and Whitewater Bay)

, with lower levels found in the northern areas (Naples Bay and Rookery Bay ). Annual geometric mean T N concentrations in Naples Bay ranged from 0.2 to 0.29 m g/L

, while the higher TN concentrations in Whitewater Bay ranged from 0.39 to 0.66 m g/L. The higher TN concentrations in the southern portions of the system likely result from the greater inputs of organic material ( i.e., total organic carbo n [ TOC ] ) from the surrounding mangrove forests and upstream wetlands/marshes.

Despite significant differences in the levels of nutrients (TN and TP), average annual chlorophyll a concentrations are relatively low across the entire region with considerable overlap across areas

, with no clear consistent spatial patterns observed. Annual geometric mean chlorophyll a concentrations ranged from 1.5 to 4.6 μg/L across the entire Southwest Coastal Estuaries area.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 32 August 2010 Due to the heterogeneous nature of the region, FIU used generally accepted geomorpho logical characteristics to group the stations. A preliminary spatial analysis of data from its monitoring program
resulted in the delineation of 1 0 groups of stations with robust similarities in water quality ( Table 7; Figures 15 through 19 ). The followi ng sections discuss w ater quality conditions within major portions of
the region. A more thorough assessment of the water quality conditions in each segment of the region is provided in FIU’s 2007 Cumulative Annual Report for the Coastal Water Quality Monitoring Network ( Boyer and Briceño 2008)

, available at: http://serc.fiu.edu/wqmnetwork/SFWMD

- CD/index.htm

.

Table 7

. Summary of sampling sites.

Area
Number Area Name Abbreviation Number of Sites

1 Cocohatchee River COCO 1

2 Naples Bay NPL 3

3 Cape Romano Marco Island MARC 8

4 Rookery Bay RB 5

5 Mangrove River MR 13

6 Whitewater Bay WWB 8

7 Gulf Island GI 12

8 Coot Bay COOT 1

9 Blackwater River E stuary BLK 2

10 Inland Wilderness Waterway zone IWW 11

Naples Bay

- Rookery Bay

Based on the FIU analysis, the area from Naples Bay to Cape Romano was divided into 4 segments: Cocohatchee River at Wiggins Pass, Cape Romano

- Marco Island, Naples Bay, and Rookery Bay. Naples Bay is the segment with the greatest anthropogenic influence. The primary cause of impairment in Naples Bay is excessive fresh water
, with the largest input being the Golden Gate Canal. Excessive fresh

w ater flowing into Naples Bay from the c anal has severely impact ed the bay

, mainly th r ough changes in the salinity regime

, which is now characterized by widely fluctuating salinit y levels

. T he Big Cypress
Basin Control District , the local arm of the S FWMD , manages the canal and is working on plans to divert
up to one

- third of the volume of fresh water now entering the bay from the Golden Gate Canal into th e Henderson Creek watershed

, which needs additional fresh water. The excessive freshwater inputs also significantly influence water quality and result in signifi cant seasonal trends for a number of parameters in addition to salinity

.

Figures 1 5 and 16 show the variation in TN and TP concentrations between the wet and dry seasons

, respectively, for Naples Bay

. N concentrations typically range between less than 0 .1 and 1.2 mg/L in Naples Bay and generally follow expected seasonal patterns , with values increasing during the wet

season and lower levels observed during the dry season. The increased TN concentrations during the wet season are likely the result of gre ater amounts of organic material from the basin being transported
to the bay in stormwater. TP concentrations are much more consistent, with values ranging between 25
and 65 μ g/L, and exhibit a less pronounced seasonal pattern.Nutri ent Criteria Technical Support Document Southwest Coastal Estuaries

Draft iv August 2010 Figure 1 3 . Estimated bycatch comparison between Fakahatchee, Faka Union, Pumpkin, and Rookery Bays.

.............................................................................................................................. 27
Figure 1 4 . Summary of TP, TN, and chlorophyll a concentrations in various portions of the Southwest Coastal Estuaries region, 1999

– 20 08.

....................................................................... 31
Figure 1 5 . Summary of wet and dry season TN and TP concentrations in Naples Bay, 2002

– 09.

............. 34
Figure 1 6 . Comparison of long

- term median concentrations in Naples Bay for selected parameters with 2007 data (from Boyer and Briceño 2008).

..................................................... 35
Figure 1 7 . Summary of salinity, nutrient, and chlorophyll a data collected by FIU in Naples Bay.

............ 36
Figure 1 8 . Comparison of long

- term median concentrations in Rookery Bay for selected parameters with 2007 data.

........................................................................................................ 37
Figure 19 . Summary of salinity, nutrient, and chlorophyll a data collected by FIU in Rookery Bay.

.......... 38
Figure 2 0 . Results of spatial analysis performed by FIU for the Ten Thousand Islands

– Whitewater Bay area.

................................................................................................ ...................................... 40
Figure 2 1 . Summary of salinity, nutrient, and chlorophyll a data collected by FIU in the Whitewater Bay and Gulf Island zones of the Ten Thousand Islands.

......................................... 41
Figure 2 2 . Proposed subdivision of estuarine and coastal waters for deriving nutrient criteria in south and southwest Florida bays and coastal waters.

.............................................................. 46
Figure 2 3 . Proposed estuarine and coastal nutrient criteria sub

- basins for the Southwest Coastal Estuaries region.

.......................................................................................................................... 47Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft i August 2010 

### Executive Summary

This report was prepared by t he Florida Department of Environmental Protection (FDEP), in cooperation with local scientists, to support the development of numeric nutrient criteria for the Southwest Coast al
Estuaries

, including Naples Bay, Rookery Bay, the Ten Thousand Islands, Whitewat er Bay

, and the surrounding areas. The primary purpose of the proposed numeric nutrient criteria is to protect healthy

, well

- balanced natural populations of flora and fauna from the effects of excess nutrient enrichment.

Many of the waters within the So uthwest C oastal Estuaries region are Class II , with a designated use of shellfish propagation or harvesting. Additionally, many of the se waters are designated as Outstanding
Florida Water s (OFWs) ( Chapter 62

- 302, Florida Administrative Code [ F.A.C. ] ).

U rban development in the region has led to intermittent adverse effects in some parts of the system

, especially in the northern portions. Most of the se impacts have result ed from channelization and drainage activities, which have dramatically changed the hydrologic and salinity regimes in the estuaries and bays. A number of Comprehensive Everglades Restoration Plan (CERP) projects

, currently planned

or under way , are intended to restore the quality, quantity, timing, and location of freshwater inflow s to the region to more natural conditions.

N utrient and chlorophyll levels are generally low but exhibit natural north

- south gradient s due to geomorphological differences across the region, with nutrients generally decreasing toward the south ( Boyer and Briceño 2008)

. Potential s ources of nutrients to the estuaries include agricultural activities,
stormwater runoff (from both natural and urban areas), atmospheric deposition, and point source discharges in the region

. C hlorophyll a in the estuaries is generally low

, with long

- term average concentrations ranging from less than 2 to 5 micrograms per liter ( μ g/L ).

Table 1 provides a checklist and description of nutrient enrichment symptoms that have occurred either historically or currently in the Southwes t Coastal Estuaries

.

Due to the relatively low nutrient and chlorophyll a levels observed, the lack of long

- term increasing
trends in nutrient and chlorophyll a concentrations, the lack of widespread biological impacts associated with nutrients, and the large number of natural conservation lands in the region , the proposed nutrient criteria were developed to maintain existing conditions , which are supportive of healthy

, well

- balanced populations of flora and fauna. Due to the natural north

- to

- south spati al gradients that occur along the
southwest Florida coast, the area was divided into more homogeneous subregions. The distribution of
nutrient and chlorophyll a data from each subregion was then used to derive criteria to en sure that the nutrient regime i n each subregion would be maintained at or below existing levels. T able s 10 a, 10b,and

10c list t he proposed criteria for total phosphorus ( TP )

, total nitrogen ( TN ) , and chlorophyll a , respectively.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft ii August 2010 Table 1. Checklist of nutrient enrichment symptoms for the S outhwest C oastal E stuaries

.

- = Empty cell/no data Response
V ariable Observed

H istorically or

C urrently? Explanation Source

Low dissolved oxygen ( DO ) (hypoxia/anoxia) Yes Localized naturally low DO conditions are common due to stratification and inputs of large amount of organic material from natural mangrove forests. Boyer 2008

Reduced clarity Yes Reduced clarity (turbidity) is an issue in Naples Bay

, where a large portion of the mangrove fringe has been replaced with vertical
seawalls

, and in areas where seagrass has been lost due to changes in the salinity regime. Thomas and Rumbold 2006

Increased chlorophyll a concentrations No No long

- term trends observed. Boyer and Briceño 2008

Phytoplankton blooms (nuisance or toxic) Yes Primarily episodic Karenia brevis blooms

. Florida Fish and Wildlife
Conservation Commission (FWCC) Fish and Wildlife Research Institute ( FWRI ) http://research.myfwc.com /features/category_main.as p?id=2309
Problematic epiphyte growth No Significant epiphyte growth on seagrasses reported in some areas. R ookery Bay National

Estuarine Research Reserve ( RBNERR )

Problematic macroalgal growth No Drift algae occurs in some areas but does not adversely affect the bay proper. O’Donnell unpublished data

Submersed aquatic vegetation ( SAV ) community changes or loss Yes SAV has been lost in some areas due to altered hydrology and salinity regimes, not from
nutrient enrichment. R ookery Bay Management
Plan 2010

Emergent or
shoreline vegetation community changes or loss Yes In Naples Bay, most of the mangrove fringe has been replaced with vertical seawalls

, or ha s decreased due to changes in freshwater inputs and salinity regime. Woithe and
Brandt

- Williams 2006

Coral/hardbottom community changes or loss No None reported

. -

Impacts to benthic community No None reported. -

Fish kills Yes Fish kills of generally limited extent and severity have occurred from low DO, cold, red tide, fishing violations

, and other unknown

causes. FWRI 2010Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 1 August 2010 

### Geographic Description and Gen e ral Information

Th is document proposes nutrient criteria for th e Southwest Coastal Estuaries region of Florida

, including Naples Bay, Rookery Bay, and the Ten Thousand Islands (Figure 1). The southwest Gulf coast is characterized by a relatively low

- energy, low

- relief coast line , with the continental shelf extending outwards for many miles, creating a shallow basin (Shirley and Brandt

- Williams 2003). The terrain in this area (the Big Cypress area of the Everglades West Coast Basin ) is very flat

, with few streams or lakes. Elevations slope from 40 feet on the Immokalee R ise in the northeast to sea level along the coast. In many areas the slope is less than 1 foot per mile.

The coastal estuaries in the system are commonly surrounded by mangrove forests that vary in width
from several hundred meters (m) in the northern p ortion to 7.5 kilometers ( km ) in the south. The northern estuaries are lagoons formed by barrier islands. South of Cape Romano

, the outer islands are
formed on a core of vermetid reef rock

, although there may be sufficient sand to form a narrow Gulf
beach.

Historically

, runoff occurred as sheetflow though cypress strand swamps and wet prairies

, and historical vegetation communities correspond ed with the area’s flat topography (Figure 2 ). Mesic or hydric
flatwoods covered t he vast majority of the land sur face (75%). Cypress and other swamp forests
occurred primarily in the eastern portion of the region and covered less than 10% each. Xeric hammock
communities were found near the coast along the coastal ridge now occupied by U .S. Highway 41. Mangrove swa mps fringed the coast al and estuarine areas

, including much of Naples Bay. Freshwater
lakes were la rgely absent from the landscape (Deuver et al. 2001; Wanless et al. 1994; Scholl 1964 ; McCoy 1962 ; 1954 Collier County soil maps SCCS).

Today, all of these habitats ha ve been impacted by varying degrees of hydrologic alteration and urban development. Natural drainage patterns within Collier County have been significantly altered by the construction of canal systems designed to lower annual peak water l evels during the rainy season to prevent flooding. The canal system includes the Golden Gate Canal, Henderson Creek Canal, Lely Canal, Lely Manor Canal, Faka Union Canal

, and borrow canals used for the construction of U.S. Highway 41
and State Road s 84, 9 51 , and 92 (Figure 3 ). A combination of fixed weirs and gates control canal flow, and flows in the system are managed to prevent excessive freshwater drainage and saltwater
encroachment.

T he northern portions of the estuarine system near Naples have exper ienced the greatest hydrologic
alterations and water quality impacts

, while the southern areas continu e to be largely undisturbed. During prosperous economic times, Collier County and the city of Naples had the highest growth rate s in
Florida , and c omplex canal systems were constructed to channelize historical wetland sheetflow through the watersheds. As a result of the construction of the canal system, t he natural freshwater inflow (quantity, timing, and quality) to the estuaries was alter ed (Shirley and Brandt

- Williams 2003). Additionally, the canal system is often managed so that fresh water is released in large pulses to avoid flooding problems in areas upstream of control structures. The changes that have occurred in
freshwater inflows have signific antly affected the salinity regime and ecology of large estuarine area s

.

Due primarily to the large expanse of wetlands

, much of southern Collier County was slow to develop and has been purchased for conservation. The large extent of conservation land has provide d a high level of protection to the southern portion of the system from the effects of urban development. As detailed in Figure 1 and Tables 1 and 2, approximately 67% of the land area in the region has been acquired for conservation (Shirley a nd Brandt

- Williams, 2003).Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 2 August 2010 The a verage open water depths of the Southwest Coastal Estuaries area range from approximately 1 m at low tide to a maximum of 5.5 m at high tide

, depending on the location. Water exchanges with in the region’s bays are generally dominated by tides. T he se are of mixed diurnal and semidiurnal character,
with 2 high and 2 low tides per day of unequal amplitudes during spring tides

, and 2 high and 2 low tides per day of nearly equal amplitudes during neap tides (Lee and Yokel 1973)

. Tid es range between about 1.1 m during spring tides and 0.5 m during neap tides.

A verage annual precipitation (rainfall) and evaporation over the area are estimated to be about 1.4 and

1.2 meters per year (m/yr) , respectively (Shirley et al. 2003)

. Bas ed on climatological averages, the highest monthly rainfall (0.20 to 0.23 m/month ; 66% of the total annual rainfall ) occur from June through October

, and the lowest monthly rainfall (about 0.02 to 0.05 m/month) from November through March (Shirley et al. 2 003

, 2004). These distributions give rise to four seasons: ( 1) early dry (December through February) ; 2) late dry (March through May) ; ( 3) early wet (June through August) ; and ( 4) late wet (September through November).

Southwest Florida is in the seasonal tropical weather belt that channels hurricanes toward or along the

coast. In 1960, Hurricane Donna’s high winds and flooding caused extensive damage to the Naples area.
The storm devastat ed vegetation and caused widespread damage to homes and buildings in the Rookery Bay

- Naples area. An earlier storm in 1918 also severe ly damage d man

- made and natural features

, and is considered responsible for destroying or significantly damaging m any of the mangrove systems in Collier County. In 1 992, Hurricane Andrew struck south Florida from the Atlantic, heading due west and exiting to the Gulf of Mexico approximately 35 miles south of the RBNERR. Damage to vegetation and structures was relatively light in Naples but extensive in Everglades National Park (ENP) south of Pavilion Key on the west coast. In 2006, Hurricane Wilma, a Category 4 storm, hit the southwest Florida coast

, with the center of the storm making landfall directly in the center of the RBNERR at Cape Romano, causing significant shore line changes in barrier islands within the Ten Thousand Islands and
deforestation within mangrove

- forested wetlands along the coast.

Although a major storm can strike Collier County at any time, projections based on storm track averaging suggest that the probability for a major storm in any year is 5 in 10, and for 2 such storms 1.5 in 10 (Jordan 1973). The probability that any of these storms will be hurricanes or major hurricanes is 5% and 1%, respectively (Gentry 1974). Such catastrophic events may h ave long

- term impacts on the Rookery Bay ecosystem and could permanently change its ecology (Alexander and Crook 1974).

Seasonal salinity variations in the area occur primarily in response to seasonal variations of net freshwater inflows (precipitation minus evaporation, plus stream and canal inflows and surface water
runoff ), with the highest salinit ies occurring in the late dry season. Daily salinity variations also occur in response to tides, with the highest salinity occurring at slack high water. During the late dry season (with high evaporation and low precipitation rates), salinity can exceed 40 practical salinity units ( psu )

. In contrast, during the late wet season, the salinity can be as low as 10 psu.

The Southest C oastal Estuarines area is co mposed of several distinct waterbodies, and each major portion of the system is discussed in greater detail below.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 3 August 2010 Figure 1. Predevelopment vegetation (data source: South Florida Water Management District [SFWMD], southwest Florida predevelopment veget ation map, 2002).Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 4 August 2010 Table 2. L and use composition for the Southwest Coast Estuaries region in h ectares (ha)

. WBID = Segment with a waterbody identification number

- = Empty cell/no data

WBID Watersheds Total

Area Mangrove Marsh Urban Upland Water Wetland

3259A Cocohatchee

- Corkscrew 1,750 402 76 765 56 415 515

3278 Okaloacoochee/

S tate R oad 29 7,038 2,302 64 131 28 2,072 3,323

3278 Fakahatchee Strand 15,005 6,874 3,205 3 46 4,653 10,303

3278 Faka Union 15,988 9,110 1,526 77 143 4,102 11,293

3278 B ig Cypress National Preserve (B CNP ) 19,667 8,011 1,410 119 76 2,472 15,562

3278I Faka Union

- South 23,303 57 46 88 910 227 22,079

3278O Marco Island 5,226 1,234 22 1,865 129 1,634 1,598

3278P Marco Island 3,016 1,380 2 26 7 1,308 1,675

3278Q Naples 2,048 178 16 1,554 9 283 202

3278R Golden Gate Naples Bay 4,122 158 - 3,086 253 575 207

3278U Rookery Bay Coastal 14,250 5,801 2,103 439 918 3,694 9,197

T

able 3. Percent of total area in c onservation and u rban land uses for the S outhwest C oast E stuaries region

. Watershed Total Area (ha) %
Conservation %
Urban

BCNP 304,506 73% 0%

Cocohatchee

- Corkscrew 51,847 23% 15%

Faka Union 50,415 76% 2%

Fakahatchee 74,303 61% 0%

Golden Gate Naples Bay 35,357 1% 52%

Marco Island 8,306 62% 23%

Naples 2,048 0% 76%

Okaloacochee

- SR29 93,330 25% 1%

Rookery Bay 43,550 49% 13%Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 5 August 2010 Figure 2

. Land use and WBIDs for the Southwest C oastal Estuaries region

.

Naples Bay

Naples Bay is a long, narrow, and shallow estuary formed by the confluence of the Gordon River and
several other small tributaries that empty into the Gulf of Mexico. The shallow, north

- south

– oriented waterbody originates at the mouth of the Gordon River in downtown Naples. The bay’s connection to the Gulf is through Gordon Pass, several miles to the south. Dollar Bay, the southern lobe of the Naples Bay system south of Gordon Pass

, is connected to Rookery Bay and the Marco River farther south by a shallow waterway with a dredged channel. The width of the bay ranges from 100 to 1

, 500 feet

, and its
de pth rang es from 1 to 23 feet . The majority of the bay is less than 5 feet deep

, with a navigational channel between 7 and 14 feet deep. The finger canals on the western side of the bay are the system’s deepest components. As part of the Evaluation of Naples Bay Water Quality and Hydrologic Data (Taylor 2005), a detailed bathymetric survey of Naples Bay was completed (Figure 3)

.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 6 August 2010 Naples Bay is the portion of the area most severely impacted by drainage and urban development
activities. The watershed , w hich previously consisted of swamps, marshes

, and sloughs that supported a natural ecosystem

, is now largely an urban/suburban landscape. Seawalls, bulkheads, and urban development have replaced e xtensive areas of mangrove forest and salt marsh. Drainage and urban
d evelopment activities have altered the volume, quality, timing

, and mixing characteristics of the freshwater flows reaching Naples Bay. Figure 4 illustrates the dramatic changes in the shoreline of Naples Bay that have occurred since 1927.

A dditionally, several dredged channels are maintained and marked for navigation throughout the area. A dredged channel through Gordon Pass extends to the top of Naples Bay, and south through Dollar Bay to Marco Island. Doctor’s Pass allows access to Venetian Bay from the Gulf of Mexico.

The b ay’s watershed once drained about 10 square miles, but it now extends to approximately 120 square miles as a result of the construction of the Golden Gate Canal system and its connection to the bay (Woithe and Brandt

- Williams 2006)

. Seasonal influxes of fresh water from the Golden Gate Canal

s ystem have greatly altered the natural salinity regime and severely stressed the biota of the estuary. On average, 200 million gallons per day (mgd) of fresh water enter Naples Bay through the canal s , producing prolonged salinity stresses that have caused sharp declines in plankton, benthic, shellfish, and
fish communities. B are sandy mud has replaced the seagrass beds once prevalent in the bay. Certain

areas also have high organic content.

A recent study prod uced for the city of Naples by t he Conservancy of Southwest Florida indicates that Naples Bay has lost 90% of its seagrass beds, 80% of its oyster reefs, and 70% of its mangrove fringe
since 1950. The b ay is considered typical of estuarine systems along the Florida coast that have been heavily altered by drainage and urban development. However , efforts are currently under way by the

c ity to improve the water quality of the bay and increase the quality and quantity of seagrass, oysters, and mangroves living within it and along its shorelines.

T he general Naples Bay area contains several distinct estuarine systems , including the Cocohatchee

Corkscrew area, Gordon River, Haldeman Creek, and Naples Ba sin

. The Cocohatchee

- Corkscrew Estuary

, located in northernmost Collier County , includes two estuarine areas . The northern portion of the estuary is a series of small mangrove

- fringed bays extending north from Wiggins Pass

, and the southern portion includes a mangrove

- fringed bay and an urbanized

, seawalled bay. The mangrove bays and pass were designated an OFW in 2004. The small coastal Naples Basin includes three mangrove

- fringed bays and a seawalled residential bay system. These systems are connected by culverts in a causeway that allows exchange between the systems.

Naples Bay is the estuarine portion of the Golden Gate / Naples Bay watershed. Drainage canals have increased the runoff to this system approximately ten fold

. Tables 2 and 3 summarize land use in the estuarine portions of the region’s individual watersheds and the percent conservation and urban land use in each of the total watersheds, respectively. The Naples and Naples Bay watersheds contain considerably more urban development and less conservation land than the more southern portions of the region

.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 7 August 2010 Figure 3. Bathymetry of Naples Bay and Dollar Bay ( d ata source: SFWMD 2005)

.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 8 August 2010 Figure 4. H istorical chan ge s in the Naples Bay shoreline since 1927 (after Schmid et al. 2006).Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 9 August 2010 Figure 5

. Naples Bay and Gordon Pass in 1953 (left) and 1999 (right) (RBNERR from U .S. Geological Survey [U SGS ] ).Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 10 August 2010 Rookery Bay and the Ten Thousand Islands

Rookery Bay and the Ten Thousand Islands are just south of Naples Bay and the city of Naples (Figure 1)

. Both estuari ne area s have been designated as aquatic preserves by the Florida legislature with the intent to protect “ the state

- owned submerged lands in areas which have exceptional biological, aesthetic, and scientific value ... for the benefi t of futur e generations.” I n 1978

, Rookery Bay joined a National Estuarine Research Reserve (NERR) network

, which comprise s 27 protected coastal areas administered by the National Oceanic and Atmospheric Administration (NOAA) in cooperation with the

coast al states in which the NERRs occur

. F DEP ‘s Office of Coastal and Aquatic Managed Areas (CAMA) serves as the state administrative agency for RB NERR.

RB NERR manage s approximately 110,000 acres, which include both the Rookery Bay Aquatic Preserve (58,076 acres) and the Cape Romano/Ten Thousand Islands Aquatic Preserve (51,470 acres) (Figure 1). Additionally, RB NERR co

- manages the Ten Thousand Islands Wildlife Refuge. RB NERR is considered the
westernmost extension of the Everglades ecosystem and contains unique features such as the larges t mangrove wetlands in the state, undeveloped barrier islands, intact tropical hardwood hammocks, and
coastal scrub habitats. T he t otal estimated surface area of open waters encomp assed within the
reserve’s boundaries is 70,000 acres, or 64 % of RBNERR

. The remaining 40,000 acres are composed primarily of mangroves, fresh water to brackish water marshes, and upland habitats. F DEP has designated all tidally connected waters within th e boundaries of RB NERR and the Cape Romano/Ten Thousand Islands Aquatic Preserves as Class II and O FWs (Rookery Bay NERR Draft Management Plan

2010

– 2015 ).

Rookery Bay is classified as a barrier

- built estuary

, with Keewaydin Island separating it from the a djacent
Gulf of Mexico. The combined Rookery Bay and Henderson Creek estuar ine system includes mangroves,
submer s ed aquatic vegetation, and fish and reef habitats with a total wetted surface area of about 5.7
km 2

. Water depths ( using lower low water as a reference point ) range between 0 and 3 m, with mean
values of 1 m in R ookery B ay and 0.75 m in Henderson Creek. The Rookery Bay E stuary is the beginning
of the transition from narrow

, highly developed coastal lagoons in the north to wider

, mangrove

forested bay systems with little urban development in the south . The Rookery Bay E stuary is approximately 6 km wide

, and the landward mangrove forest is 2 to 4 km wide. Moving south to the Ten Thousand Islands, t he Faka Union E stuary is more than 10 km w ide

, and the landward mangrove marsh system is approximately 6 km wide.

The exchanges of water and other materials between the Rookery Bay estuarine complex and the Gulf of Mexico occur through two inlets, one located at northwest end of Rookery Bay and the other at Hall Bay. The water exchanges are dominated by tides.

L and use within the Rookery Bay/Ten Thousand Island watershed s include extensive protected natural

areas ( more than 67% of the area’s lands are preserved as conservation areas ) , urban areas

, and agriculture (Shirley and Brandt

- Williams 2003). The mangrove a nd m arsh/wetland system comprises a large portion of these watersheds

, with urban development generally deceasing in a southerly direction

. Land uses for specific estuarine portions of the system are as follows:

**•** T he Faka Union E stuary basin comprise s primaril y conservation lands (97%)

, including Collier Seminole State Park and most of the Ten Thousand Island National Wildlife Refuge. The basin also includes a large portion of the Picayune Strand State Park and some of the North Golden Gate subdivision. One o f the primary outlets of
the Golden Gate Canal drainage system is at the south end of this basin. TheNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 11 August 2010 ongoing Picayune Strand Restoration Program is designed to return this discharge to a much more natural sheetflow through the conservation lands.

**•** The F akahatchee Estuary basin includes the tidal portions of the Fakahatchee Strand State Preserve and the northwestern part of ENP

. Approximately 83% of the basin is
in conservation lands

.

**•** The Okaloacoochee Estuary basin is narrow

, but salt ma r sh es extend 9.5 km inland due to the location of the first weir in the State Road 29 C anal north of U .S . Highway 41. Everglades City is located in this segment

, with urban land use only accounting for 2% of the basin. The portions of ENP and B CNP that are within the basin make up 25% of the land area

, with another 26% compris ing portions of the Florida Panther National Wildlife R efuge . Agriculture makes up 38% of the basin

.

**•** The southernmost estuary in the system

, the Big Cypress Preserve basin

, is 48% mangrove and salt marsh. Chockoloskee Island is the only developed portion of the
basin

, and urban land uses comprise only 1 %. Conservation lands cover 82% of the basin and 73% of the larger watershed area

. Wetlands constitute 88% of the land

cover , with uplands cover ing 6% of the watershed. Tables 2 and 3 provide additional
details on land use in individual watersheds

.

Al though much of the area co nsists of conservation lands with little urban development, the natural freshwater inflow (quantity, timing, and quality) to the estuaries within RB NERR has been significantly
altered as a result of the construction of the extensive canal system described for the northern portions of the system (Shirley and Brandt

- Williams 2003). Freshwater inflow varies based on the s ize of the
watershed.

The major watersheds for RBNERR are Water Management District No. 6 (Lely Basin), the Belle Meade Water Management District (Henderson Creek Basin)

, and the Southern Golden Gates Estates (Faka

Union Canal Basin) (Figure 6). These ar e subunits of the S FWMD

. Freshwater inflow to Rookery Bay comes primarily from Henderson Creek at the northeastern corner of RBNERR (Figure 6). Th e creek,
which has an average water depth of 0.8 m and a mean flow rate of 2,073,600 cubic feet per day (Wat er Resources Data, Florida 1983, FL 83 2A), drains the Belle Meade Water Management District (Gore 1984). The Lely and Lely Manor Canals are also significant sources of freshwater inflow. These waterways drain the inland areas immediate ly northwest of Ro okery Bay and have mean daily flow rates of 144,000 cubic feet per day. A substantial, but unquantifiable , amount of water also drains overland into the region via sheetflow. The Faka Union Canal, located south of Marco Island, drains the Picayune
Strand State Forest

, formerly S outhern G olden G ate E states, through a series of connected canals (within the Faka Union watershed) into the Ten Thousand Islands Estuary ( Figure 6)

.

Fixed weirs and gates control water flow downstream into the Henderson Creek/Rookery Bay Estuary and Faka Union Bay/Ten Thousand Islands Estuary

. Due to land

- draining efforts and redirected flow by
canals

, some areas in th e Ten Thousand Islands receiv e too much fresh water ( i.e., Faka Union Bay)

, while other areas do not receiv e enough ( i.e., Pumpkin Bay and bays west of Faka Union Canal)

. Weirs
retain fresh water during the dry season and release it during the wet season. Additionally, water management activities often release the fresh water in large pulses to avoid flooding problems in areas upstream of the control structure

. These practices alter the timing and amount of water released into downstream estuaries ( i.e., Henderson Creek/Rookery Bay Estuary and Faka Union/Ten Thousand
Islands Estuary ).Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 12 August 2010 Nonpoint source pollution is an additional problem associated with altered freshwater inflow

. Water running off the land can contain fertilizers and pesticides from residential lawns, agricultural areas, and golf courses that can eventually enter the estuaries

.

Figure 6

. RB NERR boundary with major features.

The y ellow line indicates the RBNERR boundary. RB= Rookery Bay, HC= Henderson Creek, BWB= Blackwater Bay, PB= Pumpkin Bay, FUB= Faka Union Bay, FB= Fakahatchee Bay .)

Faka Union
Canal

FB FUB PB BWB RB

HCNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 13 August 2010 Figure 7

. Map of R B NERR showin g r eserve boundaries surrounding conservation lands.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 14 August 2010 

### Biological Summary

General Community Types

The natural community classification system used in this report was developed by the Florida Natural Areas Inventory (FNAI) and FDEP (formerly the Florida Department of Natural Resources [FDNR])

. The community types are defined by a variety of factors, such as vegetation structure and composition, hydrology, fire regime, topography

, and soil type. The community types are named for th e most characteristic biological or physical feature (FNAI and F DNR 1990).

T he 12 natural communities described below represent the dominant upland and wetland communities
within RBNERR. The dominant wetland habitats are mangroves , saltwater marshes

, cypress sloughs, and
freshwater marshes

. These comprise more than 90% of the emergent wetland vegetation. The nonwetland assemblages

, ranked by aerial dominance

, are p ine flatwoods

, coastal strand

, coastal xeric
scrub

, cabbage palm / oak , and tropical hard wood hammocks . Figure 7 shows the approximate location and extent of the primary upland and wetland habitats within the RBNERR boundaries. T he following
natural wetland communities are found in the region :

(1) Open Waters: Resident and migratory birds make extensive use of open waters for feeding and resting. Migratory waterfowl, including several species of ducks, concentrate in open waters during fall and winter. Resident and migratory egrets, herons, pelicans, cormorants, and other piscivorous birds also feed along the open water margins or directly in this habitat. Over 219 species of fishes have been identified in the waters of Rookery Bay and the Ten Thousand Islands (FDEP unpublished data).

(2) Nonvegetated Bottom: This habitat, also associated with the open water region, comprises primarily soft mud (i.e., very fine sand and silt/clay) that is not stabilized by vegetation but also includes oyster beds and hardbottom communities. Nonvegetated bottom is more extensive in Rookery Bay than vegetate d bottom, and creates a habitat for various benthic invertebrates, including polychaetes, assorted crustaceans, and mollusks. Oyster beds, limited to the midintertidal zone, support a variety of fauna, including sponges, bryozoans mussels, barnacles, and slipper shells. Oyster reefs are found in hard and soft bottoms consisting of sand or firm mud (FDEP 1988). Hardbottom communities consisting of soft corals, sponges

, and bryozoans have been observed offshore of Keewaydin Island. Reef structures formed by the vermatid gastropod Petaloconchus sp. are found in the Ten Thousand Islands. No living vermatids have been observed recently, but the reefs support a diverse live bottom community, including bryozoans, hydroids, ascidians, sponges, and occasional co rals (FDEP 1988).

(3) Mangrove Forests: Three species of mangroves occur in RBNERR : red, black

, and white. Buttonwood, which is not a true mangrove species, is usually grouped with this assemblage because of its occurrence in higher, less tidally inundated areas. Red mangroves comprise the dominant vegetation on most of the islands and along the immediate shoreline of the bays and tidal creeks. Black mangroves form extensive forests in the periodically tidally flushed basins located landward from the shoreline. White mangroves are found in small numbers throughout the mangrove forest. Buttonwood trees occur in the higher areas of the mangrove forest along berms and high island margins, as well as along the mangrove salt marsh fringe.

Conditions that limit the distribution of mangroves and determine the extent of the mangrove ecosystem include climate, salinity, tidal fluctuation, substrate, and availableNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 15 August 2010 nutrients. The optimal conditions that exist for these factors in Rookery Bay has contributed to the development of lush, often monospecific forests. In RBNERR , distinct zones occur, with red mangrove living farther out into the water and extensive black mangrove forest occurring immediately behind.

Nearly all of the mangrove forest in RBNERR is second growth, probably ranging from 30 to 100 years old. This is a result of destructive hurricanes in 1918 and 1960 that caused extensive deforestation along the southwest Florida coast. Some forest remnants greater than 100 years old are still found along the north shore of Rookery Bay and in Henderson Creek (Conservation Foundation 1968). Regardless of age, the mangrove forests of

RBNERR are of critical value to the estuarine ecosystem. The complex branching prop roots of the red mangro ve support a large number of plants and animals. Numerous invertebrates and fishes seek shelter and food in the maze of trunks and roots. Other species, such as the mangrove tree crab, brown mangrove crab

, and mangrove snail, graze in the mangrove canopy. The insect population living as symbionts on the trunks and leaves includes ants, beetles, cockroaches, and aphids. Herbivorous grazers on the forest floor include amphipods, fiddler crabs, melampus snails

, and ladderhorn snails. A variety of birds are associated with the mangrove forest. Herons, egrets, pelicans,

cormorants
, and ibis use red mangrove islands in Rookery Bay as night roosts. These islands also serve as heron and egret rookeries. Raptors such as the bald eagle and osprey depend on the fishes and smaller birds and mammals associated with the mangroves.

The leaves of the mangrove trees are constantly being shed and rapidly decay to form detritus, which is the major food source for many of the small estuarine invertebrates that inhabit the soft bottom sediments among the mangrove roots. Lugo et al. (1980) estimated that detritus generated from the mangroves surrounding Rookery Bay provide s 32% of the energy base for the organisms in this community.

Mangrove forests also reduce the physical impact of storms, particularly wave overwash, because of their extensive above

- ground root systems. These same root systems slow freshwater runoff and act as a filter for nutrients; they also trap silt and sediments and
th us stabilize shorelines and p revent erosion.

(4) Vegetated Bottom: Seagrasses associated with open water habitat are not extensive in Rookery Bay but are considered seasonally abundant in adjacent waters such as Johnson Bay and Gullivan Bay

, and are more extensive in the shallow waters south of Cape

Romano. The dominant species is C uban shoal grass, with manatee grass, snook grass, and turtle grass occurring to a lesser extent. Seagrass beds were apparently more abundant and widely distributed in Rookery Bay years ago but have declined in the b ay due to environmental and/or human factors. Seagrasses are estimated to occupy no more than 20% of the bottom below mean high water in Rookery Bay (Yokel 1975). This important habitat plays a vital role as a nursery area and feeding ground for many of the fishes and invertebrates inhabiting the bay and adjacent waters.

(5) Saltwater Marsh: The saltwater marsh habitat is found landward or interspersed among the inland side of the mangrove

- fringing forests. Although they do not usually have a direct tidal connection, salt marshes invariably contain brackish water and are periodically inundated during higher spring tides and during storm events. The dominant plants are black needle rush, cord grass, and salt grass. Salt marshes are among the most productive systems for organic matter in any estuary and support large numbers of vertebrate and invertebrate species. In RBNERR , salt marshes are prime feeding sites for many residentNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 16 August 2010 wading or migratory game birds, raptors

, and several species of mammals (Appendix A ). Coastal ponds , a n associated habitat, are found interspersed either in salt or freshwater marshes. These small, clearly delineated areas usually hold permanent water that can be saline, brackish

, or fresh

. They are important feeding sites for numerous birds and mammals, a nd provide an ecotonal transition between saline and freshwater areas in

RBNERR

. (6) Freshwater Marsh: The freshwater marsh habitat typically borders pine flatwoods and cypress assemblages. Althou gh a distinct ecotone may exist between freshwater marshes and upland habitats such as pine flatwoods, freshwater marshes often intergrade into salt marshes with little noticeable ecotonal transition. The dominant plants are bulrushes, assorted grasses an d sedges, ferns

, and cattails.

(7) Cypress Slough/Cypress Prairie: Th is habitat is dominated by pond or bald cypress with a mixed understory throughout. C ypress habitat is restricted to areas subjected to flowing fresh water (i.e.

, sheetflow). It is ex posed at one time or another to surface waters flowing through RBNERR uplands, and therefore the quality and quantity of water are important to the system. This wetland community in the headwaters of RBNERR has been impacted by invasive plant species that have interrupted the natural hydroperiod. This interruption may also be due to water table lowering.

Native flora and fauna within RBNERR are diverse and abundant, ranging from large mammals ( such as
the West Indian manatee, Florida panther, b lack bear , and bobcat) to a diverse assemblage of microscopic plankton in coastal waters

, including algae and the larval stages of crabs, shrimp, and
fishes )

. Of particular note is the abundance of fishes and shellfish of commercial and recreational importance, in cluding blue crabs, pink shrimp, snook, tarpon, snapper, sheepshead, and flounder. RBNERR is nationally recognized for its importance in providing foraging grounds, resting areas

, and rookeries for over 150 species of wading birds, raptors

, and shorebirds, including the bald eagle, osprey, least tern, roseate spoonbill, and reddish egret.

RBNERR provides important habitats for many species listed as threatened, endangered, or of special concern by the federal government and the F WCC

. Most n otable are the West Indian manatee (endangered), Atlantic loggerhead sea turtle (threatened), gopher tortoise (species of special concern), bald eagl e (threatened), least tern (threatened), indigo snake (threatened)

, and Florida scrub jay (threatened). Co nfirmed sightings of the Florida panther (endangered) within the boundaries of RBNERR are increasing as local populations appear to be in recovery. Appendix A provides a complete
list of the endangered and threatened species known to occur in RBNERR, based on information from

FNAI.

Other notable species that occur in RBNERR include black bears and wading bird species such as the little blue heron, snowy egret, tricolored heron, white ibis, and brown pelican. The extensive shoreline and islands along the s outhwest coast contain extensive mangrove swamps and seagrass beds that provide valuable nursery and feeding habitat for many species of birds, reptiles, fish, and crustaceans.

The U.S. Fish and Wildlife Service (FWS) and S FWMD (Thomas and Rumbold 2006) assembled a

c onceptual e cological m odel for the area from Estero Bay through Rookery Bay to describe the natural and anthropogenic stressors on the various biological communities found. Figure 8 provides a summary
of the model

, showing the complex set of natural and anthropogenic factors , including waterNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 17 August 2010 management, land use changes, and urbanization, that influence the biological communities and their health. The FWS also developed a similar model for the Ten Thousand Island area (Popowski 2006).

Due to significant differences in the biological communit i es that occur along the southwest coast, the following sections discuss the biological communities that are found and their health in each major portion of the system.

Figure 8. Coastal bay and barrier island conceptual model.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 18 August 2010 Natural Communities in Naples Bay

Oysters

Oyster s were once a healthy, edible, dominant species in Naples Bay, but over the past few decades the
b ay has lost approximately 80% of its oyster reefs due to development activities that have altered freshwater flows in the watershed, dredging for navigation, and water quality degradation. F reshwater flows from the Golden Gate Canal create a longitudinal salinity gradient that varies greatly between the wet and dry seasons and cause s severe stratification in the wet summer months. This stratification
results in the limited reaeration of bottom waters

, resulting in depressed DO concentrations. This
contin ued stressor limits the amount of oyster restoration that can be conducted within Naples Bay.

Several oyster restoration efforts have been completed in the bay, with the first initiated in 2005. T he

c ity of Naples partnered with Florida Gul f Coast University and , w ith the help of community volunteers,
created t wo oyster reefs using shell

- filled mesh bags. Oysters have recruited onto the bags

, and staff continue to supplement and build up these areas with shell bags in addition to creating new reefs.

An oy ster gardening program , which provided residents with cages and oyster spat for placement under private docks, was successfully completed in 2010. Out of 10,000 spat, over 1,000 reached adulthood and were planted onto a previously created reef to facilita te a new oyster reef

. The success of the oyster restoration projects indicates that water quality in the area is adequate to support a healthy oyster community.

Seagrasses

The majority of the seagrasses that once were present in the bay are gone

, with an estimated 90% loss
since the 1950s

. Sparse areas of shoal grass ( Halodule wrig h tii ) remain in the southern part of the bay

, which is closest to Gordon Pass and farthest from the freshwater influence of the Golden Gate Canal.
The reduction of thi s fresh water is paramount to improving water quality and encouraging the expansion of seagrass beds. Seagrass beds in some areas have also been impacted by increased nutrient levels, low water clarity, dredging for navigation and development, boat wakes, and high sediment loads (Woithe and Brandt

- Williams 2006)

.

Benthic surveys are ongoing by city of Naples staff to identify and map the remaining seagrass areas.

T ransects have been established with seagrass species and abundance , sediment type, water dep th, epiphyte coverage, blade lengths, and shoot counts being recorded at 10 m intervals along each

transect. Transect monitoring occurs twice a year.

Mangroves

Naples Bay has lost 70% of its mangrove fringe. Before state laws were established to protect mangroves, these tidal coastline trees were removed from shorelines because they blocked views and harbored mosquitoes. Mangrove wetlands were also dredged and filled for residential development, streets, and other urban projects. Little value was attri buted to mangroves, and their ecological role was either unidentified or ignored. Yet mangroves provide many valuable services: they stabilize shorelines, filter pollutants from water, allow sediment to settle, sequester carbon from the atmosphere, and p rovide nursery grounds and habitat for a wide range of estuarine creatures, including commercial and recreational fish species.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 19 August 2010 M angroves have been replaced by seawalls and riprap

, resulting in increased turbidity and reduced light

p enetration through the bay’s waters. The energy created by boat wakes reflects off the perpendicular walls with little absorption of that energy, keeping the water agitated, which continually resuspends
sediments in the water column. Furthermore, the vertical natu re of the walls prevents vegetation from growing and does not provide the substrate necessary for estuarine shoreline community development. Both plants and animals have a hard time becoming established at such locations. Much of this can be alleviated by replacing seawalls with riprap and planting

, or allowing the natural recruitment of mangroves amid the riprap.

Figure 9. Shoreline mapping data collected by Taylor Engineering ( 2004 )

.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 20 August 2010 Natural Communities in Rookery Bay/Ten Thousand Islands/Whitewa ter Bay

Current and past research at the RB NERR has not focused on the direct link between nutrients and biological resources but mostly on the long

- term monitoring of seagrass beds, fisheries, and oyster reef crab population dynamics. At this point, the RB NERR does not have conclusive quantitative data indicating adverse e ffects/impairment from nutrients on biota . The purpose of this biological summary is to describe the dominant biological resources and their condition within the area managed by the

RBN ERR (Rookery Bay

– Whitewater Bay).

The dominant natural communities that make up the c oastal marine ecosystems of the RBNERR are
mangroves, seagrass es , saltwater marshes, and oyster reefs

. Table 5 lists t he number of acres of each natural community type within the RBNERR ( FDEP 2009 ). These natural community types were based on a classification system by FNAI and F DEP. The following sections describe each community type as
taken from the RBNERR Draft Management Plan 2010

- 2015 (FDEP 2009).

Table 5. Acreage of natural community types within RB NERR.

FNAI Natural Community Type Acres

Tidal Swamp (mangroves) 30,728

Seagrass Bed 2,731

Tidal marsh (saltwater marsh) 1,862

Mollusk Reef (oyster reef) 93

Mangroves (tidal swamps)

Three species of mangroves occur in RBNERR : red, black and white. Buttonwood, which is not a true mangrove species, is usually grouped with this assemblage because of its occurrence in higher, less tidally inundated areas. Red mangroves comprise the dominant vegetation on most of the islands and along the immediate shoreline of the bays and tidal creeks. Black mangroves form extensive forests in the periodically tidally flushed basins located landward from the shoreline. White mangroves are found in small numbers throughout the mangrove forest. Buttonwood trees occur in the higher areas of the mangrove forest along berms and high island margins, as well as along the mangrove saltmarsh fringe.

Conditions that limit the di stribution of mangroves and determine the extent of the mangrove ecosystem include climate, salinity, tidal fluctuation, substrate, and available nutrients. The existence of optimal conditions for these factors in Rookery Bay has contributed to the develo pment of lush, often monospecific forests. In RBNERR , distinct zones occur

, with red mangrove living farther out into the water and extensive black mangrove forest occurring immediately behind.

Nearly all of the mangrove forest in the Reserve is second growth, probably ranging from 30 to 100 years old. This is a result of destructive hurricanes in 1918 and 1960 that caused extensive deforestation along the southwest Florida coast. Some forest remnants greater than 100 years old are still found along the north shore of Rookery Bay and in Henderson Creek (Conservation Foundation 1968).

Regardless of age, the mangrove forests of RBNERR are of critical value to the estuarine ecosystem. The complex branching prop roots of the red mangrove support a large number of plants and animals.
Numerous invertebrates and fishes seek shelter and food in the maze of trunks and roots. Other species such as the mangrove tree crab, brown mangrove crab

, and mangrove snail graze in the mangroveNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 21 August 2010 canopy. The insect population living as symbionts on the trunks and leaves includes ants, beetles, cockroaches, and aphids. Herbivorous grazers on the forest floor include amphipods, fiddler crabs, melampus snail s, and ladderhorn snails. A variety of birds are associated with the mangrove forest. Herons, egrets, pelicans, cormorants

, and ibis use red mangrove islands in Rookery Bay as night roosts. These islands also serve as heron and egret rookeries. Raptors such as the bald eagle and osprey depend on the fishes and smaller birds and mammals associated with the mangroves.

The leaves of the mangrove trees are constantly being shed. These rapidly decay to form small particulate material called detritus. Detr itus is the major food source for many of the small estuarine
invertebrates that inhabit the soft bottom sediments amo ng the mangrove roots. Lugo et al. (1980) estimated that detritus generated from the mangroves surrounding Rookery Bay provide s 32% of th e energy base for the organisms in this community.

Mangrove forests also reduce the physical impact of storms, particularly wave overwash, because of
their extensive above

- ground root systems. These same root systems slow freshwater runoff and act as
a filter for nutrient s; they also trap silt and sediments and th us stabiliz e shorelines and prevent erosion.

Seagrasses

Seagrasses are not extensive in Rookery Bay

, but are considered seasonally abundant in Johnson Bay
and are more extensive in the shallow waters south of Cape Romano ( FDEP 2009 )

. R ecent observations
within RBNERR indicate that seagr ass is not as abundant as in neighboring counties and throughout southwest Florida. When seagrass is present, it typically is patchy a nd sparse. Light attenuation could be one contributing factor for this reduced coverage. The water is typically tea colored

, and sediments are often resuspended within the water column. F ive documented species of seagrass are found within

RBNERR boundar ies: turtle grass ( Thalassia testudinum ) ; shoal grass ( Halodule wrightii ) ; manatee grass ( Syringodium filiforme ) ; paddle grass ( Halophila decipiens ) ; and star grass ( Halophila engelmannii )

. Seagrass beds are important habitat serving as a nursery area and feeding ground for many fi sh and invertebrate species inhabiting Rookery Bay and adjacent waters ( FDEP 2009 ).

Previous seagrass studies in RBNERR have been done as part of long

- term monitoring, acquisition, ecosystem analysis, and isolated research projects over the past 4 decades. Backwater bays in the Ten
Thousand Islands historically had greater seagrass coverage than more recent data indicate (Carter et al.

1973 ; Browder et al. 1986 ; Locker 2005). An ecosystems analysis by Carter et al

. (1973) in the early
1970s found that seagrasses were more prevalent in Fakahatchee Bay than in Faka Union Bay. Fifty

seven percent of Fakahatchee Bay was found to have seagrasses; however, 29% of the bay had only trace amounts, 18% had medium amounts, and 10% had heavy amounts. In comparison, Faka Union Bay had 23.1% seagrasses, with 17.8% of the bay having trace amounts and 5.3% having heavy amounts. The species of seagrasses found were H. decipiens

, H. wrightii, and T. testudinum . A later study by

B rowder et al. (1989), which focused more on fishes, found fewer seagrasses in Faka Union and Fakahatchee Bays during th e study. In 2005, a study by Locker found that the only seagrass in Fakahatchee Bay was H. decipiens

, with n o seagrass found in Faka Union Bay.

Johnson Bay seagrass coverage was monitored as part of a S FWMD grant from 2000 to 2009. According to data collected in 2008, the annual average percent coverage for the study transects w as ju st under
30%. All 5 species found in RBNERR were fo und at this site; however

, H. wrightii was the dominate species, followed by H . englemanni . During the 2008 monitoring at this location , t he majority of the

seagrasses had moderate to heavy epiphytic growth (Schmid et al. unpublished data 2008). Data fro mNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 22 August 2010 prior years were not comparable due to a change in fixed transect locations as a result of a migrating sandbar that covered the original transects.

Seagrass m onitoring at Cape Romano has been irregular for over a decade. In 1998

, as part of an acquisition process for RBNERR , staff collected data on the seagrass bed located in the open waters off the southern part of Cape Romano

. Fixed transects were placed perpendicular to the shore for nearshore seagrass coverage

, and random quadrate points w ere generate d for seagrass located on the shoals at Cape Romano and in Gullivan Bay. Percent coverage and species of seagrass were
documented

, along with water quality measurements. All five species of seagrass found in RBNERR

were seen here; however, T. testudinum

, H. wrightii , and S. filiforme were the only seagrasses found in the quadrates. Seagrass coverage at Cape Romano used to be 100% of the random quadrates much of
the time (J. Schmid

, personal communication

, 2010 ) (see Figure 10 ).

A few years later, a side

- scan sonar project was undertaken to determine SA V coverages within RBNERR ( Locker 2006 ). A seagrass monitoring project at Cape Romano began in 2010 as part of a S FWMD grant. Percent coverage, species abundance, and epiphytic coverage estim ates were recorded using quadrates on a transect across the Cape Romano shoal (see Figure 11 ). The average coverage of the quadrates was less than 40% during the sampling period in April. The 2 species present were H. wrightii and T.
testudinum

. H. wrig htii had less than 3% coverage and was found mostly at the edges of the seagrass

area. T

. testudinum had less than 35% coverage; however, this was the predominant seagrass species. Seagrasses had moderate to heavy epiphyte coverage ( Figure 10 , right ) ( Schmid et al. unpublished 2010).

Additional seagrass studies currently under way within RBNERR boundaries include a seagrass mapping study led by W. Judson Kenworthy of NOAA and a light attenuation study by Susan Denham, a Graduate Research Fellow funded through the National Estuarine Research Reserve System ( NERRS ) /NOAA program. No published data for either project were available for this report.

Saltwater Marshes (tidal marshes)

S altwater marsh habitat is found landward or interspersed among the inland side of the mangrove

fringing forests. Although it does not usually have a direct tidal connection, it invariably contains brackish water and is periodically inundated during the higher spring tides and storm events. The dominant plants are black needle rush, cord grass, and salt grass. Salt marshes are among the most productive systems for organic matter in any estuary and support large numbers of vertebrate and invertebrate species. In RBNERR , they are prime feeding sites for many resident wading or migratory game birds, raptors

, and several species of mammals . C oastal ponds , an associated habitat, are found interspersed either in salt or freshwater marshes. These small, clearly delineated areas usually hold permanent water that can be saline, brack ish

, or fresh. They form important feeding sites for numerous birds and mammals, a nd also provide an ecotonal transition between saline and freshwater areas in

RBNERR

.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 23 August 2010 Figure 10. Quadrate on the shoal of Cape Romano in 1998 (left) ; i

mage of seagrass taken on the same shoal in 2009 (right).

Figure 11. Map of the 2010 Cape Romano quadrate loc ations along a fixed transect.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 24 August 2010 Oyster Reefs

The Eastern oyster ( Crassostrea virginica ) is the dominant bivalve in R B NERR that forms biogenic reefs

, mostly in the midintertidal zone. Oysters are not commercially harvested in southwest Florida

, and therefore their valuable ecological functions are often the focus of research and restoration activities. One ecological function of oysters is the removal of phytoplankton, particulate organic carbon, sediments, pollutants, and microorganisms from the water through filter feeding. T he t ransfer of organic matter links the benthic and pelagic environments. The reef structure provides habitat, sites for laying eggs and nesting, and refuge from predation or desiccation.

Oyster reefs support a variety of fauna

, including sponges, bryozoans, mussels, barnacles

, and slipper shells ( FDEP 2009 ). Additionally, several crab species (mud crabs, porcelain crabs) and fish s pecies (skilletfish, toadfish, gobies) ar e reef residents (Tolley et al. 2005). Many of the organisms living on the reefs serve as forage for other fish species and birds. Studies have been conducted in southwest Florida estuaries (including Faka Union B ay and other s ) to determine the influence of salinity on the habitat use of oyster reefs (Tolley et al. 2005), the impacts of salinity and freshwater inflow on oyster reef

co mmunities (Tolley et al. 2006), and oyster reef crab populations as a tool for managing freshwater
inflow in R R NERR (Shirley et al. 2004).

Fisheries

Commercial fisheries in R B NERR include blue crab ( Calinectes sapidus ), stone crab ( Menippe
mercenaria ), and mullet ( Mugil cephalus ), while recreational fishers typically target snook ( Centropomus
undecimalis ), tarpon ( Megalops atlanticus ), red drum ( Scianops ocellatus ), lane and mangrove snapper ( Lutjanus synagris

, Lutjanus griseus ), spotted seatrout ( Cynoscion nebulosus ), sheepshead ( Archosargus probatocephalus ), Florida pompano ( Trach inotus carolinus ), black drum ( Pogonias cromis ), and southern kingfish ( Menticirrhus americanus ). There are 230 recorded species of fish from RBNERR, including some freshwater and exotic species.

Fisheries in RBNERR have been impacted by recreational and commercial fishing, watershed alterations ( canals ) , agricultural runoff, stormwater runoff, red tide blooms, hypoxia

, and cold stress events.
Studies o f fisheries have focused on the Faka Union canal system and to a lesser extent the Henderson
Creek watershed. Past and present studies on fisheries include Carter et al. (1973), Lindall et al. (1973), Yokel (1975), Colby et al. (1985), Browder et al. (1986), Shirley et al. (2005)

, and O’Donnell (unpublished
data ). The i ndirect effects of canal drainage include changes in bottom substrate and bottom vegetation cover (Browder 1986). Canal systems can also affect fish distributions compared with areas receiving
more natural freshwater inflows.

Rookery Bay’s current fisheries study and water quality program indicate s that Fakahatchee Bay has a

more natural watershed compared with Faka Union Bay, which receives canal drainage, and Pumpkin Bay, which receives less fresh water in the wet, rainy season. Results from 1999 th rough 2009 indicate

30 species of fish with significant differences (nonparametric Kruskal

- Wallis one

- way analysis of variance [ ANOVA ] on ranks) in abundance between Faka Union Bay and the other 2 bays (O’Donnell unpublished
data ; Table 6 ). These differen ces could be attributed to salinity, substrate

, or vegetation cover but most likely are influenced by the canal drainage into Faka Union Bay.

A few freshwater species such as the largemouth bass ( Microptera salmoides ), Mayan cichlid ( Cichlasoma urophthal mus ), and sunfish ( Lepomis spp

. ) have survived for short periods in Faka UnionNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 25 August 2010 Bay due to the large volume of fresh water inundating the estuary. Species diversity, measured by species richness (O’Donnell unpublished data ; Figure 1 2 ), is significantly higher in Fakahatchee and Pumpkin Bays than in Faka Union and Rookery Bays . Both Faka Union and Rookery Bays have canals and
water control structures that alter freshwater flows, wh ile Fakahatchee and Pumpkin Bays receive fresh

water t hrough more natural watersheds.

In Rookery Bay’s shark nursery/top predator study, bull sharks ( Carcharhinus leucas ) dominate the catches (over 50% overall), especially in Faka Union Bay in the wet season, where almost all sharks caught are juvenile bull sharks. This result is due to low salinities (canal influenced) and the bull shark ’s ability to acclimate to them. The other juvenile sharks u s ing R B NERR estuaries

— bonnethead (S phryna
tiburo ) , lemon ( Negaprion brevirostris )

, blacktip ( Carcharhinus limba tus )

, and nurse ( Ginglymostoma
cirratum )— need higher salinities to survive.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 26 August 2010 Table 6. Fish species showing significant differences between Faka Union Bay and Fakahatchee and Pumpkin Bays, using the Kruskal

- Wall is one
- way ANOVA on ranks

. Significant difference if Z

- value is > 1.96 ; numbers shown with an asterisk and shading are significant

. FH = Fakahatchee Bay, FU = Faka Union Bay, PB = Pumpkin Bay Empty cell/no data

Species Total

Count Mean

FH Mean
FU Mean

PB Z- value

FH

- FU Z- value

FH - PB Z- value

FU

- PB

LOWEST ABUNDANCE IN
FAKA UNION BAY - - - - - - -

Lagadon rhomboides 14

, 087 12.69 3.27 12.10 9.57 * 2.36 * 7.20 *
Synodus foetens 3, 891 2.95 2.14 2.66 4.52 * 0.03 4.49 *
Bairdiella chrysoura 2, 300 2.38 0.65 1.55 6.16 * 2.46 * 3.71 *
Lutjanus synagris 2, 120 1.16 0.54 2.53 4.67 * 3.26 * 7.93 *
Syngnathus scovelli 1, 818 1.54 0.42 1.66 8.02 * 2.20 * 10.22 *

Gobiosoma robustum 1, 513 1.56 0.39 1.06 6.16 * 2.26 * 3.91 *
Orthopristis chrysoptera 1, 187 1.68 0.08 0.60 10.01 * 6.53 * 3.48 *
Sphroides nephalus 1, 118 0.98 0.56 0.68 4.91 * 3.00 * 1.91

Prionotus tribulus 892 0.87 0.42 0.49 3.35 * 1.89 1.45

Etropus crossotus 831 0.91 0.26 0.49 8.33 * 6.34 * 1.99 *
Archosargus probatocephalus 828 0.43 0.21 1.01 1.94 1.13 3.07 *

Prionotus scitulus 464 0.48 0.15 0.30 8.02 * 4.96 * 3.05 *
Paralichthys albigutta 367 0.29 0.18 0.27 2.76 * 1.28 1.48
Opsanus beta 366 0.46 0.07 0.20 7.22 * 4.05 * 3.17 *
Syngnathus louisianae 323 0.22 0.13 0.30 3.17 * 1.24 4.41 *
Chloroscombrus chrysurus 297 0.31 0.03 0.26 2.47 * 0.83 3.30 *

Monacanthus hispidus 228 0.16 0.03 0.27 4.34 * 0.96 5.30 *
Chilomycterus schoepfi 165 0.14 0.01 0.18 5.97 * 1.46 7.44 *
Chaetodipterus faber 65 0.09 0.03 0.02 3.72 * 4.23 * 0.51
Hippocampus zosterae 54 0.030 0.002 0.076 2.50 * 1.70 4.20 *

Chasmodes saburrae 41 0.054 0.002 0.026 3.73 * 1.12 2.62 *
Mycteroperca microlepis 20 0.032 0.000 0.008 3.50 * 2.23 * 1.27

HIGHEST ABUNDANCE IN
FAKA UNION BAY - - - - - - -

Cynoscion arenarius 1,496 0.71 1.40 0.87 6.11 * 1.09 5.02 *
Microgobius gulosus 1,039 0.57 1.00 0.51 5.41 * 1.15 4.25 *
Microgobius thallassinus 636 0.26 0.77 0.24 4.15 * 0.27 3.88 *
Eugeres plumieri 142 0.008 0.273 0.002 3.59 * 0.55 4.14 *

Gobiosox strumosus 24 0.004 0.044 0.000 2.84 * 0.71 3.55 *
Sciaenops ocellata 24 0.000 0.048 0.000 3.01 * 0.00 3.01 *

Gobiosoma bosc 22 0.000 0.044 0.000 3.89 * 0.00 3.89 *
Freshwater species 4 0.000 0.008 0.000 2.45 * 0.00 2.45 *Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 27 August 2010 Figure 12. Species richness comparison between Fakahatchee, Faka Union, Pumpkin, and Rookery Bays.

Figure 13. Estimated b ycatch comparison between Fakahatchee, Faka Union, Pumpkin, and Rookery Bays. 8.80

7.17 8.72

5.72

0 1 2 3 4 5 6 7 8 9 10

Fakahatchee Bay Faka Union Bay Pumpkin Bay Rookery BayMEAN-Species per sample 

# Species Richness

Significant Difference from Fakahatchee Bay and Pumpkin Bay 

# * * *

0 10 20 30 40 50 60 70 80 90

1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 MEAN
Estimated

Bycatch

liters

Fakahatchee Bay Faka Union Bay Pumpkin Bay Rookery BayNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 28 August 2010 

### Water Quality Conditions

Existing Water Quality Standards

Florida’s water quality criteria are provided in Chapter 62

- 302, F.A.C. The existing criteria that are of greatest concern for this effort are for nutrients , chlorophyll, and DO

. The existing nutrient criterion applicable to Class II and III marine waters is narrative

, stating that: “ In no case shall nutrient concentrations of a body of water be altered so as to cause an imbalance in natural populations of aquatic flora or fauna. ” There is currently no state water quality criteri on for chlorophyll specified in Chapter 62

- 302, F.A.C. ; however, the Impaired Surface Waters Rule (IWR ) ( Chapter 62

- 303, F.A.C.) does

us e an annual average chlorophyll concentration of 11 mg/L as a threshold for identifying impaired marine (nonfresh) waters. In accordance with the IWR, a waterbody can also be deemed impaired
based on a 50 % increase in chlorophyll concentrations based on historical conditions.

The DO crit erion currently applicable to Class II and III marine waters in Florida states that the
concentration of DO: “ Shall not average less than 5.0 in a 24

- hour period and shall never be less than 4.0. Normal daily and seasonal fluctuations above these levels shall be maintained. ” As detailed in the Overview of FDEP Approaches for Nutrient Criteria Development in Marine Waters

, the current DO
criteri on w as developed more than 40 years ago

, was based on very limited information

, and has been determined to be inappropriate for many Florida waters

. A revised DO criterion more appropriate for Florida waters is being developed using additional, more recent information. All water quality criteria currently applicable to Florida’s wa ters can be found in Chapter 62

- 302, F.A.C.

Designated Uses

Under Section 62

- 302.400, F.A.C., a number of waters in the S outhwest C oastal Estuaries region are
Class II waters
, which have the designated use of propagation or harvesting of shellfish. The Class II
waters within th is region include the following :

**•** Cocohatchee River ;

**•** Wiggins Pass ;

**•** Dollar Bay ;

**•** Little Hickory Bay ;;

**•** Inner and Outer Clam Bay

**•** Inner and Outer Doctors Bay ;

**•** Connecting waterways

— from Wiggins Pass south to Outer Doctors Bay ; and

**•** Tidal bays and passes

— Naples Bay and south and easterly through Rookery Bay and
the Ten Thousand Islands

.

The state waters in the region not listed above are designated as Class III marine waters

.

Outstanding Florida Waters

M any of the waters within the S outhwest C oastal Estuaries region are designated as O FWs, which provides for “special protection due to their natural attributes” (Section 403.061, Florida Statutes [ F.S. ] ). These waters are listed in Section 62

- 302.700, F.A.C. The intent of an OFW desi gnation is to maintain ambient water quality conditions , even if those conditions are more stringent than the stateNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 29 August 2010 water quality criteria applicable to the waterbody’s surface water classification ( i.e., Class II or Class III)

. Most OFWs are associated w ith managed areas in the state or federal park system, such as aquatic preserves, national seashores, or wildlife refuges. Other OFWs may also be designated as “Special Waters” based on a finding that the waters are of exceptional recreational or ecologic al significance and
are identified as such in Rule 62

- 302, F.A.C.

The following waters within the S outhwest C oastal Estuaries region are OFWs:

**•** Barefoot Beach acquisitions ;

**•** Delnor

- Wiggins Pass State Recreation Area ;

**•** Wiggins Pass Estuarine Area and the Cocohatchee River system ;

**•** Rookery Bay State Aquatic Preserve ;

**•** Rookery Bay National Estuarine Research Reserve (RBNERR) ;

**•** Rookery Bay acquisitions ;

**•** Collier

- Seminole State Park ;

**•** Cape Romano

– Ten Thousand Islands State Aquatic Preserve ;

**•** Fakahatchee Strand State Preserve ; and

**•** Florida Panther National Wildlife Refuge

.

Summary of Existing Water Quality

Historically, water quality in the S outhwest C oastal Estuaries region was strongly influenced by the quantity, timing, and quality of freshwater inflow from the es tuaries’ associated watersheds. Due to increased development and extensive drainage and channelization activities, the hydrology and historical freshwater flow patterns of the region’s estuaries have been severely altered, which has in
turn resulted adver sely impacted the environmental integrity of many of the se estuaries, mostly in terms of widely varying salinity patterns (Browder et al. 1998 ; Shirley et al. 2005) and the reported introduction of large quantities of organic

- rich sediments from accelerated rates of freshwater inflow (Locker 2005). Much of the scientific literature for the area, especially the Ten Thousand Islands and Rookery Bay, has focused on the issue of altered hydrology and the need for a more natural pattern of freshwater inflow (e. g., Browder et al. 1988 ; Shirley et al. 2005). Even though the entire region has been influenced to some degree by the changes in the quantity, timing, distribution of freshwater inflows to varying degrees, excessive nutrients have not been identified as problematic except in localized areas.

Typically, m ost temperate estuaries are N limited (Vitousek and Howarth 1991)

, while upstream
freshwater tributaries are P limited (Smith 1990). In contrast, i n the southern Everglades area , both freshwater wetlands and saline estuaries are generally P limited (Fourqurean et al. 1993; Boyer et al. 1999; Noe et al. 2001). Therefore, estuaries along the Everglades West Coast are unique in their oligotrophic nature and marine supply of the limiting nutrients. Since the source of P to the se estuar ies is the coastal Gulf of Mexico rather than the watershed, Childers et al. (2006) has call ed the Shark R iver an ‘‘upside

- down estuary’’ (Chen and Twilley 1999).

Dr. Joe Boyer and his colleagues at Florida International University (FIU) have performed much of the water quality monitoring within the region

. The FIU Coastal Water Quality Monitoring Network hasNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 30 August 2010 collected monthly water quality data at 22 sites in Whitewater Bay and 2 6 sites in the Ten Th ousand Islands beginning in September 1992

, and 1 7 sites in the Naples Bay

- Cape Romano area starting in January 1999. All of the data collected as part of the FIU monitoring program for the period of record
are available at: http://serc.fiu.edu/wqmnetwork/SFWMD

- CD/index.htm . A summary of water quality in the southwest coastal region is provided in the 2007 Cumulative Annual Report for the Coastal Water Quality Monitoring Network (Boyer and Briceño 2008)

, which is also available at the website listed
above. Contour maps showing the spatial distributions of all measured variables (quarterly) are also
available

.

In an analysis of the monitoring data

, Boyer (2006) used a combination of principa l components analysis (PCA) and multivariate cluster analysis to spatially aggregate monitoring sites located along the southwest Florida coast based on similar water quality characteristics. One of the most interesting findings was that P dec reases, while N increases, from north to south in area.

The analysis also suggested that the nutrient gradients likely resulted from changes in coastal geomorphology

, geological setting

, and watershed characteristics over this gradient . In the southern region

, the sediments are composed of carbonates , but they change to siliceous quartz sand to the
north around Cape Romano (Gleason 1984). During the process of biogenic carbonate formation

, P is scavenged from the water column (Bosence 1989). Therefore, one would exp ect the southern estuaries of the region to be more P limited than those in the north.

Figure 14 summarizes TP, TN, and chlorophyll a concentrations for various estuaries within the area based on data collected from 1999 through 2008 by FIU

. B ased on the differences in geology, coastal geomorphology, and watershed characteristics, N and P concentrations within the region showed the expected north

- south gradients

, with TP concentrations being highest in the northern areas (Naples Bay and Rookery Bay) and considerably lower in the southern portion (Whitewater Bay)

. Annual geometric mean TP concentrations ranged from 13 to 30 μg/L in Whitewater Bay

, while the annual mean concentrations in Rookery Bay ranged from 28 to 48 μg/L.

In contrast to TP

, TN concentrations were highest in the southern portions of the region (Ten Thousand Islands and Whitewater Bay)

, with lower levels found in the northern areas (Naples Bay and Rookery Bay ). Annual geometric mean T N concentrations in Naples Bay ranged from 0.2 to 0.29 m g/L

, while the higher TN concentrations in Whitewater Bay ranged from 0.39 to 0.66 m g/L. The higher TN concentrations in the southern portions of the system likely result from the greater inputs of organic material ( i.e., total organic carbo n [ TOC ] ) from the surrounding mangrove forests and upstream wetlands/marshes.

Despite significant differences in the levels of nutrients (TN and TP), average annual chlorophyll a concentrations are relatively low across the entire region with considerable overlap across areas

, with no clear consistent spatial patterns observed. Annual geometric mean chlorophyll a concentrations ranged from 1.5 to 4.6 μg/L across the entire Southwest Coastal Estuaries area.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 31 August 2010 Figure 14. Summary of TP
, TN , and chlorophyll a concentrations in various portions of the S outhwest

C

oastal Estuaries region
, 1999

– 2008.

NPL=Naples Bay, RB=Rookery Bay, WWB=Whitewater Bay , TTI=Ten Thousand Islands.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 32 August 2010 Due to the heterogeneous nature of the region, FIU used generally accepted geomorpho logical characteristics to group the stations. A preliminary spatial analysis of data from its monitoring program
resulted in the delineation of 1 0 groups of stations with robust similarities in water quality ( Table 7; Figures 15 through 19 ). The followi ng sections discuss w ater quality conditions within major portions of
the region. A more thorough assessment of the water quality conditions in each segment of the region is provided in FIU’s 2007 Cumulative Annual Report for the Coastal Water Quality Monitoring Network ( Boyer and Briceño 2008)

, available at: http://serc.fiu.edu/wqmnetwork/SFWMD

- CD/index.htm

.

Table 7

. Summary of sampling sites.

Area
Number Area Name Abbreviation Number of Sites

1 Cocohatchee River COCO 1

2 Naples Bay NPL 3

3 Cape Romano Marco Island MARC 8

4 Rookery Bay RB 5

5 Mangrove River MR 13

6 Whitewater Bay WWB 8

7 Gulf Island GI 12

8 Coot Bay COOT 1

9 Blackwater River E stuary BLK 2

10 Inland Wilderness Waterway zone IWW 11

Naples Bay

- Rookery Bay

Based on the FIU analysis, the area from Naples Bay to Cape Romano was divided into 4 segments: Cocohatchee River at Wiggins Pass, Cape Romano

- Marco Island, Naples Bay, and Rookery Bay. Naples Bay is the segment with the greatest anthropogenic influence. The primary cause of impairment in Naples Bay is excessive fresh water
, with the largest input being the Golden Gate Canal. Excessive fresh

w ater flowing into Naples Bay from the c anal has severely impact ed the bay

, mainly th r ough changes in the salinity regime

, which is now characterized by widely fluctuating salinit y levels

. T he Big Cypress
Basin Control District , the local arm of the S FWMD , manages the canal and is working on plans to divert
up to one

- third of the volume of fresh water now entering the bay from the Golden Gate Canal into th e Henderson Creek watershed

, which needs additional fresh water. The excessive freshwater inputs also significantly influence water quality and result in signifi cant seasonal trends for a number of parameters in addition to salinity

.

Figures 1 5 and 16 show the variation in TN and TP concentrations between the wet and dry seasons

, respectively, for Naples Bay

. N concentrations typically range between less than 0 .1 and 1.2 mg/L in Naples Bay and generally follow expected seasonal patterns , with values increasing during the wet

season and lower levels observed during the dry season. The increased TN concentrations during the wet season are likely the result of gre ater amounts of organic material from the basin being transported
to the bay in stormwater. TP concentrations are much more consistent, with values ranging between 25
and 65 μ g/L, and exhibit a less pronounced seasonal pattern.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 33 August 2010 Figure 16 depicts the t ypical seasonal patterns and long

- term median concentrations for a number of parameters based on the FIU monitoring data. Figure 17 provides a more detailed illustration of the seasonal and long

- term (1999 to 2007) trends in salinity, nutrients, and chlor ophyll a

. Both salinity and DO decrease during the summer wet season as expected. Salinity levels decrease during the wet season in response to greater freshwater inflows, while the lower DO levels during the summer likely result
from a combination of higher water temperatures and increased organic loads that consume DO. As
with TN and TP

, chlorophyll, TOC, and water temperature generally increase during the summer wet

season in response to the increased freshwater inflows . pH and turbidity may exhibit long

- term seasonal trend s but, as shown for 2007, are much more variable over shorter periods and respond rapidly to shorter

- term events. Based on the FIU data collected since 1999, no long

- term trends in nutrients or chlorophyll are apparent (Figure 17 ).

Figures 18 and 19 provide similar summaries of the FIU data for Rookery Bay

, located just south of Naples and Naples Bay. The water quality in Rookery Bay shows seasonal trends similar to those noted for Naples Bay. Due to the extensive mangrove forests , Rookery Bay can have greater TOC inputs and slightly higher nutrient and chlorophyll levels.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 34 August 2010 Figure 15. Summary of wet and dry season TN and TP concentrations in Naples Bay
, 2002

– 09. 

### TN for Naples Bay 2006-2009

0 0.2 0.4 0.6 0.8

1 1.2 1.4 1.6 1.8

2

Wet 06 Dry 06 Wet 07 Dry 07 Wet 08 Dry 08 Wet 09 Dry 09TN (mg/l) 

### 25th

Min

Median

Max

75th



### TP Naples Bay 2002-2009

0.000 0.020 0.040 0.060 0.080 0.100 0.120 0.140 0.160 0.180

Wet
02 Dry
02 Wet
03 Dry
03 Wet
04 Dry
04 Wet
05 Dry
05 Wet
06 Dry
06 Wet
07 Dry
07 Wet
08 Dry
08 Wet
09 Dry
09TP (mg/l) 25th

Min

Median

Max

75thNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 35 August 2010 Figure 16. Comparison of long

- term median concentrations in Naples Bay for selected parameters
with 2007 data (from Boyer and Brice ño 2008)

.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 36 August 2010 Figure 17. Summary of salinity, nutrient, and chlorophyll a data collected by FIU in Naples Bay.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 37 August 2010 Figure 18. Comparison of long

- term median concentrations in Rookery Bay for selected parameters
with 2007 data

.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 38 August 2010 Figure 19

. Summary of salinity, nutrient, and chlorophyll a data collected by FIU in Rookery Bay.

Ten Thousand Islands

– Whitewater Bay

The spatial analysis of the FIU data for the Ten Thousand Island

– Whitewater Bay portion of the system resulted in the delineation of 6 groups of stations with similar water quality characteristics: ( 1) Whitewater Bay proper ; ( 2) the Mangrove River group

, which includes the Shark, Harney, Broad, and Lostmans Rivers; ( 3) the Inland Wilderness Waterway zone

, located along the inside passage , which includes the Chatham River as well as sites off Everglades City; ( 4) the Blackwater River Estuary ; ( 5) the Gulf Island group; and ( 6) Coot Bay

, which includes a single site.

Whitewater Bay is a shallow, semienclosed body of water with a relatively long residence time (months)
that receives diffusive freshwater input from the Everglades marsh and mangrove fringe. Its location at the edge of the P- limited Everglades and its long water residence time explain the presence of very low P concentrations, while the high evaporation rate , w hich tend s to concentrate salt and dissolved organic matter (DOM)

, result s in higher salinities and TOC concentration s

. Although both Whitewater Bay and the Mangrove River group have similar sources of fresh water , the long water residence time in Whitewater Bay affects water quality enough to separate Whitewater Bay from the Mangrove River
stations. Figure 21 summariz es water quality for selected parameters based on data fr om the FIUNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 39 August 2010 monitoring program ( Boyer and Briceño 2008) . The area is characterized by wide fluctuation in salinity
levels

, low TP concentrations , and moderate chlorophyll levels.

Estuaries in the M angrove Rivers cluster are directly influenced by the Shark Slough of the Everglades and therefore have a huge watershed relative to their volume. The terrestrial freshwater inputs to the southern mangroves are orders of magnitude greater than for the nor thern Ten Thousand Islands

. As such, concentrations of P in incoming waters are very low , w hile DOM inputs are high (Boyer 2005 ; Childers et al. 2006). The output of TON and TOC in the southern estuaries is clearly enhanced by the production of organic m atter in the mangrove forest (Twilley 1985 ; Boto and Wellington 1988).

An interesting anomaly in the Mangrove Rivers group is the inclusion of Faka Union Bay in the northern
Ten Thousand Islands (Fig ure 20 ). The reason for this is that the Faka Union Canal drains the Southern Golden Gate Estates, a failed development that built 813 miles of roads and 138 miles of canals during the 1960s to drain the swamps of Collier County in southwest Florida. Wet season overdrainage through the Faka Union Ca nal has resulted in a decline in salinity of 8 to 12 psu in Faka Union Bay and has significantly affected fish, oyster, and seagrass communities (Browder et al. 1989 ; SFWMD 1994). Because of its unusual hydrology and large watershed, the Faka Union Canal site is more similar to the Mangrove River sites than to other sites in the northern Ten Thousand Islands

.

The Inner Waterway ha s extensive channelization but lower freshwater input than the Mangrove River

group to the south and less exchange with the Gu lf of Mexico due to its small inlets. For these reasons,
it s water quality is between that of the estuaries to the south and north. Most of the Inner Waterway is part of E NP ’s Wilderness Waterway, a 99

- mile ( 159

- km) back

- country canoeing route that runs along the western edge of E NP from Flamingo to Everglades City.

The Gulf Island zone has very low freshwater input due to the poorly drained watershed of the Big Cypress Basin. Instead of mangrove river channels

, there are many mangrove islands set in a lower tidal energy environment situated behind the Cape Romano Shoals in the Gulf of Mexico. Water quality is dominated by the Gulf , although small freshwater inputs from land are a regular occurre nce

. A current restoration project to construct 87 addit ional culverts at 30 separate sites under Tamiami Trail will increase watershed connectivity to the estuaries ( additional information is available at: http://www.evergladesplan.or g/pm/projects/docs _30_sgge.cfm ). S alinity and nutrient regimes are expected to change with increased terrestrial flows.

T he Blackwater River cluster has the highest salinity and P. The Blackwa ter River is about 8 miles long

, with flow v arying seasonal ly in accordance with rainfall. There is considerable agriculture (tomatoes, etc.) in the Blackwater River watershed, which may contribute P to the system via drainage ditches

. This
area is also being developed with low

- density residen tial areas and golf courses.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 40 August 2010 Figure 20. Results of spatial analysis performed by FIU for the Ten Thousand Island s– Whitewater Bay

area.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 41 August 2010 Figure 21. Summary of salinity, nutrient, and chlorophyll a data collected by FIU in the Whitewater Bay and Gulf Island zones of the Ten Thousand Islands.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 42 August 2010 

### S ources of Nutrients

Sources of nutrients to the Southwest Coastal Estuaries include freshwater inputs from the upland tributaries and canals, point source discharges, urban stormwater, agricultural runoff, saline ground water, the Gulf of Mexico, and atmospheric deposition . There are four point sources in the northern
watersheds and only one small point source (Everglades City ) in the southern portion of the region

. Table 8 lists the poi nt sources in the region.

The spatial differences in sources and the geochemical differences result in significant gradients across
the area. The Southwest Coastal Estuaries a re geomorphologically diverse and have diffuse and

, in

some cases , undefined watersheds. Due to the nonpoint source nature of runoff from the Everglades and Big Cypress Basin

, it is almost impossible to quantify the sources and loads of fresh water and nutrients to most estuaries, especially those in the southern portion of the system. Since the sources
and loads of nutrients can no t be accurately quantified, it is difficult to study nutrient biogeochemistry using standard schemes of estuarine ecology

— i.e., mixing diagrams.

Nonpoint source pollution

, including agricultural operations; excess fertilizer from urban lawns, landscapes, and golf courses; faulty or old septic tanks; and stormwater runoff are potential sources of anthropogenic nutrients into R B NERR. To FDEP’s knowledge , there is no published research on the

a ssimilative capacity of these systems or nutrient loading models for RB NERR.

Table 8. List of facilities permitted for surface water discharge in the Southwest Coastal Estuaries region.

Facility ID Facility Name Description Permitted Capacity ( mgd ) Design Capacity ( mgd )

FL0026271 City of Naples Wastewater
Treatment Plant Domestic Wastewater
Treatment Plant 10 10

FL0141356 Collier County South Regional

W ater Reclamation Facility (W RF ) Domestic Wastewater
Treatment Plant 8 8

FL0141399 Collier County N orth WRF Domestic Wastewater
Treatment Plant 13.5 8.5

FL0141704 Port of the Islands

– South Domestic Wastewater
Treatment Plant 0.2 0.2

Fl0027618 City of Everglades, City Wastewater Treatment Facility ( WWTF ) Domestic Wastewater

Treatment Plant 0.115 0.115



### Waters on the 303(d) List

Due to the adverse water quality impacts associated with the urban development and the drainage and
channelization activities that have occurred in the region , a number of areas have been identified as impaired based on the assessment methodolog y in the IWR ( Chapter 62

- 303, F.A.C. ). A ppendix B list s all verified impairments for estuarine and coastal waterbodies within the region (FDEP 2010a). Most of the impairments are for DO , fecal coliform

, and chlo rophyll/nutrients

. Naples Bay is also listed as impaired for iron and copper. The majority of the impaired segments are located in the northern portions of the system ( i.e., Naples Bay and Cocohatchee River)

, where the greatest impacts from urban develop ment,Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 43 August 2010 drainage, and channelization have occurred. However, Rookery Bay is also listed as impaired for nutrients/chlorophyll and DO

.

Copper has been iden tif ied a s a major pollutant in Naples Bay . A geographic information system ( GIS ) analysis located “h ot spots” at the stormwater outfalls that drain the city’s 28 stormwater ponds, streets, and other impervious surfaces

. These ponds are the logical source of the copper

, since copper
sulfate has been applied to them for decades as an herbicide to kill alg ae. FDEP verified the copper impairment

, and Naples Bay was placed on the impaired waters list for this metal. NOAA has also found
that oysters in Naples Bay have one of the highest levels of copper sampled in the nation.

Based on a closer evaluation of the data used in the assessments, the listing for DO appear s to be an artifact of an inappropriate DO criterion that currently does not take into account natural conditions . As described previously, the Rookery Bay Estuary has extensive mangrove forest s that are ecologically critical components of the system. The mangroves continuously shed their leaves and produce
considerable quantities of organic material. As the organics decay, oxygen is consumed

, resulting in naturally lower DO levels in the bay

. This phenomenon of naturally low DO levels (below the existing water quality criteri on ) is commonly observed throughout the state.

Due to the widespread occurrence of naturally low DO levels in Florida estuarine and coastal systems, a s described in the document

, Overview of FDEP Approaches for Nutrient Criteria Development in Marine Waters, Florida is currently evaluating the appropriateness of the current criteri on , which was based on
limited information collected more than 40 years ago. Based on the observations that Rookery Bay has limited anthropogenic inputs and supports a healthy biological community, the observed DO levels used

to verify the impairment likely represent a natural condition that full y supports the designated use of the bay.

As for t he listing for nutrients in Rookery Bay , FDEP has determined that the listing was based on a flaw in the original analysis and p l ans to delist the bay for nutrients during the next assessment cycle. The listing was primarily based on chlorophyll a data collected during 2006 by the FDEP District Office in Fort Myers . However, t he data were collected as a part of a study targeting isolated nutrient sources such as golf courses, wastewater sprayfields, and dead

- end canals, and were not representative of the general conditions within the bay or WBID. M ost of the sites included in this study were located in the most inland portions of the WBID

, with some of the sites appearing to be more fresh water than estuarine or marine. Since the data from this targeted study made up a large majority of the data used in the IWR assessment, the results of the assessment indicated an annual average chlorophyll a level above the threshold for impairment.

W hen the annual average chlorophyll concentration for Rookery Bay is recalculated incorporating
additional

, more representative data collected by FIU as part of its extensive south Florida coastal and estuary monitoring program, the result is well below the threshold for listing (Figure 20 ) . The FIU data

were not u sed in the original assessment because FIU did not enter the data into STORET

, which is the primary data source for the IWR assessments. Therefore, the listing for chlorophyll/nutrients in Rookery Bay is not reflective of the overall health of the waterbo dy and is inaccurate.

In summary, water quality conditions observed in the southern portions of the system likely represent largely natural conditions

, while those in the northern regions represent areas more highly impacted by urban development . H oweve r, impacts are caused by multiple factors

, and nutrient levels do not appear to result in significant widespread biological problems

.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 44 August 2010 

### Criteria Development

Due to the relatively low nutrient and chlorophyll a levels observed, the lack of long

- term increasin g trends in nutrient and chlorophyll a concentrations, the lack of widespread biological impacts associated with nutrients, and the large number of natural conservation lands in the basin, the proposed nutrient criteria were developed to maintain the existing conditions that are supportive of healthy

, well

- balanced populations of flora and fauna. As described previously, nutrients concentrations across the Southwest
Coastal Estuaries region are characterized by spatial, north

- south gradients due to th e natural geochemical changes that occur within the region. Due to this natural spatial variation, the first step in the derivation of appropriate nutrient criteria was to separate the area into more homogeneous subregions. The distribution of nutrient and chlorophyll a data from each subregion was then used to derive criteria that would assure the nutrient regime in each subregion would be maintained at or below existing levels. More details on the regionalization approach and the derivation of the nutr ient criteria for each subregion are provided blow.

Regionalization

As discussed previously, FIU has u s ed the data collected as part of its Coastal Water Quality Monitoring
Network t o spatially aggregate monitoring sites located along the southwest Florida coast based on
similar water quality characteristics (Boyer 2006). Based on the unique water quality and geologic characteristics observed along the Southwest C oastal Estuaries area , E NP and FIU have jointly proposed
that the estuarine and coastal waters of south Florida be divided into sub

- basins for the purpose of deriving nutrient criteria.

On behalf of ENP, FIU recently completed an extensive statistical characterization of coastal waters from Biscayne Bay to Dry Tortugas to Pine Island Sound. The recent analys is was similar to the earlier spatial regionalization method used by FIU, but u s ed a longer period of record and a modified set of parameters. The analysis , which used a combination of Principal Component Analysis and Hierarchical Clustering of multiple (from 8 to 13) parameters, produced a division of the bays as shown in F igure 23
and T able 9

. Appendix A contains m ore detail on the a nalysis conducted by Henry Briceño, Joe Boyer,
and Peter Harlem from FIU. Additionally, the GIS layers with information on the sub

- basins

, as well as FIU’s working files with data and statistical analysis

, are available at FIU’s ftp site provided earlier

.

FDEP plans to use t his regionalization scheme as the basis for numeric criteria for each sub

- basin. A final step in the process will be to evaluate the similarity of the derived criteria with the purpose of combining sub

- basins with similar criteria ( i.e., criteria that are not statistically different) for TP, TN, and
chloro phyll a

.

On the basis of the statistical analysis performed, the southwest Florida bays and coastal waters were
divided into 14 sub

- basins, as detailed in Table 9 and illustrated in Figure 22 and 2 3

. The area from Whitewater Bay to the Ten Thousand Islands was subdivided into 8 sub

- basins , and the region from Pine Island to Rookery Bay was divided into 6 sub

- basins

.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 45 August 2010 Table 9 a . Proposed regionalization for the Whitewater Bay to the Ten Thousand Island s a rea of the
Southwest Coastal Est uaries

. Sub

- Basin
Number Sub

- Basin Map Code Sub

- Basin Name

1 WWB Whitewater Bay

2 PD Ponce De Leon

3 SRM Shark River mouth

4 MR Mangrove River

5 CTZ Coastal Transition Zone

6 IWW Inner Waterway

7 GI Gulf Islands

8 BLK Blackwater River

Table 9 b

. Proposed regionalization for the Pine Island Sound to Rookery Bay area of the Southwest
Coastal Estuaries.

Sub

- Basin
Number Sub

- Basin Map Code Sub

- Basin Name

1 MARC Marco Island

2 NPL Naples Bay

3 CI Collier Inshore

4 EB Estero Bay

5 SCB San Carlos Bay

6 PIS Pine Island SoundNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 46 August 2010 Figure 22. Proposed subdivision of estuarine and coastal waters for deriving nutrient criteria in south
and southwest Florida bays and coastal waters

.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 47 August 2010 Figure 23. Proposed estuarine and coastal nutrient criteria sub

- ba sins for the Southwest Coastal
Estuaries region.



### Proposed Numeric Nutrient Targets

Methodology

For consistent application and to provide an appropriate level of protection, water quality criteria need to include magnitude, frequency, and duration components

. The magnitude is a measure of how much of a pollutant may be present in the water without an unacceptable adverse effect

. Duration measure s how long the pollutant may be above the magnitude, and frequency relates to how often the magnitude may be exceeded without adverse effects. It is prefer able to derive the magnitude component of a criterion through a cause

- effect relationship (such as that measured through toxicity testing). The magnitude would then be set at a level that would protect a majority of the sensitive aquatic organisms inhabiting the system. Absent a demonstrated cause

- effect relationship, the magnitude may be set at a level designed to maintain the current data distribution, accounting for natural temporal variability, when the current conditions are protective of the designated uses of the waterbody. Since a criterion derived based on the existing data distribution has no direct link to any observed cause

- and

- effect relationship, it is assumed that maintaining the current data distribution will preserve the uses
associated with that distribution.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 48 August 2010 The frequency and duration components of the criteria are best established as additional descriptors of
the reference condition data distribution. Specifically, these components should be part of a statistical test designed to determi ne whether the long

- term distribution of data has shifted upward (or in some cases, downward) from the reference distribution. This test would then be used to determine whether future monitoring data are consistent with the magnitude (long

- term average) d efined by the reference
dataset. It is critical to account for the natural variability surrounding the magnitude expression and to
control for statistical errors.

The derivation of the magnitude, frequency

, and duration components of the numeric nutrien t criteria
for the Southwest Coast is described briefly below. More details concerning the statistical approaches
used can be found in the document

, Overview of FDEP Approaches for Nutrient Criteria Development in
Marine Waters (FDEP 2010).

Magnitude

The magnitude component can be set at a variety of values based on the frequency and duration that will be used to determine compliance. For the “healthy existing conditions” approach, FDEP established the magnitude at (1 ) an adjusted long

- term central tend ency (geometric mean) of the distribution, expressed as a long

- term geometric mean never to be exceeded; and (2 ) an annual geometric mean, not
to be exceeded more than twice over a five - year period. The long

- term average condition was adjusted
to a level that represents an insignificant increase from the baseline. Allowing for an insignificant increase accounts for uncertainty in the estimate of the mean and partially addresses the fact that the
reference

- based approach fails to identify a threshold of i mbalance, and thus is highly prone to excessive Type I error ( i.e., identifying a healthy system as impaired)

. For the purpose of antidegradation evaluations, the EPA has established that a 10% change in a water quality parameter represents an insignifica nt departure from the historical condition, known as a de minimus change (U .S. Sixth Circuit Court 2008). Therefore, the long

- term geometric mean limit was derived to allow for up to

a 10% increase in the long

- term geometric mean, which was calculated as the geometric mean of the annual geometric means of the long

- term dataset for each segment of the waterbody.

Frequency and Duration

Because it is not always practical to assess compliance with the criteria on the same long

- term basis, FDEP also developed c riteria expressed as an annual geometric mean so that estuaries could be assessed
annual ly

. It should be noted that the duration and frequency components of the criteria must be linked to the response time frame of the sensitive endpoint. Short

- term averaging periods (e.g., 1 to 30 days) might be appropriate for nutrient criteria where a sufficiently robust cause

- effect relationship has demonstrated that a eutrophic response occurs over such time frames. If however, such a short

- term response cannot be demonstrated, or there is no indicati on of use impairment, longer averaging periods
should be used.

Since the duration and frequency components of the criteria must be consistent with the derivation of the magnitude component, the long

- term geometric mean target cannot simply be applied as an annual

mean. Doing so would result in an unacceptab ly high Type I failure rate

, since approximately 50 % of the individual yearly means are expected to be above the long

- term mean. Therefore, the long

- term targe t must be adjusted to allow for the application to a shorter duration with an acceptable Type I error rate
of no more than 10 %.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 49 August 2010 An annual criterion with an approximate 10 % Type I error rate for a given frequency was derived by appropriately accounting for the annual variability above the mean. This annual target concentration was derived as an upper percentile of the distribution of the annual geometric mean concentrations. Previous proposals by the EPA have u s ed 3- year assessment periods to express the d uration nutrient criteria components. Although it is possible to construct a test that achieves the 10 % Type I error rate target over a 3

- year period, a slightly longer period (5 years) will provide better control for Type II error and will more fully capture climatic cycles ( e.g ., El Niño, La Niña ), which tend to be longer than 3 years in Florida (and may actually be on a multidecadal scale). Furthermore, a 5- year period is more consistent
with both the s tate’s 5- year 303(d) assessment and National Pollu tant Discharge Elimination System ( NPDES ) permit renewal cycles.

Given a 5- year a ssessment period, FDEP derived criteria expressed as an annual geometric mean by using the 75 th percentile of the annual geometric means from the long

- term dataset. FDEP
demo nstrated that setting the criteria at this percentile results in a magnitude that, when expressed as an annual geometric mean not to be exceeded more than twice during a 5- year period, will achieve the targeted 10 % error rate

. The magnitude component of t he criteria (not to be exceeded more than twice
in a 5- year period) was established to allow for 2 separate assessments , as follows :

**•** As an annual geometric mean for a network of stations in a specified segment of the waterbody; and

**•** As an annual geometric mean for a single station in a given segment.

The two expressions of magnitude differ in the handling of within

- segment spatial variability. The network average magnitude was calculated based on the distribution of spatially aver aged annual geometric means, while the single

- site magnitude was calculated using the distribution of station annual geometric means. The u se of the network average magnitude is appropriate for assessing overall
segment status. However, a network average is only representative of overall segment status if it is relatively homogeneous. I f the segment is not well mixed, is very large, or contains localized nutrient sources, then isolated areas of enrichment may potentially be masked in the network spatial average. Therefore, the single

- station annual geometric mean has the benefit of assessing localized enrichment
patterns. F DEP has not decided whether both expressions of magnitude are needed in all cases, and is seeking additional feedback from local exp erts and stakeholders.

Summary of the Proposed Criteria

FDEP proposes three sets of potential criteria: (1 ) a long

- term g eometric mean concentration; (2 ) an annual geometric mean of values from a network of stations over a given area, not to be exceeded more than twice in a five

- year period; and (3 ) a n annual geometric mean of values from a single location, not
to be exceeded more than twice in a five

- year period.

Table 10 provides t he proposed long

- term targets for the protection of a healthy, well

- balan ced aquatic community

, as well the annual limits for each sub

- basin

, in the Southwest Coastal Estuaries region. The next step in finalizing the proposed criteria is to evaluate the similarities among the different sub

- basins to determine if any of the m co uld be combined for criteria development. The process of evaluating the similarities among sub

- basins is currently under way , and the results will be provided once the analysis has been completed.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 50 August 2010 Table 10 a

. Proposed numeric TP criteria for sub

- basins within the Southwest Coastal Estuaries region

.

- = Empty cell/no data
Sub

- Basin Map Code Sub

- Basin

Name Existing Long

- Term
Geometric

Mean
Concentration Maximum
Allowed Long

- Term
Geometric

Mean Annual Geometric
Mean for Network of
Stations (2 of 5 year exceedance rate) Annual Geometric Mean for Single Site (2 of 5 year exceedance rate)

Whitewater Bay to Ten
Thousand
Islands Area - - - - -

WWB Whitewater Bay 19.4 21.3 26.6 27.2

PD Ponce De Leon 19.2 21.1 25.0 25.3

SRM Shark River mouth 16.9 18.6 22.8 24.1

MR Mangrove River 17.4 19.2 22.4 23.5

CTZ Coastal Transition

Zone 29.2 32.1 36.1 37.6

IWW Inner Waterway 27.9 30.7 34.9 36.3

GI Gulf Islands 33.0 36.2 40.7 42.4

BLK Blackwater River 44.9 49.4 55.7 58.3

Naples Bay to Rookery Bay Area - - - - -

MARC Marco Island 37.0 40.7 46.0 48.0

NPL Naples Bay 39.5 43.5 50.2 51.4

CI Collier Inshore 26.7 29.4 33.5 34.0Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 51 August 2010 Table 10 b

. Proposed numeric TN criteria for sub

- basins within the Southwest Coastal Estuaries a rea.

- = Empty cell/no data
Sub

- Basin Map Code Sub

- Basin

Name Existing Long

- Term
Geometric

Mean
Concentration Maximum
Allowed Long

- Term
Geometric

Mean Annual Geometric
Mean for Network
of Stations (2 of 5 year exceedance rate) Annual Geometric Mean for Single Site (2 of 5 yea r exceedance rate)

Whitewater Bay to Ten
Thousand
Islands Area - - - - -

WWB Whitewater Bay 0.63 0.69 0.84 0.87

PD Ponce De Leon 0.40 0.44 0.54 0.55

SRM Shark River mouth 0.56 0.61 0.77 0.79

MR Mangrove River 0.55 0.61 0.74 0.75

CTZ Coastal Transition

Zone 0.48 0.52 0.63 0.64

IWW Inner Waterway 0.53 0.58 0.71 0.73

GI Gulf Islands 0.36 0.40 0.46 0.48

BLK Blackwater River 0.34 0.37 0.43 0.44

Naples Bay to Rookery Bay Area - - - - -

MARC Marco Island 0.26 0.29 0.32 0.33

NPL Naples Bay 0.27 0.29 0.32 0.33

CI Collier Inshore 0.22 0.24 0.27 0.27Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 52 August 2010 Table 10 c

. Proposed numeric chlorophyll a criteria for sub

- basins within the Southwest Coastal
Estuaries a rea.

- = Empty cell/no data
Sub

- Basin Map Code Sub

- Basin

Name Existing Long

- Term
Geometric

Mean
Concentration Maximum
Allowed Long

- Term
Geometric

Mean Annual Geometric
Mean for
Network of Stations (2 of 5 year exceedance rate) Annual Geometric Mean for Single Site (2 of 5 year exceedance rate)

Whitewater Bay to Ten
Thousand
Islands Area - - - - -

WWB Whitewater Bay 2.7 3.0 4.0 4.3

PD Ponce De Leon 2.3 2.6 3.0 3.1

SRM Shark River mouth 1.8 2.0 2.4 2.5

MR Mangrove River 3.1 3.4 4.0 4.3

CTZ Coastal Transition

Zone 3.2 3.5 4.0 4.4

IWW Inner Waterway 4.1 4.5 5.3 5.5

GI Gulf Islands 2.9 3.2 3.6 3.9

BLK Blackwater River 3.4 3.7 4.2 4.5

Naples Bay to Rookery Bay Area - - - - -

MARC Marco Island 4.3 4.7 5.4 5.9

NPL Naples Bay 3.9 4.2 4.8 5.2

CI Collier Inshore 2.3 2.5 3.1 3.2Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 53 August 2010 

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Draft 57 August 2010 

# Appendix A: Threatened and Endangered Species

(Data Taken from Draft Rookery Bay NERR Management Plan)Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 58 August 2010Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 59 August 2010Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 60 August 2010 

# Appendix B: Impaired Waters ListNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 61 August 2010OGC CaseNumberPlanning UnitWBIDWater SegmentNameWaterbodyTypeWaterbodyClass11998 303(d)Parameters ofConcernParametersAssessed Using the2007 ImpairedSurface Waters Rule(IWR)ConcentrationCausing ImpairmentPriority for TMDLDevelopment209-2718Southw est Coast8065SOUTHWEST COASTGULF 5COASTAL3MBacteria (in Shellfish)09-2719Florida Gulf Coast8999FLORIDA GULFCOASTCOASTAL3MMercury (Based onfish consumptionadvisory)Mercury (Based on fishconsumption advisory)Hg > 0.3 mg/KgHigh*09-2698Southw est Coast3259ACOCO-HATCHEERIVERESTUARY2ColiformsFecal Coliform > 43 colonies per 100 mlLow09-2699Southw est Coast3259ACOCO-HATCHEERIVERESTUARY2Iron>0.3 mg/LMedium09-2709Southw est Coast3278R(3259G)NAPLES BAYCOASTALESTUARY2Copper>3.7 mg/LMedium09-2710Southw est Coast3278R(3259G)NAPLES BAYCOASTALESTUARY2Fecal Coliform > 43 colonies per 100 mlLow09-2711Southw est Coast3278R(3259G)NAPLES BAYCOASTALESTUARY2Iron>0.3 mg/LMedium09-2712Southw est Coast3278R(3259G)NAPLES BAYCOASTALESTUARY2Dissolved Oxygen < 4.0 mg/LMedium09-2715Southw est Coast3278UROOKERY BAYCOASTALESTUARY2Dissolved Oxygen < 4.0 mg/LMedium09-2716Southw est Coast3278UROOKERY BAYCOASTALESTUARY2Nutrients (Chlorophyll-a)TN = 0.32 mg/L; TP =0.04 mg/L; BOD = 2.2mg/LMedium09-2717Southw est Coast3278UROOKERY BAYCOASTALESTUARY2Fecal Coliform> 400 colonies per 100mlLowWhere a parameter w as only identified as impaired under the IWR, a priority of “medium” w as assigned. Exceptions are w aters w here the impairment poses a threat to potable w ater orhuman health, w hich have been assigned a “high” priority, and fecal coliform impairments, w hich have been assigned a “low ” priority. All other listings as of this cycle are prioritized basedon the follow ing: it is the Department's intent that listings w ith a "High" priority be addressed w ithin the next 5 years, listings w ith a "Medium" priority be addressed w ithin 5-10 years as resouand listings w ith a "Low " priority be addressed w ithin the next 10 years.Fish advisory data is based on "2006 Fish Advisories" file created 07/11/2006 and updated 08/13/2007 by FDEP.5 - Navigation, utility, and industrial useg y y g g ( ) yof the integrated list; individual entries have been removed from the list.2Where a parameter w as 1998 303(d) listed, the priority for TMDL development is the year provided and is assigned based on the consent decree schedule.3PP- Planning Period (January, 1995 through December, 2004);VP- Verified Period (January, 2000 through June 30, 2007)The Group 1 Everglades West Coast Basin Verified List is based on IWR Run 32.Beach advisory data is based on "2006 Beach Advisories" file created 04/16/2007 by FDEP.1Florida's w aterbody classifications are defined as:1 - Potable w ater supplies2 - Shellfish propagation or harvesting3F - Recreation, propagation, and maintenance of a healthy, w ell-balanced population of fish and w ildlife in fresh w ater3M - Recreation, propagation, and maintenance of a healthy, w ell-balanced population of fish and w ildlife in marine w ater4 - Agricultural w ater suppliesNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 62 August 2010 

# Appendix C: Summary of Regionalization MethodNutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 63 August 2010 

### April 30, 2010

Dr. Joffre Castro Everglades National Park South Florida Ecosystem Office 950 N Krome Ave; 3 rd 

### floor Homestead, Fl 33030

Dear Dr. Castro,

This is a transmittal letter to accompany the report entitled, “Summary of Statistical Classification and Clustering of South Florida Estuarine and Coastal Waters” prepared by Florida International University for the National Park Service, as supportive ma terial for derivation of Numeric Nutrient Criteria for South Florida coastal and estuarine waters. A map with the outlines of the classified areas has been attached to this e- mail. Additionally, a set of zip -files have been uploaded to the NPS folder in SE RC’s ftp site, containing shape files and metadata, as well as a copy of the summary report. You will receive the code and password to access the ftp site, via e- mail.

Please do not hesitate to contact me, if you need additional information. Best regards,

Henry O. Briceño Southeast Environmental Research Center Florida International University 11200 SW 8 th 

### St, OE # 148 Miami, Fl 33199Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 64 August 2010



## Summary of Statistical Classification and Clustering of South Florida Estuarine and Coastal Waters

Prepared by:

Henry Briceño, Joseph Boyer and Peter Harlem Florida International University Southeast Environmental Research Center Miami, Florida

Delivered to: Joffre Castro

National Park Service Everglades National Park Homestead, Florida

Miami April 30 th 

### , 2010

TASK AGREEMENT #: J5297-08-0085 C OOPERATIVE AGREEMENT#: H5000-06-0104Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 65 August 2010



## Summary of Statistical Classification and Clustering of South Florida Estuarine and Coastal Waters

PREVIOUS WORK: Classification and grouping of South Florida coastal waters into spatial WQ clusters have been performed by Boyer et al. (1997) and Briceño and Boyer (2010) in Florida Bay (FB); by Caccia and Boyer (2005), Hunt and Todt (2006), and Briceño et al. (2010) in Biscayne Bay (BB); by Boyer (2006) in the Whitewater Bay

- Ten Thousand Islands (WWB -TTI) region; and by Boyer and Briceño (2009) in the Florida Keys (FK). No previous subdivision exists for Pine Island

- Rookery Bay area (PI

- RB). In all studies where subdivi sions have been reported, a combination of Principal Component and Cluster Analysis was used for grouping FIU’s sampling sites, except in the work by Hunt and Todt (2006) where a direct cluster analysis was performed to group the stations. Caccia and Boyer (2005) used FIU WQ data from 1994 to 2003 to subdivide Biscayne Bay into five spatial zones, and Hunt and Todt (2006) combined DERM and FIU data and also found five geographic domains in Biscayne Bay. Boyer et al. (1997) subdivided Florida Bay into four classes and Briceño and Boyer (2010) obtained six water classes. The process by which the bays were subdivided considered several biogeochemical variables and followed an ecological approach, so its results mimic very closely those geographical patterns of: water circulation and residence time (Wang et al. 1994, 2003, 2007; Brand 2001; Cosby et al. 2005;); salinity (Robblee et al. 1989; Boyer et al. 1997; Fourqurean and Robblee 1999; Nuttle et al. 2000; Cosby et al. 2005); TP and TN (Fourqurean et al. 1993; Fourqurean and Robblee 1999; Hitchcock et al. 2007); phytoplankton biovolumes and type (Phlips and Badylak 1996; Phlips et al. 1999; Steidinger et al. 2001; Hunt and Nuttle 2007); seagrass distribution (Zieman et al., 1989,1991; Roblee et al. 1991; Fourqur ean et al. 2003); and bottom composition (Wanless et al. 1984).

OBJECTIVE The main objective of this work is to subdivide south Florida’s estuaries and coastal waters into basins with similar geomorphological and geochemical characteristics to support the derivation of numeric nutrient criteria.

METHODOLOGY

Data source Florida International University WQMN ( http://serc.fiu.edu/wqmnetwork ).

Period of Record The PORs were selected depending upon data availability, variable set completeness, and data quality as shown in Table 1. For BB we reassessed our recent subdivision of Central and South BB (from 09/30/93 to 9/18/08) with a new one that includes North BB and Manatee Bay and Barnes Sound (6/7/96 to 9/24/09), and for FB we adopted the recently published subdivision of Briceño and Boyer (2010) whose POR is from 3/14/91 to 12/07/07. Some of Briceño and Boyer’s abbreviations for the basins have been modified to maintain a consistent nomenclature throughout the area of interest.

Water Quality data FIU WQMN field water column measurements and sampling were performed monthly. Reported measurements included surface and bottom salinity (PSU), temperature (°C), diss olved oxygen (mg/l), and turbidity (NTU). Laboratory determinations under NELAC certified analytical procedures included Total Nitrogen (TN), Total Phosphorus (TP), Total Organic Carbon (TOC), Total Organic Nitrogen (TON), Chlorophyll a (CHLA), Nitrate+Nitrite (NO x- ), Nitrite (NO 2- ),Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 66 August 2010 Nitrate (NO 3- ), Ammonium (NH 4+ ), Inorganic Nitrogen (DIN, calculated), Soluble Reactive Phosphate (SRP), and Silicate (SiO 2 ).

FACTOR ANALYSIS AND CLUSTERING

We re

- assessed the subdivisions in the FK, WWB -TTI and BB, and for the first time subdivided the SoFlo (South Florida) west coast estuaries from Pine Island to Rookery Bay (PI- RB). We followed an ecological (multivariate) approach to classify the estuarine and coastal waters. Biogeochemical variables with less than 10% non- detects were selected for Factor Analysis (StatView 5.0.1). Factor Analysis of standardized data used Orthotran/Varimax rotation and PC extraction. Scores were retained and their
mean, st andard deviation, median, and median absolute deviation at each sampling station were used for hierarchical cluster analysis (SYSTAT 8.0) with Ward distance calculations. A group of small lakes along the Everglades –Florida Bay ecotone (Frankovich et al. 2010) were provisionally incorporated in FB as an additional water type (Coastal Lakes, CL). We are in the process of collecting pertinent water quality data to validate and confirm this grouping. Table 1 summarizes the inputs and results of the whole data processing, indicating the POR, variables used for Factor Analysis, number of stations included, the % variance accounted and the resulting clusters after the Hierarchical cluster analysis.

Three GIS map layers (shape files) were prepared for this study (Table 2). These layers portray the model boxes as polygons and the FIU station locations as points with the third layer showing the land areas of South Florida. The latter was made by combini ng the U.S Census Bureau land area maps for each county into a single layer; however, for Miami -Dade County, a shoreline derived from Lidar data and more accurate than the Census version was used.Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 67 August 2010 Finally, this statistical clustering is a first cut at p artitioning ecological regions of the bays and coastal areas according to overall water quality characteristics (Table 3). We plan to further compare pertinent nutrient variables among groups in an effort to determine their statistical significance. Should zones not be significantly different, similar nutrient criteria will be applied to reduce complexity.

TABLE 3Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 68 August 2010 REFERENCES

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