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 National Estuary Research Reserve

Collier County

City of Naples

August 20, 2010
Nutrient 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 Florida 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: Threatened and Endangered Species ............................................................. 57

Appendix B: Impaired Waters List ...................................................................................... 60

Appendix C: Summary of Regionalization Method............................................................. 62
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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

Table 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 10. Quadrate on the shoal of Cape Romano in 1998 (left); image of seagrass taken on the 

same shoal in 2009 (right)...........................................................................................................23

Figure 11. Map of the 2010 Cape Romano quadrate locations along a fixed transect. ............................23

Figure 12. Species richness comparison between Fakahatchee, Faka Union, Pumpkin, and 

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

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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 Florida 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: Threatened and Endangered Species ............................................................. 57

Appendix B: Impaired Waters List ...................................................................................... 60

Appendix C: Summary of Regionalization Method............................................................. 62
Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

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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

Table 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 10. Quadrate on the shoal of Cape Romano in 1998 (left); image of seagrass taken on the 

same shoal in 2009 (right)...........................................................................................................23

Figure 11. Map of the 2010 Cape Romano quadrate locations along a fixed transect. ............................23

Figure 12. Species richness comparison between Fakahatchee, Faka Union, Pumpkin, and 

Rookery Bays. ..............................................................................................................................27
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collected monthly water quality data at 22 sites in Whitewater Bay and 26 sites in the Ten Thousand 

Islands beginning in September 1992, and 17 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 principal 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 decreases, 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 expect 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. Based 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 TN concentrations in Naples Bay ranged from 0.2 to 0.29 mg/L, while the 

higher TN concentrations in Whitewater Bay ranged from 0.39 to 0.66 mg/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 carbon [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

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Due to the heterogeneous nature of the region, FIU used generally accepted geomorphological 

characteristics to group the stations. A preliminary spatial analysis of data from its monitoring program 

resulted in the delineation of 10 groups of stations with robust similarities in water quality (Table 7; 

Figures 15 through 19). The following sections discuss water 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 RomanoMarco IslandMARC 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 Estuary 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

water flowing into Naples Bay from the canal has severely impacted the bay, mainly through changes in 

the salinity regime, which is now characterized by widely fluctuating salinity levels. The Big Cypress 

Basin Control District, the local arm of the SFWMD, 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 the 

Henderson Creek watershed, which needs additional fresh water. The excessive freshwater inputs also 

significantly influence water quality and result in significant seasonal trends for a number of parameters 

in addition to salinity. 

Figures 15 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 greater 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 μg/L, and exhibit a less pronounced seasonal pattern. 
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Figure 13. Estimated bycatch comparison between Fakahatchee, Faka Union, Pumpkin, and 

Rookery Bays. ..............................................................................................................................27

Figure 14. Summary of TP, TN, and chlorophyll a concentrations in various portions of the 

Southwest Coastal Estuaries region, 1999–2008. .......................................................................31

Figure 15. Summary of wet and dry season TN and TP concentrations in Naples Bay, 2002–09..............34

Figure 16. Comparison of long-term median concentrations in Naples Bay for selected 

parameters with 2007 data (from Boyer and Briceño 2008). .....................................................35

Figure 17. Summary of salinity, nutrient, and chlorophyll a data collected by FIU in Naples Bay.............36

Figure 18. 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 20. Results of spatial analysis performed by FIU for the Ten Thousand Islands–Whitewater 

Bay area.......................................................................................................................................40

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..........................................41

Figure 22. Proposed subdivision of estuarine and coastal waters for deriving nutrient criteria in 

south and southwest Florida bays and coastal waters. ..............................................................46

Figure 23. Proposed estuarine and coastal nutrient criteria sub-basins for the Southwest Coastal 

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

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Executive Summary

This report was prepared by the Florida Department of Environmental Protection (FDEP), in cooperation 

with local scientists, to support the development of numeric nutrient criteria for the Southwest Coastal 

Estuaries, including Naples Bay, Rookery Bay, the Ten Thousand Islands, Whitewater 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 Southwest Coastal Estuaries region are Class II, with a designated use of

shellfish propagation or harvesting. Additionally, many of these waters are designated as Outstanding 

Florida Waters (OFWs) (Chapter 62-302, Florida Administrative Code [F.A.C.]). 

Urban development in the region has led to intermittent adverse effects in some parts of the system, 

especially in the northern portions. Most of these impacts have resulted 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 inflows to 

the region to more natural conditions. 

Nutrient and chlorophyll levels are generally low but exhibit natural north-south gradients due to 

geomorphological differences across the region, with nutrients generally decreasing toward the south

(Boyer and Briceño 2008). Potential sources 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. Chlorophyll a in the estuaries is generally low, with long-term average 

concentrations ranging from less than 2 to 5 micrograms per liter (μg/L). 

Table 1 provides a checklist and description of nutrient enrichment symptoms that have occurred either 

historically or currently in the Southwest 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 spatial 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 ensure that the 

nutrient regime in each subregion would be maintained at or below existing levels. Tables 10a, 10b,and 

10c list the proposed criteria for total phosphorus (TP), total nitrogen (TN), and chlorophyll a, 

respectively.
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Table 1. Checklist of nutrient enrichment symptoms for the Southwest Coastal Estuaries. - = Empty cell/no data

Response

Variable

Observed 

Historically or 

Currently?

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.

Rookery 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.

Rookery 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 

has 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 2010
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Geographic Description and General Information

This document proposes nutrient criteria for the 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 coastline, 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 Rise 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 portion 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 corresponded with the area’s flat topography (Figure 2). Mesic or hydric 

flatwoods covered the vast majority of the land surface (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 swamps fringed the coastal and estuarine areas, including much of Naples Bay. Freshwater 

lakes were largely 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 have 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 levels 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 Roads 84, 951, 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.

The northern portions of the estuarine system near Naples have experienced the greatest hydrologic 

alterations and water quality impacts, while the southern areas continue to be largely undisturbed. 

During prosperous economic times, Collier County and the city of Naples had the highest growth rates in 

Florida, and complex canal systems were constructed to channelize historical wetland sheetflow through 

the watersheds. As a result of the construction of the canal system, the natural freshwater inflow 

(quantity, timing, and quality) to the estuaries was altered (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 significantly affected the salinity regime and ecology of large estuarine areas. 

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 provided 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 and Brandt-Williams, 2003).
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The average 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 within the 

region’s bays are generally dominated by tides. These 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). Tides range between about 

1.1 m during spring tides and 0.5 m during neap tides. 

Average 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). Based 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. 2003, 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 devastated vegetation and caused widespread damage to homes and buildings in the Rookery 

Bay-Naples area. An earlier storm in 1918 also severely damaged man-made and natural features, and 

is considered responsible for destroying or significantly damaging many of the mangrove systems in 

Collier County. In 1992, 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 shoreline 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 have 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 salinities 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 Coastal Estuarines area is composed of several distinct waterbodies, and each major 

portion of the system is discussed in greater detail below.
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Figure 1. Predevelopment vegetation (data source: South Florida Water Management District 

[SFWMD], southwest Florida predevelopment vegetation map, 2002).
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Table 2. Land use composition for the Southwest Coast Estuaries region in hectares (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/

State Road 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 Big Cypress National 

Preserve (BCNP) 

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

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

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

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Figure 2. Land use and WBIDs for the Southwest Coastal 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

depth ranges 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). 
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Naples Bay is the portion of the area most severely impacted by drainage and urban development

activities. The watershed, which 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 extensive areas of mangrove forest and salt marsh. Drainage and urban 

development 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. 

Additionally, 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 bay’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 

system 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 canals, 

producing prolonged salinity stresses that have caused sharp declines in plankton, benthic, shellfish, and 

fish communities. Bare sandy mud has replaced the seagrass beds once prevalent in the bay. Certain 

areas also have high organic content. 

A recent study produced for the city of Naples by the 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 bay 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 

city 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. 

The general Naples Bay area contains several distinct estuarine systems, including the CocohatcheeCorkscrew area, Gordon River, Haldeman Creek, and Naples Basin. 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 tenfold. 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. 
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Figure 3. Bathymetry of Naples Bay and Dollar Bay (data source: SFWMD 2005). 
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Figure 4. Historical changes in the Naples Bay shoreline since 1927 (after Schmid et al. 2006).
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Figure 5. Naples Bay and Gordon Pass in 1953 (left) and 1999 (right) (RBNERR from U.S. Geological 

Survey [USGS]).
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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 estuarine areas 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 benefit of future generations.” In 1978, Rookery Bay joined a 

National Estuarine Research Reserve (NERR) network, which comprises 27 protected coastal areas 

administered by the National Oceanic and Atmospheric Administration (NOAA) in cooperation with the 

coastal states in which the NERRs occur. FDEP‘s Office of Coastal and Aquatic Managed Areas (CAMA) 

serves as the state administrative agency for RBNERR. 

RBNERR manages 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, RBNERR co-manages the Ten Thousand Islands Wildlife Refuge. RBNERR is considered the 

westernmost extension of the Everglades ecosystem and contains unique features such as the largest 

mangrove wetlands in the state, undeveloped barrier islands, intact tropical hardwood hammocks, and 

coastal scrub habitats. The total estimated surface area of open waters encompassed within the 

reserve’s boundaries is 70,000 acres, or 64% of RBNERR. The remaining 40,000 acres are composed 

primarily of mangroves, freshwater to brackish water marshes, and upland habitats. FDEP has 

designated all tidally connected waters within the boundaries of RBNERR and the Cape Romano/Ten 

Thousand Islands Aquatic Preserves as Class II and OFWs (Rookery Bay NERR Draft Management Plan 

2010–2015). 

Rookery Bay is classified as a barrier-built estuary, with Keewaydin Island separating it from the adjacent 

Gulf of Mexico. The combined Rookery Bay and Henderson Creek estuarine system includes mangroves, 

submersed aquatic vegetation, and fish and reef habitats with a total wetted surface area of about 5.7 

km2

. Water depths (using lower low water as a reference point) range between 0 and 3 m, with mean 

values of 1 m in Rookery Bay and 0.75 m in Henderson Creek. The Rookery Bay Estuary is the beginning 

of the transition from narrow, highly developed coastal lagoons in the north to wider, mangroveforested bay systems with little urban development in the south. The Rookery Bay Estuary is 

approximately 6 km wide, and the landward mangrove forest is 2 to 4 km wide. Moving south to the 

Ten Thousand Islands, the Faka Union Estuary is more than 10 km wide, 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.

Land use within the Rookery Bay/Ten Thousand Island watersheds 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 and marsh/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:

• The Faka Union Estuary basin comprises primarily 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 of the primary outlets of 

the Golden Gate Canal drainage system is at the south end of this basin. The 
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ongoing Picayune Strand Restoration Program is designed to return this discharge to 

a much more natural sheetflow through the conservation lands. 

• The Fakahatchee 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 marshes extend 9.5 km inland 

due to the location of the first weir in the State Road 29 Canal 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 BCNP that are within the basin make 

up 25% of the land area, with another 26% comprising portions of the Florida 

Panther National Wildlife Refuge. 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 covering 6% of the watershed. Tables 2 and 3 provide additional 

details on land use in individual watersheds. 

Although much of the area consists of conservation lands with little urban development, the natural 

freshwater inflow (quantity, timing, and quality) to the estuaries within RBNERR 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 size 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 (FakaUnion Canal Basin) (Figure 6). These are subunits of the SFWMD. Freshwater inflow to Rookery Bay 

comes primarily from Henderson Creek at the northeastern corner of RBNERR (Figure 6). The creek, 

which has an average water depth of 0.8 m and a mean flow rate of 2,073,600 cubic feet per day (Water 

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 immediately northwest of Rookery 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 Southern Golden Gate Estates, 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 the Ten Thousand Islands receive too much fresh water (i.e., Faka Union Bay), 

while other areas do not receive 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). 
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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. RBNERR boundary with major features. 

The yellow line indicates the RBNERR boundary. 

RB= Rookery Bay, HC= Henderson Creek, BWB= Blackwater Bay, PB= Pumpkin Bay, 

FUB= Faka Union Bay, FB= Fakahatchee Bay.)

FakaUnion 

Canal

FB

FUB

PB

BWB

RB

HC 
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Figure 7. Map of RBNERR showing reserve boundaries surrounding conservation lands.
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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 the most 

characteristic biological or physical feature (FNAI and FDNR 1990).

The 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 pine flatwoods, coastal strand, coastal xeric 

scrub, cabbage palm/oak, and tropical hardwood hammocks. Figure 7 shows the approximate location 

and extent of the primary upland and wetland habitats within the RBNERR boundaries. The 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 vegetated 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 corals (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 available 
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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 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 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 provides 

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 

thus stabilize shorelines and prevent 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 Cuban 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 bay 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 resident 
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wading or migratory game birds, raptors, and several species of mammals (Appendix A). 

Coastal 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, brackish, or fresh. They are important feeding sites for numerous birds and 

mammals, and 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. Although 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 and sedges, ferns, and cattails. 

(7) Cypress Slough/Cypress Prairie: This habitat is dominated by pond or bald cypress with a 

mixed understory throughout. Cypress habitat is restricted to areas subjected to flowing 

fresh water (i.e., sheetflow). It is exposed 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, black 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, including 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 FWCC. Most notable are the West Indian manatee 

(endangered), Atlantic loggerhead sea turtle (threatened), gopher tortoise (species of special concern), 

bald eagle (threatened), least tern (threatened), indigo snake (threatened), and Florida scrub jay 

(threatened). Confirmed 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 southwest 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 SFWMD (Thomas and Rumbold 2006) assembled a 

conceptual ecological model 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 water 
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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 communities 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.

 
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Natural Communities in Naples Bay

Oysters

Oysters were once a healthy, edible, dominant species in Naples Bay, but over the past few decades the 

bay 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. Freshwater 

flows from the Golden Gate Canal create a longitudinal salinity gradient that varies greatly between the 

wet and dry seasons and causes severe stratification in the wet summer months. This stratification 

results in the limited reaeration of bottom waters, resulting in depressed DO concentrations. This 

continued 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. The 

city of Naples partnered with Florida Gulf Coast University and, with the help of community volunteers, 

created two 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 oyster 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 facilitate 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 wrightii) 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 this 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. 

Transects have been established with seagrass species and abundance, sediment type, water depth, 

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 attributed 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 provide nursery grounds and habitat for a wide range of estuarine creatures, including 

commercial and recreational fish species. 
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Mangroves have been replaced by seawalls and riprap, resulting in increased turbidity and reduced light 

penetration 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 nature 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). 
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Natural Communities in Rookery Bay/Ten Thousand Islands/Whitewater Bay

Current and past research at the RBNERR 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 RBNERR does not have conclusive quantitative data 

indicating adverse effects/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 

RBNERR (Rookery Bay–Whitewater Bay). 

The dominant natural communities that make up the coastal marine ecosystems of the RBNERR are 

mangroves, seagrasses, saltwater marshes, and oyster reefs. Table 5 lists the 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 FDEP. 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 RBNERR.

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 distribution 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 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 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 mangrove 
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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. These rapidly decay to form small 

particulate material called detritus. Detritus 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 provides 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 thus stabilize 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). Recent observations 

within RBNERR indicate that seagrass is not as abundant as in neighboring counties and throughout 

southwest Florida. When seagrass is present, it typically is patchy and 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. Five documented species of seagrass are found within 

RBNERR boundaries: 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 fish 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. Fiftyseven 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 

Browder et al. (1989), which focused more on fishes, found fewer seagrasses in Faka Union and 

Fakahatchee Bays during the study. In 2005, a study by Locker found that the only seagrass in 

Fakahatchee Bay was H. decipiens, with no seagrass found in Faka Union Bay. 

Johnson Bay seagrass coverage was monitored as part of a SFWMD grant from 2000 to 2009. According 

to data collected in 2008, the annual average percent coverage for the study transects was just under 

30%. All 5 species found in RBNERR were found at this site; however, H. wrightii was the dominate 

species, followed by H. englemanni. During the 2008 monitoring at this location, the majority of the 

seagrasses had moderate to heavy epiphytic growth (Schmid et al. unpublished data 2008). Data from 
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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 monitoring 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 were generated 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 SAV coverages within RBNERR 

(Locker 2006). A seagrass monitoring project at Cape Romano began in 2010 as part of a SFWMD grant. 

Percent coverage, species abundance, and epiphytic coverage estimates 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. wrightii 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)

Saltwater marsh habitat is found landward or interspersed among the inland side of the mangrovefringing 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. Coastal 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, brackish, or fresh. They form important feeding sites for numerous 

birds and mammals, and also provide an ecotonal transition between saline and freshwater areas in 

RBNERR.
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Figure 10. Quadrate on the shoal of Cape Romano in 1998 (left); image of seagrass taken on the same 

shoal in 2009 (right).

Figure 11. Map of the 2010 Cape Romano quadrate locations along a fixed transect.
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Oyster Reefs

The Eastern oyster (Crassostrea virginica) is the dominant bivalve in RBNERR 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. The transfer 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 species 

(skilletfish, toadfish, gobies) are 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 Bay and others) 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 

communities (Tolley et al. 2006), and oyster reef crab populations as a tool for managing freshwater 

inflow in RRNERR (Shirley et al. 2004). 

Fisheries

Commercial fisheries in RBNERR 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 (Trachinotus 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 of 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 indirect 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 indicates 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 through 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 differences 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 urophthalmus), and sunfish (Lepomis spp.) have survived for short periods in Faka Union 
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Bay due to the large volume of fresh water inundating the estuary. Species diversity, measured by 

species richness (O’Donnell unpublished data; Figure 12), 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, while Fakahatchee and Pumpkin Bays receive fresh

water through 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 using RBNERR estuaries—bonnethead (Sphryna 

tiburo), lemon (Negaprion brevirostris), blacktip (Carcharhinus limbatus), and nurse (Ginglymostoma 

cirratum)—need higher salinities to survive.
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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. 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* 
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Figure 12. Species richness comparison between Fakahatchee, Faka Union, Pumpkin, and Rookery 

Bays.

Figure 13. Estimated bycatch 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 Bay

MEAN - 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 Bay
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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 criterion for chlorophyll specified in 

Chapter 62-302, F.A.C.; however, the Impaired Surface Waters Rule (IWR) (Chapter 62-303, F.A.C.) does 

use 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 criterion 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 

criterion was 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 waters 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 Southwest Coastal Estuaries region are

Class II waters, which have the designated use of propagation or harvesting of shellfish. The Class II 

waters within this 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

Many of the waters within the Southwest Coastal Estuaries region are designated as OFWs, 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 designation is to 

maintain ambient water quality conditions, even if those conditions are more stringent than the state 
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water quality criteria applicable to the waterbody’s surface water classification (i.e., Class II or Class III). 

Most OFWs are associated with 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 ecological significance and 

are identified as such in Rule 62-302, F.A.C. 

The following waters within the Southwest Coastal 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 Southwest Coastal Estuaries region was strongly influenced by the 

quantity, timing, and quality of freshwater inflow from the estuaries’ 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 adversely impacted the environmental integrity of many of these 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, most temperate estuaries are N limited (Vitousek and Howarth 1991), while upstream 

freshwater tributaries are P limited (Smith 1990). In contrast, in 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 these estuaries

is the coastal Gulf of Mexico rather than the watershed, Childers et al. (2006) has called the Shark River 

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 has 
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Draft 30 August 2010

collected monthly water quality data at 22 sites in Whitewater Bay and 26 sites in the Ten Thousand 

Islands beginning in September 1992, and 17 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 principal 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 decreases, 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 expect 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. Based 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 TN concentrations in Naples Bay ranged from 0.2 to 0.29 mg/L, while the 

higher TN concentrations in Whitewater Bay ranged from 0.39 to 0.66 mg/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 carbon [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.
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Figure 14. Summary of TP, TN, and chlorophyll a concentrations in various portions of the Southwest 

Coastal Estuaries region, 1999–2008. 

NPL=Naples Bay, RB=Rookery Bay, WWB=Whitewater Bay, TTI=Ten Thousand Islands.
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Due to the heterogeneous nature of the region, FIU used generally accepted geomorphological 

characteristics to group the stations. A preliminary spatial analysis of data from its monitoring program 

resulted in the delineation of 10 groups of stations with robust similarities in water quality (Table 7; 

Figures 15 through 19). The following sections discuss water 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 RomanoMarco IslandMARC 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 Estuary 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

water flowing into Naples Bay from the canal has severely impacted the bay, mainly through changes in 

the salinity regime, which is now characterized by widely fluctuating salinity levels. The Big Cypress 

Basin Control District, the local arm of the SFWMD, 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 the 

Henderson Creek watershed, which needs additional fresh water. The excessive freshwater inputs also 

significantly influence water quality and result in significant seasonal trends for a number of parameters 

in addition to salinity. 

Figures 15 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 greater 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 μg/L, and exhibit a less pronounced seasonal pattern. 
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Figure 16 depicts the typical 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 chlorophyll 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 trends 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.
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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 09

TN (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

09

TP (mg/l)

25th

Min

Median

Max

75th 
Nutrient 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 Briceño 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, which tends to concentrate salt and dissolved organic 

matter (DOM), results in higher salinities and TOC concentrations. 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 summarizes water quality for selected parameters based on data from the FIU 
Nutrient 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 Mangrove 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 northern Ten Thousand Islands. As 

such, concentrations of P in incoming waters are very low, while 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 matter 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 (Figure 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 Canal 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 has extensive channelization but lower freshwater input than the Mangrove River

group to the south and less exchange with the Gulf of Mexico due to its small inlets. For these reasons, 

its water quality is between that of the estuaries to the south and north. Most of the Inner Waterway is 

part of ENP’s Wilderness Waterway, a 99-mile (159-km) back-country canoeing route that runs along the 

western edge of ENP 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 occurrence. A current 

restoration project to construct 87 additional culverts at 30 separate sites under Tamiami Trail will 

increase watershed connectivity to the estuaries (additional information is available at: 

http://www.evergladesplan.org/pm/projects/docs _30_sgge.cfm). Salinity and nutrient regimes are 

expected to change with increased terrestrial flows. 

The Blackwater River cluster has the highest salinity and P. The Blackwater River is about 8 miles long, 

with flow varying seasonally 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 residential 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 Islands–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

Sources 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 point sources in the region.

The spatial differences in sources and the geochemical differences result in significant gradients across 

the area. The Southwest Coastal Estuaries are 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 cannot 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 RBNERR. To FDEP’s knowledge, there is no published research on the 

assimilative capacity of these systems or nutrient loading models for RBNERR. 

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 

Water Reclamation Facility (WRF) 

Domestic Wastewater 

Treatment Plant

8 8 

FL0141399 Collier County North 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 methodology in the IWR (Chapter 62-303, F.A.C.). Appendix B lists all 

verified impairments for estuarine and coastal waterbodies within the region (FDEP 2010a). Most of the 

impairments are for DO, fecal coliform, and chlorophyll/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 development, 
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 identified as a major pollutant in Naples Bay. A geographic information system (GIS) 

analysis located “hot 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 algae. 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 appears 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 forests 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 criterion) is commonly observed throughout the state. 

Due to the widespread occurrence of naturally low DO levels in Florida estuarine and coastal systems, as 

described in the document, Overview of FDEP Approaches for Nutrient Criteria Development in Marine 

Waters, Florida is currently evaluating the appropriateness of the current criterion, 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 fully supports the designated use of 

the bay.

As for the listing for nutrients in Rookery Bay, FDEP has determined that the listing was based on a flaw 

in the original analysis and plans 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, the 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. Most 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. 

When 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 used 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 waterbody 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. However, 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 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 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 the 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 nutrient criteria 

for each subregion are provided blow.

Regionalization

As discussed previously, FIU has used the data collected as part of its Coastal Water Quality Monitoring 

Network to 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 Coastal Estuaries area, ENP 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 analysis was similar to the earlier spatial 

regionalization method used by FIU, but used 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 Figure 23 

and Table 9. Appendix A contains more detail on the analysis 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 this 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 

chlorophyll 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 23. 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 9a. Proposed regionalization for the Whitewater Bay to the Ten Thousand Islands area of the 

Southwest Coastal Estuaries. 

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 9b. 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 Sound
Nutrient 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-basins 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 measures 

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 preferable 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. 
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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 determine 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) defined 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 nutrient 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 tendency (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 imbalance, 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 insignificant 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 criteria expressed as an annual geometric mean so that estuaries could be assessed 

annually. 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 indication 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 unacceptably 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 target 

must be adjusted to allow for the application to a shorter duration with an acceptable Type I error rate 

of no more than 10%. 
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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 used 3-year assessment periods to express the duration 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 state’s 5-year 303(d) assessment and National Pollutant Discharge Elimination System 

(NPDES) permit renewal cycles.

Given a 5-year assessment period, FDEP derived criteria expressed as an annual geometric mean by 

using the 75th percentile of the annual geometric means from the long-term dataset. FDEP 

demonstrated 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 the 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 averaged annual 

geometric means, while the single-site magnitude was calculated using the distribution of station annual 

geometric means. The use 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. If 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. FDEP has not decided whether both expressions of magnitude are needed in all cases, and is

seeking additional feedback from local experts and stakeholders.

Summary of the Proposed Criteria

FDEP proposes three sets of potential criteria: (1) a long-term geometric 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) an annual geometric mean of values from a single location, not 

to be exceeded more than twice in a five-year period.

Table 10 provides the proposed long-term targets for the protection of a healthy, well-balanced 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 them could 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. 
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Table 10a. 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 34.0
Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

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Table 10b. Proposed numeric TN criteria for sub-basins within the Southwest Coastal Estuaries area. - = 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 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 0.27
Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 52 August 2010

Table 10c. Proposed numeric chlorophyll a criteria for sub-basins within the Southwest Coastal 

Estuaries area. - = 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 3.2
Nutrient Criteria Technical Support Document Southwest Coastal Estuaries

Draft 53 August 2010

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Appendix A: 

Threatened and 

Endangered Species

(Data Taken from Draft Rookery Bay NERR Management Plan)
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Appendix B: 

Impaired Waters List
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Draft 61 August 2010 OGC Case Number Planning Unit WBID Water Segment Name Waterbody Type Waterbody Class1 1998 303(d) Parameters of Concern

Parameters 

Assessed Using the 

2007 Impaired 

Surface Waters Rule 

(IWR)

Concentration 

Causing Impairment

Priority for TMDL 

Development2

09-2718 Southw est Coast 8065 SOUTHWEST COAST GULF 5 COASTAL 3M Bacteria (in Shellfish)09-2719 Florida Gulf Coast 8999 FLORIDA GULF COAST COASTAL 3M Mercury (Based on fish consumption advisory) Mercury (Based on fish consumption advisory) Hg > 0.3 mg/Kg High*09-2698 Southw est Coast 3259A COCO-HATCHEE RIVER ESTUARY 2 Coliforms Fecal Coliform > 43 colonies per 100 ml Low09-2699 Southw est Coast 3259A COCO-HATCHEE RIVER ESTUARY 2 Iron > 0.3 mg/L Medium09-2709 Southw est Coast 3278R (3259G) NAPLES BAY COASTAL ESTUARY 2 Copper > 3.7 mg/L Medium09-2710 Southw est Coast 3278R (3259G) NAPLES BAY COASTAL ESTUARY 2 Fecal Coliform > 43 colonies per 100 ml Low09-2711 Southw est Coast 3278R (3259G) NAPLES BAY COASTAL ESTUARY 2 Iron > 0.3 mg/L Medium09-2712 Southw est Coast 3278R (3259G) NAPLES BAY COASTAL ESTUARY 2 Dissolved Oxygen < 4.0 mg/L Medium09-2715 Southw est Coast 3278U ROOKERY BAY COASTAL ESTUARY 2 Dissolved Oxygen < 4.0 mg/L Medium09-2716 Southw est Coast 3278U ROOKERY BAY COASTAL ESTUARY 2 Nutrients (Chlorophyll-a) TN = 0.32 mg/L; TP = 0.04 mg/L; BOD = 2.2 mg/L Medium09-2717 Southw est Coast 3278U ROOKERY BAY COASTAL ESTUARY 2 Fecal Coliform > 400 colonies per 100 ml Low

 5 - Navigation, utility, and industrial use g y y g g ( ) y of the integrated list; individual entries have been removed from the list.

2

 Where 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 or 

 human 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 based on 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 resou  and 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.

 Where 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.

3 PP - Planning Period (January, 1995 through December, 2004); VP - Verified Period (January, 2000 through June 30, 2007)1

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.

 Florida's w aterbody classifications are defined as: 

 1 - Potable w ater supplies  2 - Shellfish propagation or harvesting 3F - Recreation, propagation, and maintenance of a healthy, w ell-balanced population of fish and w ildlife in fresh w ater 3M - Recreation, propagation, and maintenance of a healthy, w ell-balanced population of fish and w ildlife in marine w ater 4 - Agricultural w ater supplies
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Appendix C: 

Summary of 

Regionalization Method
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April 30, 2010 

Dr. Joffre Castro 

Everglades National Park 

South Florida Ecosystem Office 

950 N Krome Ave; 3rd 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 material 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 SERC’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 8th St, OE # 148 

Miami, Fl 33199 
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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 30th, 2010 

TASK AGREEMENT #: J5297-08-0085 COOPERATIVE AGREEMENT#: H5000-06-0104 
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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 subdivisions 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; Fourqurean 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), dissolved 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 (NOx-), Nitrite (NO2-), 
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Nitrate (NO3-), Ammonium (NH4+), Inorganic Nitrogen (DIN, calculated), Soluble Reactive Phosphate 

(SRP), and Silicate (SiO2). 

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, standard 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 combining 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. 
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Finally, this statistical clustering is a first cut at partitioning 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 3 
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