NAPLES BAY SURFACE WATER IMPROVEMENT & 

MANAGEMENT PLAN RECONNAISANCE REPORT 

FEBRUARY 2006 

 

Debra Childs Woithe, Inc. 

and 

Sherry Brandt-Williams, Ph.D. 
February 2006 i Naples Bay SWIM Reconnaissance 

TABLE OF CONTENTS 

Table of Contents.............................................................................................................................i

List of Acronyms and Abreviations ............................................................................................ iii

Acknowledgements.........................................................................................................................v

1 Introduction............................................................................................................................1

PROJECT DESCRIPTION ................................................................................................................................2

IMPAIRED WATERS RULE STATUS.................................................................................................................3

GOVERNMENT UNITS WITH JURISDICTION...................................................................................................6

PARTICIPANTS AND CONTRIBUTORS............................................................................................................6

2 History of the Basin ...............................................................................................................9

BEFORE 1860...............................................................................................................................................9

1860 TO 1930 ..............................................................................................................................................9

1930 TO PRESENT ......................................................................................................................................11

3 Geographic Analysis............................................................................................................18

ESTUARIES ................................................................................................................................................18 

TOPOGRAPHY, FLOOD ZONES, SOILS .........................................................................................................20 

LAND USE/LAND COVER...........................................................................................................................22 

SUB-BASIN AND DRAINAGE CHARACTERISTICS.........................................................................................28 

SPECIES AND HABITAT ..............................................................................................................................37 

PUBLICLY OWNED/CONSERVATION LANDS...............................................................................................41 

AQUIFER....................................................................................................................................................43 

SANITARY SEWER SERVICE .......................................................................................................................43 

4 Information Review.............................................................................................................45

CURRENT DATA.........................................................................................................................................46

Preferred Water Quality Data ............................................................................................................46

Collier County, SFWMD, FDEP (DBHYDRO and STORET) ............................................................46

FFWCC...............................................................................................................................................48

Petroleum Storage Tanks and Hazardous Waste................................................................................51

Wastewater .........................................................................................................................................51

STUDIES.....................................................................................................................................................54

Coastal Bays and Barrier Islands Ecological Conceptual Model ......................................................54

Evaluation of Naples Bay Water Quality and Hydrologic Data.........................................................55

Compilation, Evaluation, and Archiving of Existing Water Quality Data for Southwest Florida......55

Effects Of Increased Urban And Agricultural Landuse On The Anthropogenic Loading To 

Southwest Florida Estuaries ....................................................................................................57

Effects of Water Control Structures on Estuaries...............................................................................58

Environmental Impact Statement On Improving the Regulatory Process in Southwest Florida, 

Lee and Collier Counties, Florida. ..........................................................................................58

An Integrated Surface Water Quality Monitoring Program for the South Florida Coastal Waters...60

Big Cypress Basin Water Quality Monitoring Report: 1979 – 1988 ..................................................61

Naples Bay Study ................................................................................................................................62

MODELING AND PLANS .............................................................................................................................64

SWFFS Water Quality Strategy Document.........................................................................................64

City of Naples Basin V Stormwater System Improvement Plan Phase I: Basin Assessment and 

Conceptual Improvement Plan.................................................................................................66

The Southwest Florida Feasibility Study (SWFFS) ............................................................................67

Big Cypress Basin Integrated Hydrologic-Hydraulic Model..............................................................68

Five Year Plan -- 2002-2006 For The Big Cypress Basin of The South Florida Water 

Management District................................................................................................................69

BCB Region Science Plan...................................................................................................................69
February 2006 ii Naples Bay SWIM Reconnaissance 

Gordon River Extension Basin Study, Phase IV .................................................................................70

Big Cypress Basin Watershed Management Plan: Hydrologic Hydraulic Assessment for Golden 

Gate Canal Watershed Improvements Phase I – Retrofit of Golden Gate Canal 

Weir Number 1.........................................................................................................................71

Big Cypress Basin Watershed Management Plan, Flood Control Element........................................71

South Lee County Watershed Plan .....................................................................................................74

Central and Southern Florida Project Comprehensive Review Study Final Integrated Feasibility 

Report and Programmatic Environmental Impact Statement (PEIS) ......................................75

City of Naples Basin VI Assessment Report........................................................................................75

City of Naples Interim Basin III Design Development Report............................................................76

City of Naples Stormwater Management Program - Phase 1 Master Plan Draft Report...................76

Gordon River Watershed Study. .........................................................................................................78

PROJECTS ..................................................................................................................................................79

Collier County Capital Improvement Projects ...................................................................................79

City of Naples Ten Year Stormwater Funding Plan............................................................................79

Golden Gate Canal/Henderson Creek Water Transfer.......................................................................81

Gordon River Water Quality Park......................................................................................................81

Lely Area Stormwater Improvement Project (LASIP) ........................................................................82

Westlake Outfall Improvements and the Twin Lakes Interconnect .....................................................83

Gordon River Greenway.....................................................................................................................83

Northern Golden Gates Estates Regional Offsite Mitigation Area (ROMA) ......................................83

Beach Re-nourishment........................................................................................................................84

Transportation ....................................................................................................................................84

PROGRAMS ................................................................................................................................................87

Background.........................................................................................................................................87

NPDES (MS4) Municipal Separate Storm Sewer System Permits......................................................88

Collier County Stormwater Management Master Planning and Regulation......................................89

Collier County Transfer of Development Right (TDR) Program........................................................90

Southwest Florida Resource Conservation & Development Council (RD&CD), Inc.........................90

Rookery Bay National Estuarine Research Reserve (RBNERR).........................................................91

Conservation Collier ..........................................................................................................................91

Collier County Restoration Mapping..................................................................................................91

RECOMMENDATIONS .................................................................................................................................92

Evaluation of Naples Bay Water Quality and Hydrologic Data.........................................................92

Reconnaissance Observations ............................................................................................................93

Working Group Meetings....................................................................................................................95

REFERENCES CITED...................................................................................................................................97
February 2006 iii Naples Bay SWIM Reconnaissance 

LIST OF ACRONYMS AND ABREVIATIONS 

As Arsenic 

ASR Aquifer Storage and Recovery 

BCB-RCT Big Cypress Basin Restoration Coordination Team 

BCB – SFWMD Big Cypress Basin division of South Florida Water Management District 

BOD Biologic Oxygen Demand, Biochemical Oxygen Demand 

CERP Comprehensive Everglades Restoration Plan 

Cd Cadmium 

CDM Camp Dresser & McKee 

Cfs Cubic feet per second 

CHNEP Charlotte Harbor National Estuary Program 

CIWQFS Comprehensive Integrated Water Quality Feasibility Study 

COD Chemical oxygen demand 

Cr Chromium 

CREW Corkscrew Regional Ecosystem Watershed 

CSWCD Collier Soil and Water Conservation District

Cu Copper 

CWA Clean Water Act 

DBHYDRO SFWMD’s environmental data retrieval system 

DDT Dichloro-diphenyl-trichloroethane

DHI Danish Hydrologic Institute 

DO Dissolved oxygen 

DP Dissolved phosphorus 

EIS Environmental Impact Statement 

EMAP Environmental Monitoring and Assessment Program funded by EPA 

FDEP Florida Department of Environmental Protection 

FDOH Florida Department of Health 

Fe Iron 

FEMA Federal Emergency Management Act

FFWCC Florida Freshwater Fish and Wildlife Conservation Commission 

FGCU Florida Gulf Coast University 

FIRM Flood Insurance Rate Map

FIU Florida International University 

FLUCCS Florida Land Use, Cover and Forms Classification System developed by 

FDOT 

FWC Florida Fish and Wildlife Commission 

FWRI Florida Wildlife Research Institute (Part of FWC, formerly named the 

Florida Marine Research Institute (FMRI)) 

GIS Geographic Information System 

GWIS Groundwater Information System 

Hg Mercury 

HMW High molecular weight 

IN Inorganic nitrogen 

IWR Impaired Waters Rule 

LEGACY Data from 1998 and earlier that was maintained in first edition EPA 

MSTBU Municipal Service Taxing Benefit Unit

NADP National Atmospheric Deposition Program 

NAWQA National Water Quality Assessment Program 

NH3, NH4 Ammonia, ammonium 
February 2006 iv Naples Bay SWIM Reconnaissance 

LIST OF ACRONYMS AND ABREVIATIONS (continued) 

NO2 Nitrite

NO3 Nitrate

NOAA National Oceanic and Atmospheric Administration 

NPDES National Pollutant Discharge Elimination System 

NWIS National Water Information System 

ON Organic nitrogen 

ONRW Outstanding National Resource Water 

PAH Polycyclic aromatic hydrocarbons 

Pb Lead 

PDF Portable Document Format using Adobe Reader/Acrobat 

PMP Project Management Plan 

PEL Probable effect limit 

PSU Practical salinity units a calculated measure of parts per thousand 

QAPP Quality Assurance Program Plan 

QAQC Quality Assurance Quality Control 

RBNERR Rookery Bay National Estuarine Research Reserve 

ROMA Regional Offsite Mitigation Area 

SBIO Florida Department of Environmental Protection's Statewide Biological 

Database 

SFWMD South Florida Water Management District 

Si Silicon, Silicates 

SMP Submitochondrial particles 

SOFIA South Florida Information Access run by USGS 

STORET Storage and Retrieval EPA data repository (1999 to date) 

SWFFS Southwest Florida Feasibility Study 

SWIM Surface Water Improvement and Management 

TBT Tributytin

TDS Total dissolved solids 

TEL Threshold effect limit 

TIP Transportation Improvement Program 

TKN Total kjeldahl nitrogen 

TN Total nitrogen 

TOC Total organic carbon 

TP Total phosphorus

TSI Trophic State Index 

TSS Total Suspended Solids 

USACE United States Army Corps of Engineers 

USEPA United States Environmental Protection Agency 

USF University of South Florida 

USFWS United States Fish and Wildlife Service 

USGS United States Geological Survey 

WATSTOR USGS Water Data Storage and Retrieval System 

WBID Water Body Identification 

WMD Water Management District 

Zn Zinc 
February 2006 v Naples Bay SWIM Reconnaissance 

ACKNOWLEDGEMENTS 

This Naples Bay Surface Water Improvement and Management Reconnaissance Report 

was produced for the South Florida Water Management District by Debra Childs Woithe, 

Inc. Debra Woithe and Sherry Brandt-Williams, Ph.D., co-authored the report. Carla N. 

Palmer, P.E., Stormwater Management Division Director for the South Florida Water 

Management District, provided programmatic oversight and guidance and co-edited the 

report. Liz Abbott, PMP, lead project manager for the South Florida Water Management 

District, managed and co-edited the project. Special thanks to Scott Legg of Atlas 

Management, Inc. working for the South Florida Water Management District, and the 

numerous other participants and contributors for providing guidance and assistance with 

data and references for the report. 
February 2006 1 Naples Bay SWIM Reconnaissance 

Figure 1. The Naples Bay Basin Study Area. 

This report characterizes the Naples Bay Basin, past and present, and reviews information 

pertinent to the development of a Surface Water Improvement and Management (SWIM) Plan. It 

is an inventory of monitoring data, modeling efforts, studies, projects, plans and programs within 

the Study Area. Additional details of information within the main report and less relevant 

information that is not included in the main body of the report are provided in Appendix A. 

Credible sources of information were reviewed and summarized as presented. Interpretation and 

application of data was not within the scope of this effort, and was reserved for future efforts. 

Much of the text and graphic material in this report was taken directly from the source document. 

1 INTRODUCTION 

Naples Bay, on the coast of Collier County, Florida, is a long, narrow estuary formed by the 

confluence of the Gordon River, and 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 further south by a shallow waterway with a dredged 

channel. The Naples Bay Basin is a flat, low elevation region with the City of Naples and Naples 

Bay in its southwestern corner (Figure 1). 

Moving northeast from Naples Bay, the 

Basin becomes increasingly more rural and 

is dominated by agriculture and forested 

wetlands. 

The 120 square mile Naples Bay Basin 

lies within the Big Cypress Basin, and 

shares borders with the CorkscrewCocohatchee Basin to the north, Faka-Union 

Canal Basin to the east, and the Henderson 

Creek and District VI Basins along the 

southeast. The Naples Bay Basin is 

bounded by the Gulf of Mexico to the west 

and partially by Immokalee Road to the 

north. Its easternmost extent is along 

Everglades Boulevard., with a southeastern 

boundary crossing near the I-75-CR 951 

junction, and terminating at the Gulf of 
February 2006 2 Naples Bay SWIM Reconnaissance 

Mexico within the northwestern corner of the Rookery Bay Reserve. 

During the past century, the Bay and its watershed have been heavily altered by drainage, 

agriculture, and most recently urban development activities. As a result, Bay water clarity and 

water quality, freshwater inflows, and surface water levels and natural habitats in the Basin are 

much different than their historic conditions. The Bay once received drainage from a 10 squaremile basin, but an extensive system of large drainage canals have extended the Basin to the east 

and north and enlarged it to approximately 120 square miles. On the edges of the Bay itself, 

extensive areas of mangroves and salt marsh have been replaced by canals, seawalls and 

bulkheads in the past 60 years. The headwaters of the Gordon River and other Naples Bay 

tributaries (including Rock and Haldeman Creeks) have been extensively channelized. This 

drainage canal system lowered surface water levels and facilitated extensive agricultural 

development. Urban development followed close behind. The most significant of these drainage 

features is the Golden Gate Canal which receives water from a series of canals to the north and 

east and empties into the Gordon River just north of Naples Airport. 

A water body of regional and statewide significance, Naples Bay is currently ranked in Tier 2 

of the SFWMD Priority Water Body List. The list was updated and approved in 2001 according 

to FDEP based criteria. The development of a SWIM plan for Naples Bay was authorized by the 

SFWMD Governing Board in 2003 (Bauer, 2003). In preparation for that effort, this Naples Bay 

SWIM Reconnaissance Report was authorized in 2005. 

PROJECT DESCRIPTION 

The project objective was to identify sources of existing data, identify gaps in existing data, 

and identify related programs within the Study Area. The intent of the report is to provide a 

meaningful resource for the development of the Naples Bay SWIM Plan. Information pertaining 

to the Naples Bay Basin was documented, reviewed and summarized in order to assess the Study 

Area in terms of current water quality, water quantity, and ecological features. In general, this 

scope of work consists of a review of existing studies and data, work group meetings, GIS 

mapping of land use and other data, and problem identification. All data and documents cited in 

this narrative were provided to SFWMD. 

This project consisted of six tasks, defined below: 

Task 1. Review of Studies and Data. Review and concisely summarize existing studies and 

relevant data. List and describe data sources compiled. Focus review process on technical 

aspects related to surface water movement/storage and factors affecting these activities. 

Task 2. Land Use/Land Cover and Conservation Land Mapping. Map current and future land 

use/land cover, publicly owned land and land of potential significance for acquisition/ 
February 2006 3 Naples Bay SWIM Reconnaissance 

conservation. Aerial calculations and summaries. 

Task 3. Working Group Meetings. Up to three inter-agency meetings to identify and 

characterize data, issues and other information for inclusion in the report. 

Task 4. Additional GIS Mapping. Compile, document and provide relevant spatial data 

available for the study. Create maps for report. 

Task 5. Problem Identification. Identify and summarize problems such as flooding; water 

quality; rare, endangered or protected ecosystems; and gaps in information that would be 

necessary to develop solutions and complete a SWIM plan. 

Task 6. Reconnaissance Report. Summarize findings and list information gaps for above 

tasks. Provide a synopsis of available data and issues. 

IMPAIRED WATERS RULE STATUS 

Section 303(d) of the Federal Clean Water Act (CWA) requires states to list waters that do 

not meet applicable water quality standards and to establish Total Maximum Daily Loads 

(TMDLs) for those waters on a prioritized schedule. The 303(d) List is based primarily on the 

state’s 1996 305(b) Water Quality Assessment Report, which uses a watershed approach to 

evaluate surface waters, ground waters, and wetlands. In 1998, EPA approved Florida’s 1998 

303(d) Impaired Waters List, which was based on existing, readily available data or best 

professional judgment However in 1999, the Florida Watershed Restoration Act, Section 

403.067, F.S. was enacted by the Florida Legislature. This law requires FDEP to adopt by rule, a 

scientific methodology for analyzing environmental data and determining whether a water body is 

impaired or healthy. All water bodies on the 1998 303(d) List are required to be either 1) verified 

as impaired, 2) de-listed as they are meeting water quality standards, or 3) placed on a planning 

list if insufficient data exists (Category 3). FDEP’s 2002 update to Florida’s 1998 303(d) 

Impaired Waters List for Group 1 Basins was adopted August 2002 by FDEP Secretarial order 

and submitted to EPA October 2002. The verified list and de-list lists were amended by FDEP 

Secretarial order March 2003. The 2002 update was developed in accordance with EPA 

guidelines for Integrated Water Quality Monitoring and Assessment Reports. 

TMDL’s establish the maximum amount of pollutants a water body can assimilate without 

exceeding water quality standards. The Florida Watershed Restoration Act, Chapter 99-223, 

Laws of Florida, addresses processes for refining the list and for calculating and allocating 

TMDLs. According to EPA guidelines, waters expected to attain and maintain applicable water 

quality standards through other Federal, State, or Local requirements do not need to be included 

on the 303(d) list. (www.dep.state.fl.us/water, Eric Livingston, FDEP, personal communication). 
February 2006 4 Naples Bay SWIM Reconnaissance 

SFWMD and FDEP will be working closely on BMPs and data modeling pertaining to both 

SWIM and TMDLs. 

The Naples Bay Basin is a Group 1 Basin in FDEP’s South District, and is in the Southwest 

Coast Planning Unit of the Everglades West Coast Basin. Planning units comprise a group of 

smaller assessment units referred to as WBIDs, for water body identification. Nine of the fortyone WBIDs in the Southwest Coast Planning Unit occur within the Naples Bay Basin (Table 1, 

Figure 2). Other WBIDs have boundaries that overlap the Naples Bay Basin, though their water 

body and watershed are not considered to be within the Basin. See Section 3, Geographic 

Analysis, for further discussion of basin and sub-basin delineation. Information from the FDEP 

2002 Updated Master List and 2003 amendments lists was compiled into Table 1, below, for ease 

of reference. All information from those FDEP 303(d) lists for relevant WBIDs is provided in 

Appendix A1. 

The status of each WBID is summarized according to the most limiting parameter in Figure 

2. According to information provided in the 303(d) lists, the primary parameter of concern is 

dissolved oxygen (DO). Two water bodies, the Gordon River Canal and Henderson Creek Canal, 

are verified impaired due to low DO. Biological oxygen demand (BOD) is the causative pollutant 

in the Gordon River and Henderson Creek Canals. 

Though several WBIDs meet standards for some parameters (turbidity and fecal coliform), all 

WBIDs have planning list status for at least one parameter. Planning list status includes no data, 

insufficient data, and sufficient data showing potential impairment (Categories 3a, 3b, and 3c). 

WBIDS on the planning list will undergo Impaired Water Rule assessments for TMDLs and 

receive a new listing in fall of 2006 after further monitoring is conducted. The projected year for 

TMDL development of all necessary WBIDs in the Naples Bay Basin is 2007. 

Table 1. FDEP 303(d) Waterbody Status (compiled from the Updated Master List (October 2002), and the 

Amended Verified and De-list Lists (March 2003)).

WBID Water Body Name Proposed Status Parameter Priority 

3259C Gordon River Planning List DO Low 

 No Data BOD Low 

 Planning List Total Coliforms Low 

 Insufficient Data Fecal Coliforms Low 

 De-listed Nutrients - 

3258 D Gordon River Canal Verified List DO Medium 

3259 E Henderson Creek Canal Verified List DO Medium 

3259 F Golden Gate Canal Planning List DO - 

 Meets Standard Turbidity - 

3259 G Naples Bay Planning List 

Nutrients 

(chlorophyll) Low 

 Planning List DO Low 

3259H Henderson Creek Canal Planning List DO - 

3259 Q Outer Clam Bay No data - - 

3259 T Lake Avalon Mid-Lake Insufficient Data - - 

3259 Y Vanderbilt Way Insufficient Data - 
February 2006 5 Naples Bay SWIM Reconnaissance 

Figure 2. FDEP 303(d) WBID and Verified Impaired Waterbody Status (data source: FDEP, 2005).
February 2006 6 Naples Bay SWIM Reconnaissance 

GOVERNMENT UNITS WITH JURISDICTION 

Governmental units that have jurisdiction over Naples Bay and its drainage basin include 

Federal and State agencies and the SFWMD. The Basin also lies entirely within Collier County 

and the boundaries of the Southwest Florida Regional Planning Council (SWFRPC). The City of 

Naples is located entirely within the Study Area, as is the Pelican Bay Municipal Service Taxing 

Benefit Unit (MSTBU). Special Districts within the Study Area that are relevant to surface water 

improvement and management are listed below (Table 2). The function of the Special District, 

year established, local government with authority over the district, and Florida Statute that 

governs their operation are included. A Special District is identified as independent if no other 

governmental entities have control over their budget or governing board membership. The 

information in Table 2 is from the Florida Department of Community Affairs (FDCA) Special 

District Information Program Official List of Special Districts On-Line. None of the special 

districts within the Study Area are included in the SFWMD GIS data set, and, while some of their 

geographic boundaries are apparent, they are not readily available for mapping. 

PARTICIPANTS AND CONTRIBUTORS 

SFWMD requested participation in this project from government agency representatives with 

expertise in the subject matter and Study Area. A half-day working group meeting was held 

March 1, 2005 to identify available information, data and their sources that should be included in 

the Reconnaissance Report. All issues and sources of information discussed at workshop were 

considered in the development of this Reconnaissance Report. Many other organizations and 

individuals were contacted for information and to follow up on leads discussed at the workshop. 

A second half-day working group meeting was held June 1, 2005 to review and receive comments 

on the draft report. Additional information, suggested clarifications and corrections were 

incorporated into the final report as appropriate. The seventy-two working group participants and 

other contributors to the project are acknowledged on the following page. 

The information gathering process was initiated in February 2005, and accelerated following 

the March meeting. Input from the twenty participants of the first meeting was recorded. 

Between meetings, information was gathered and reviewed with many suggestions and leads 

followed through phone and/or email communication. A comprehensive set of notes from these 

discussions was maintained. All information (data, studies, projects, etc.) was logged into a 

spreadsheet designed to track and manage the information. The tracking matrix was maintained 

and updated throughout the project, with fields for item name, source, contact person, description, 

comments, status, format, reviewer name and review status. The spreadsheet contained over 200 

records at the time of project completion. All information, both digital and paper, was organized 

and stored for use in the review process and for delivery with the final report. Information from 
February 2006 7 Naples Bay SWIM Reconnaissance 

the fifteen participants of the second working group meeting was recorded on tape. The tracking 

matrix and notes were updated as additional information was gathered and reviewed for the final 

report. 

Table 2. Special Districts within the Study Area. 

District Function 

Local Gov. 

Authority 

Year 

Establis

hed 

Indep

ende

nt 

Statutory 

Authority 

City of Naples Airport 

Authority Airport/Aviation City of Naples 1969 No Ch. 332, F.S. 

Collier County Airport 

Authority Airport/Aviation Collier County 1993 No Ch. 332, F.S. 

Cedar Hammock 

Community 

Development District 

Community 

Development Collier County 1999 Yes Ch. 190, F.S. 

Heritage Greens 

Community 

Development District 2 

Community 

Development Collier County 1993 Yes Ch. 190, F.S. 

Lely Community 

Development District 

Community 

Development Collier County 1990 Yes Ch. 190, F.S. 

Naples Heritage 

Community 

Development District 

Community 

Development Collier County 1996 Yes Ch. 190, F.S. 

Pelican Marsh 

Community 

Development District 

Community 

Development Collier County 1993 Yes Ch. 190, F.S. 

Pine Air Lakes 

Community 

Development District 

Community 

Development Collier County 1994 Yes Ch. 190, F.S. 

Collier County 

Community 

Redevelopment Agency 

Community 

Redevelopment Collier County 2000 No 

Ch. 163, Part III, 

F.S. 

East Naples Bay 

Special Taxing District 

Environmental 

Protection & 

Navigation City of Naples 1987 No 

Section 

165.041(2).F.S. 

Moorings Bay Special 

Taxing District 

Environmental 

Protection & 

Navigation City of Naples 1987 No 

Section 

165.041(2).F.S. 

Collier County 

Industrial Development 

Authority 

Industrial 

Development Collier County 1978 No 

Ch. 159, Part III, 

F.S. 

Collier Mosquito 

Control District Mosquito Control Collier County 1950 Yes Ch. 582, F.S. 

Collier Soil & Water 

Conservation District 

Soil & Water 

Conservation Collier County 1984 Yes Ch. 582, F.S. 

Collier County WaterSewer District Water & Sewer Collier County 1978 No Ch. 153.53, F.S. 

Immokalee Water & 

Sewer District Water & Sewer Collier County 1978 Yes Ch. 153.53, F.S. 

Big Cypress 

Stewardship District Water Control Collier County 2004 Yes 

Section 298.01, 

F.S. 
February 2006 8 Naples Bay SWIM Reconnaissance 

Participants and Contributors 

Abbott, Liz - SFWMD 

Addison, David - Southwest Florida Conservancy 

Baldus, Gretchen - Collier County 

Bartareau, Tad - RBNERR 

Bauer, Mike - City of Naples 

Beever, Jim - FFWCC 

Beever, Lisa - CHNEP 

Bell, Susan - USF 

Bellow, Ted - Independent 

Bickford, Karen - FDEP 

Boyer, Joe - FIU 

Broker, Michael - SFWMD 

Burd, Jim - FWRI 

Burr, David - SWFRPC 

Byrne, Mike - USGS 

Calixte, Jean Paul - USDA 

Carlson, Ed - Audubon 

Carol, Pat - Gordon River Greenway 

Ceilly, David - Conservancy of Southwest Florida 

Cochrane, John - CCSWC 

Deuver, Mike - SFWMD 

Doering, Peter - SFWMD 

Dryden, Kim - USFWS 

Estevez, Ernest - Mote Marine 

Gotfredson, Kevin - Collier County 

Hall, Tim - Turrell and Associates 

Hatcher, Mac - Collier County 

Heckler, Jennifer - Conservancy of Southwest Florida 

Herbst, Hal - SFWMD 

Howard, Tim - SFWMD 

Jue, Sally - FNAI 

Kurtz, Gerald - Collier County 

Legg, Scott - SFWMD 

Lieberman, Tim - SFWMD 

Livingston, Eric - FDEP 

Lucas, Cyle - Pelican Bay Services Division 

McAlpin, Gary - Collier County 

McCallister, Paul - City of Naples 

Nagle, Steve - SFWMD 

Nath, Anantha - SFWMD 

Nelson, Jennifer - FDEP 

O'Connell, Gregg - FDEP 

O’Kiefe, Kathleen - FWRI 

Palmer, Carla - SFWMD 

Patino, Eduardo - USGS 

Polizo, Tony - NRCS 

Potts, Andy - SFWMD 

Preston, Steve - Collier County 

Prinos, Scott - USGS 

Prymas, Angela - SFWMD 

Razem, Frank - SFWMD 

Rippe, Michael - FDOT 

Rumbold, Darren - SFWMD 

Ryziw, Vlad - City of Naples 

Savarese, Mike - FGCU 

Shirley, Mike - RBNERR 

Silvanima, Jay - FDEP 

Sloane, Gail - FDEP 

Starn, Janet - SFWMD 

Sulecki, Alexandra - Collier County 

Thomas, Daryl - USFWS 

Tinsley, Megan - Southwest Florida Water Quality Consortium 

Truby, Jill - FWRI 

Urbanic, Mike - CCSWC 

Valera, Ricardo - Collier County 

Watkins, Rhonda - Collier County 

Whalen Stadler, Tabitha - RBNERR 

Williams, Bryan - FDOT (PBS&J) 

Wilt, Jim - FDOT (PBS&J) 

Whiley, Robert - Collier County 

Woody, Theresa - South Florida Ecosystem Restoration Task Force 

Worley, Kathy - Conservancy of Southwest Florida 
February 2006 9 Naples Bay SWIM Reconnaissance 

2 HISTORY OF THE BASIN 

BEFORE 1860 

The southwest coast of Florida was under water until about 5000 years ago. The gentle ridges and 

embayments conducive to mangrove island formation are remnants of several different long-term sea 

rises that created shorelines at seven different levels within the Pleistocene era, and are now referred to as 

terraces. The two lowest levels, Talbot and Pamlico, are evident in Collier County. These elevations were 

estimated to be 25 to 42 feet above sea level in the mid-20th century for the Talbot terrace and 20 to 25 

feet above sea level for the Pamlico. All of the Study Area is part of the Pamlico terrace, with the 

potential exception of the extreme northeast corner which may lie on the Talbot terrace. 

Earliest documented human settlements, the Calusa Indians, date from 2500 years ago. The Spanish 

attempted to colonize the area in the early 1500s, but met with fierce resistance from the Calusas. After 

40 years of fighting and disease introduction the Calusa population was gone, and no permanent Spanish 

settlements remained. In 1821 when the U.S. acquired Florida from Spain, there were about 5000 

Seminoles living in the Collier County area. In 1855, these native-Americans had been driven further east 

into the Big Cypress and Everglades areas. 

The early Naples Bay Basin was characterized by surface water sheet-flow, with historic vegetation 

communities corresponding with the Basin’s flat topography (Figure 3, Southwest Florida PreDevelopment Vegetation Map). The vast majority of the Basin (75%) was covered with Mesic or Hydric 

Flatwoods. Cypress and other swamp forests were primarily in the eastern portion of the basin and 

covered less than 10% each. Xeric hammock communities were near the coast along the coastal ridge 

now occupied by US41. Mangrove swamps fringed the coast and 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) 

1860 TO 1930 

Roger Gordon and Joe Wiggins arrived in Naples in the late 1860's. Although the river in this study 

was named after Gordon and passes were named after each, they did not stay. The first permanent settlers 

were John and Madison Weeks, taking residence along the Gordon River in 1876. In 1886, over 3,000 

acres between the Gulf of Mexico and what came to be known as Naples Bay was purchased by a group 

of Tallahassee businessmen calling themselves the Naples Town Improvement Company. 

In 1887, the Naples Town Improvement Company was reorganized by General John S. Williams and 

Walter N. Haldeman, prominent Kentucky men, into the Naples Company with ambitious plans for 

Naples development. One of the Gordon River’s tributaries is named after Haldeman. The Naples 
February 2006 10 Naples Bay SWIM Reconnaissance 

Figure 3. Pre-Development Vegetation (Data source: SFWMD, Southwest Florida Predevelopment Vegetation Map, 

2002). 
February 2006 11 Naples Bay SWIM Reconnaissance 

Figure 5. Road from Naples to Gordon Pass circa 

1935 (State Library & Archives of Florida).

Figure 4. Naples Hotel in downtown Naples circa 

1906 (State Library & Archives of Florida).

Hotel (Figure 4) and a 600 foot pier were built in 1888. By 1890, the Naples Company was bankrupt and 

the Naples Bay area remained isolated and sparsely settled for the next 40 years. 

The Tamiami Trail, built to connect Miami with Tampa, was completed in Collier County in 1928, 

and was largely funded by Barron Collier. 

Based on the promise of completion of this 

road, the area to the west of Dade, Hardy and 

Monroe and south of Lee counties was accepted 

as the 62nd Florida county and named after 

Collier in 1923. The first train delivered 

tourists in 1927 to the depot that is now an 

historic building on 10th Street and 5th Avenue 

South. The county population was about 1200 

and Naples had less than 400 residents. The 

building of the Tamiami Trail and the railroad 

were the first major impediments to surface 

water, overland flow in this area. (Baum 

1973, Tebeau 1957) 

1930 TO PRESENT 

In 1930, a protected channel, 3-feet deep and 40-feet wide, was dredged from Naples Bay to Marco 

Island. In 1940, the federal government completed the channel, 6-feet deep and-70 feet wide, from the 

southern boundary of Naples to the Big Marco Pass, a total of 10 miles. In 1945, the federal government 

relocated the channel east of Hurricane Pass due 

to storm damage. Landscape characteristics of 

the area between Naples and Gordon Pass at the 

time can be seen in Figure 5. Today vessels 

must leave a sheltered bay channel at Wiggins 

Pass, travel in the Gulf, then re-enter a sheltered 

channel at Gordon Pass. The dredged channels 

and other shoreline changes can be seen in the 

nautical charts and aerial photographs in 

Figures 6 through 9. 

A U.S. Army Air Field was constructed at 

the Naples Airport in 1943 (Figure 10), and 
February 2006 12 Naples Bay SWIM Reconnaissance 

Figure 6. Nautical chart of Naples Bay, Dollar Bay and the Gulf of Mexico in 1931 (US Coast and 

Geodetic Survey, 1931).
February 2006 13 Naples Bay SWIM Reconnaissance 

Figure 7. Nautical chart of Naples Bay, Dollar Bay and Gulf of Mexico in 1984 (NOAA-NOS, 1984).
February 2006 14 Naples Bay SWIM Reconnaissance 

Figure 8. 2000 Satellite image, Naples Bay, Dollar Bay, and the Gulf of Mexico (data source: SFWMD).
February 2006 15 Naples Bay SWIM Reconnaissance 

 

 Figure 9. Naples Bay and Gordon Pass in 1953 (left) and 1999 (right) (RBNERR, source: USGS).
February 2006 16 Naples Bay SWIM Reconnaissance 

Figure 11. Population Growth in Collier County, 1930 

– 2000 (Collier County 2001 Demographic and Economic Profile 

U.S. Bureau of the Census, 1930-1990-2000 Collier County 

Comprehensive Planning Section July 2000).

Figure 10. Clearing on the site of Naples Airport 

circa 1935 (State Library & Archives of Florida).

by 1944 there were over 200 soldiers stationed 

in Naples, almost doubling the population. By 

1953, the airport was conveyed to the city and 

county, a bank had been built and residents had 

funded several parks and civic improvements. 

Port Royal and Aqualane Shores were the first 

developments to dredge canals and create 

waterfront property. A hospital, expanded 

water treatment plant, schools and businesses 

were built at the same time, and by 1960 the 

population count was almost 5000. 

Construction of the City of Naples 

drainage system began in the 1940s in “Old 

Naples”, with additional construction in the 

50’s and 60’s as Ridge Lakes and Coquina Sands subdivisions were built. The Cove and Public Works 

Pumping Stations were added in the mid-1960s. Drainage systems were added for the Moorings, Port 

Royal and Royal Harbor in the late 60’s and early 70’s with the Lantern Lane station located in Port 

Royal. During the same time period, many small lakes were constructed to deal with drainage issues, 

further altering the natural system in an area where lakes were notably absent. 

Hurricane Donna passed directly over Naples in 1960, destroying the pier and causing extensive 

inland damage. The influx of insurance and disaster funding stimulated growth, and Naples became the 

fastest growing city in the nation. Meanwhile, the Gulf American Corp. began development of 113,000 

acres of pine and cypress forests in the county's interior − Golden Gate Estates. Gulf American dug 180 

miles of canals, some of them 19-feet deep, and built 800 miles of roads. The southern portion is now 

Picayune Strand and is slated for restoration. 

Historic drainage of this mostly undeveloped area 

was south through the Faka-Union Canal. 

However, the northern section of Golden Gates 

Estates is developed and drainage currently enters 

the Gordon River through the Golden Gate Canal; 

effectively increasing the original Naples Bay 

watershed from about 10 square miles to over 100. 

Collier County’s population continued to rise 

exponentially, passing the quarter million mark in 

2000. The burden on infrastructure increases by 

almost 100,000 people every winter (Figure 11). 
February 2006 17 Naples Bay SWIM Reconnaissance 

Figure 12. Gordon Pass and Key Island.

In 1970, the Naples City Council conducted a small water quality survey of Naples Bay. The results 

led to three City of Naples sewage system expansions in order to reduce the amount of sewage entering 

the Bay. In 1972, when the Naples Bay Study was begun by The Conservancy of Southwest Florida (the 

Conservancy), there were 117 residential canals in the Naples Bay complex. Some canals were in the 

City where adjacent residences had central sewer systems, but many were in the county where septic 

tanks were used for sewage treatment. In 1979, Port Royal and Aqualane Shores Phase 2 dedicated their 

canals to the City. Oyster Bay, Golden Shores and Royal Harbor developments retained their canals as 

private property. 

In early 1988, plans were announced to 

purchase and develop the northern end of 

Key Island (Figure 12) which is the 

southern land mass bordering Gordon Pass. 

While the Conservancy opposed this plan, 

the Naples City Council did allow the 42 

single-family homes. In 1993, 2,300 acres 

of Key Island became part of RBNERR, 

including those portions along Gordon Pass. 

The result of 60 years of canal drainage, 

agricultural activities and urban 

development activities has been reduced water clarity, increased concentrations of contaminants and 

nutrients, and reduced dissolved oxygen levels in the Bay. The Bay once received drainage from about 

10 square miles, but with the construction of the Golden Gate Canal system it receives surface water input 

form approximately 120 square miles. Extensive areas of mangroves and salt marsh have been replaced 

by canals, seawalls and bulkheads. Development activities in the watershed have altered the volume, 

quality, timing and mixing characteristics of freshwater flows reaching Naples Bay. Natural tributaries - 

Gordon River, Rock Creek, and Haldeman Creek - have been altered by urban infrastructure that have 

significantly changed the historic flowways to the Bay and impacted its biology. Seasonal influxes of 

fresh water from the Golden Gate Canal system have altered the natural salinity regime of the bay, 

resulting in declines in seagrass beds, and harmful impacts to all levels of flora and fauna in the aquatic 

ecosystem. (Tebeau 1957, Baum 1973, Naples Bay Study 1979, Collier County Comprehensive Planning Section 

2000, City of Naples Engineering Division 1996)
February 2006 18 Naples Bay SWIM Reconnaissance 

Figure 13. County, City and SFWMD basins and subbasins (data sources: SFWMD, Collier County). 

3 GEOGRAPHIC ANALYSIS 

This section describes the Naples Bay Basin primarily through maps using data available in GIS 

format. Spatial data available for the Study Area were compiled, reviewed and documented. The spatial 

data used to create the maps in the report were provided on DVD in ESRI compatible GIS format, with 

available metadata. 

The Naples Bay Basin (as defined 

by the SFWMD for the purposes of this 

Reconnaissance Report and upcoming 

SWIM Plan) forms the boundary of the 

Study Area. There are 32 sub-basins 

within the Naples Bay Basin. Collier 

County, the City of Naples, FDEP and 

other organizations have different 

delineations for the basins and subbasins within the Study Area (Figure 

13). This is a basin boundary for 

planning purposes only and may change 

as more information becomes available 

from local drainage assessments and 

refined topographical efforts. The 

various reports, studies, etc. within this 

report may use the terms basin, subbasin and watershed differently, as their 

geographic scopes differ. 

ESTUARIES 

Naples Bay is a relatively narrow and shallow estuary ranging in width from 100 to 1500 feet, and in 

depth 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 14). Data were collected from 

a hydrographic survey vessel with onboard geophysical sensors. From the 2004-2005 field data, one-half 

foot bathymetric contours were processed into a combination of 5 ft and 25 ft cells in raster GIS data sets. 
February 2006 19 Naples Bay SWIM Reconnaissance 

Figure 14. Bathymetry of Naples Bay and Dollar Bay (data source: SFWMD, 2005).
February 2006 20 Naples Bay SWIM Reconnaissance 

Substrates in the Bay and its canals are muddy, permeable sediments. Certain areas also have high 

organic content. Several dredged channels are maintained and marked for navigation throughout the 

Study 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. There are several marine facilities, including marinas, boat ramps, hotels, resorts, and other 

establishments within the Study Area. 

Tidal exchange occurs through Gordon Pass at the southern end of the Bay. Average daily tide range 

at Gordon Pass is 2.1 feet. The highest tides occur every two weeks during the “spring tides” at full and 

new moons. Spring tide ranges average 2.8 feet at Gordon Pass. Tidal ranges increase slightly moving 

north from Gordon Pass to the US 41 Bridge in downtown Naples as a result of amplification caused by 

the elongated shape of Naples Bay. Tidal ranges decrease in the Gordon River north of the bridge 

because tidal flow is limited by the constricted shape of Naples Bay in the vicinity of the bridge. 

Salinities in Naples Bay vary both seasonally (wet season and dry season) and daily (incoming and 

outgoing tides). Average salinities at the US 41 Bridge range from 0 to 10 PSU in the wet season and 

occasionally approach 35 PSU (the salinity of the open Gulf) in the dry season. Salinity at the Gulf of 

Mexico near Gordon Pass is typically 35 PSU. The largest range in daily salinity is most often seen in the 

area of Naples Bay off Bayview Park. Low salinity surface layers move into this area during outgoing 

tides. Incoming tides force the low salinity waters north and inhibit the discharge of tributaries like 

Haldeman Creek. 

During the wet season, the deeper portions of northern Naples Bay become stratified and form layers 

of different salinity water. Low salinity water flowing out of the Golden Gate Canal and other tributaries 

flows over the denser, high salinity bay waters. The result is a series of horizontal layers with increasing 

salinities from bay surface to bottom. In the northern Bay, these layers often do not mix. Since oxygen is 

produced in the upper layers, this lack of mixing results in low oxygen concentrations in the bottom 

layers. The Bay once received drainage from about 10 square miles, but with the construction of the 

Golden Gate Canal system it receives surface water input from approximately 120 square miles. 

Stratification problems are believed to have increased with both the increased freshwater flow and with 

the construction of deep, dead end canals. Stratification is less of a problem in the lower Bay where 

horizontal mixing from tidal currents is greater (Simpson et al., 1979). 

TOPOGRAPHY, FLOOD ZONES, SOILS 

In general, ground elevation increases gradually from Naples Bay and the coast towards the northeast 

portion of the Basin (Figure 15). The lowest areas of the Naples Bay Basin are the mangrove forests and 

the Bay at sea-level in the Basin’s southwest corner. The highest elevations in the Basin are 

approximately 20 ft NGVD in the far northeastern corner near Immokalee. The majority of the Basin has 

elevations of 10 ft or less with a slow rise to the northeast. Elevations above 15 ft do not occur until north 
February 2006 21 Naples Bay SWIM Reconnaissance 

Figure 15. Topographic Elevation (data source: SFWMD, Revised Elevation for the Southwest Florida Feasibility 

Study Area, 2004). 
February 2006 22 Naples Bay SWIM Reconnaissance 

of Oil Well Road (CR858). An exception is found along the US41 corridor within a mile of the coast. 

This road follows a north-south oriented coastal ridge with elevations between 10 ft and 15 ft. 

Areas within the FEMA flood zone extend between roughly 3,000 and 15,000 ft. inshore (Figure 16). 

Revisions made to the Flood Insurance Rate Maps (FIRM) by FEMA, as shown in this report, will be 

effective November 17th, 2005. A large portion of the Basin is covered by hydric soils (Figure 17). 

Though much of the Basin can be characterized as a mosaic of hydric and upland soils, the coastal ridge 

in the western edge of the Basin is dominated by upland soils. A revision to the Collier County soils map 

is being done by USDA NRCS to correct for a 100-foot line offset in the GIS data that has been 

identified. The revised soil map reflecting the positional shift should be available in the near future. 

LAND USE/LAND COVER 

SFWMD current and future land use/land cover maps used in this Reconnaissance Report were 

created using FLUCCS (Figures 18, 19) to support CERP efforts in Southwest Florida. Their 1995-base 

SFWMD land use/land cover was updated to 2000-base conditions using the 2000-aerial photography and 

other sources. Partial updates were made for 2004 conditions. Future land use/land cover for 2025 and 

2050 were developed from county future plans, other GIS data, and local expert knowledge. Other 

sources of current and future land use are available; however they are not as well suited for Naples Bay 

SWIM purposes. Collier County has a FLUCCS map updated by Wilson Miller, Inc. using 2001 aerial 

photography. Unfortunately, the map covers only the western portion of the County. The SFWMD 2000 

FLUCCS map, developed as part of its District-wide, 5-year mapping program, was not available in time 

to meet CERP modeling needs. The Southwest 2000 FLUCCS, updated for SFWMD by URS, remains 

the preferred data set for CERP. A compiled, generalized future land use map is available from the 

SWFRPC and local governments have their own future land uses maps, however they do not use 

FLUCCS, and therefore do not allow direct comparison from one time period to the other. Land use/land 

cover acreages for the Basin for each of the three time periods are summarized in Table 3. 
February 2006 23 Naples Bay SWIM Reconnaissance 

Figure 16. Flood Zones (data sources: Collier County/ FEMA Flood Insurance Rate Map (FIRM), to be adopted 

November 2005).
February 2006 24 Naples Bay SWIM Reconnaissance 

Figure 17. Hydric Soils and Hydrologic Soil Group (data source: USDA NRCS Soil Survey Geographic Database 

(SSURGO), 1995). 
February 2006 25 Naples Bay SWIM Reconnaissance 

Figure 18. Current Land Use/Land Cover (FLUCCS) (data source: SFWMD, 2000 Update for Land Use/Land 

Cover for Southwest Florida, 2004). 
February 2006 26 Naples Bay SWIM Reconnaissance 

Figure 19. Future Land Use/Land Cover (FLUCCS) (data source: SFWMD, Spatial Distribution of Land 

Use/Land Cover for Southwest Florida Feasibility Study Area, 2004).
February 2006 27 Naples Bay SWIM Reconnaissance 

 Table 3. 2004, 2025, and 2050 Land Use/Land Cover in the Basin. 

Land Use/Land Cover 2004 2025 2050 

Mobile Home Park 464 464 464 

Low Density Residential 19,151 33,213 15,359 

Medium Density Residential 12,081 18,023 36,122 

High Density Residential 6,223 10,948 10,794 

Commercial and Services 2,583 3,469 3,996 

Industrial 1,205 1,711 1,764 

Extractive 413 144 144 

Institutional 890 890 890 

Recreational 5,621 5,880 5,880 

Open Land 2,251 0 0 

Agriculture 8,507 905 233 

Rangeland 1,278 70 70 

Upland Forest 15,539 893 893 

Water 4,938 4,938 4,938 

Wetland 18,667 18,667 18,667 

Barren Land (Beaches, Sand) 448 43 43 

Transportation, Communication & 

Utilities 2,567 2,568 2,568 

Sum 102,826 102,826 102,826 

The decrease in low density residential uses is attributed to the increase in medium and high density 

residential uses. The general rules followed for modeling future land use distribution assumed no 

development of areas designated as the wetland by the wetland FLUCCS code. Since the wetland 

distribution is according to FLUCCS, it does not reflect changes that might occur due to wetland fill 

permits or mitigation. 

The five most common categories which comprise 73% of the current land use in the Study Area are 

listed below: 

• Low density residential = 19% 

• Wetland = 18% 

• Upland forest = 15% 

• Medium density residential = 12% 

• Agriculture and Rangeland = 9% 

The US41 corridor from North Naples to Belle Meade occupies the Basin’s western edge. This 

corridor is the most heavily developed area in the Basin. It is almost entirely medium and high density 

residential together with commercial land uses. The only exception is a large area of mangrove forest 

south and east of Naples Bay. The majority of the Basin’s agricultural lands are located in the higher 

elevation areas north of Oil Well Road and east of Immokalee road in the Basin’s northeastern corner. 
February 2006 28 Naples Bay SWIM Reconnaissance 

Figure 21. A portion of the Collier County Primary and 

Secondary Drainage Map, Naples Bay vicinity (Collier County). 

Significant changes are projected for the distribution of land use/land cover in the Basin between the 

current conditions and 2050. The largest projected future land uses (by percentage of basin area) are 

listed below: 

• Medium density residential = 35% 

• Wetland = 18% 

• Low density residential = 15% 

• High density residential = 10% 

• Recreational = 6% 

Upland forest and agricultural/rangeland are each projected to occupy less than 1% of the Basin in 

2050. The 2050 land use projections place almost all of the high density residential and commercial land 

west of CR951. The eastern portion of the Basin will be a mosaic of wetlands and low density residential 

development with several large blocks of medium density residential and a small amount of commercial 

development. 

SUB-BASIN AND DRAINAGE CHARACTERISTICS 

Canals and other drainage barriers and conveyances have altered the historic patterns in the Naples 

Bay Basin to the extent that the basin is now best described in terms of these features. The canals tend to 

be aligned along section and half section boundaries in north-south or east-west patterns (Figure 20). 

There are eleven major canals within the Naples Bay Basin. 

• Golden Gate Main Canal 

• Orange Tree Canal 

• Corkscrew Canal 

• Curry Canal 

• Cypress Canal 

• CR 951 Canal 

• Green Canal 

• Harvey Canal 

• I-75 Canal 

• Airport Road Canal 

• Lely Canal

A primary and secondary canal 

system forms a major public surface 

water/stormwater network in Collier 

County. A sample of the high 

resolution, detailed drainage maps 

depicting that system in the Naples Bay 

vicinity is in Figure 21. The West 

Collier and East Collier maps are 
February 2006 29 Naples Bay SWIM Reconnaissance 

Figure 20. Naples Bay Basins, Sub-basins, Canals and Hydrography (data source: SFWMD 2005). 
February 2006 30 Naples Bay SWIM Reconnaissance 

designed for large format plotting and viewing. The County’s extensive stormwater management system 

is displayed using their draft stormwater management GIS data in Figure 22. SFWMD canals and 

structures are in Figure 23. GIS data sources available from SFWMD for canals and control structures 

vary slightly. All sources are shown in Figure 23. They are referred to in the GIS data as SFWMD 

Canals, Big Cypress Basin Canals, and SWFFS Canals. SWFFS data were developed for regional models 

and are subject to revisions. BCB data were used in MIKE SHE models. See GIS metadata for additional 

information. The City of Naples has Master Drainage AutoCad maps that document pipes, inlets, 

manholes, and other conveyance features that are not shown here. 

The 32 sub-basins in the Naples Bay Basin (Table 4) are generally named for the conveyance features 

within them (Figures 24 and 25). The acreage of each sub-basin is listed below. The minimum sub-basin 

size is 225 acres, the maximum is 8,820 acres, and the mean is 3,213 acres. 

 Table 4. Sub-basins of the Naples Bay Basin. 

Sub-basin name Area (acres) Sub-basin name Area (acres) 

951 N 781 Gordon River N 1,474 

951 S 967 Gordon River S 456 

Airport S 3,481 Green 1,358 

Corkscrew Canal N 4,579 Haldeman Creek 1,970 

Corkscrew Canal S 1,348 Harvey 5,324 

Curry 1,863 I-75 #1 3,485 

Cypress E 4,341 I-75 #2 3,102 

Cypress W 4,953 I-75 #3 2,760 

GG #1 2,585 Lely N 7,404 

GG #2 621 Lower Haldeman Creek 2,665 

GG #3 8,820 Naples Bay 3,893 

GG #4 4,699 Naples Shore 8,075 

GG #5 4,049 Orange Tree 2,076 

GG #6 2,702 Rock Creek 1,569 

GG #7 2,952 Santa Barbara 5,244 

Gordon River Central 3,006 Winter Park 225 

 Sum 102,826 

The Big Cypress Basin Watershed Management Plan identifies several “flood control problem areas” 

within the Study Area. Flood control problem areas are defined as areas where at least one of the 

following items occurs during the design storm event (using land use and cover that was current at the 

time of the study): 

• The maximum flood elevations exceed the canal bank elevation 

• The maximum flood elevation is within 1.5 feet of the canal bank elevation 

• Water velocities exceed 2.5 feet per second, creating a potential for erosion 

• Structures within the canal do not meet District right of way criteria 
February 2006 31 Naples Bay SWIM Reconnaissance 

Figure 22. Collier County Stormwater Management Features (data source: Collier County, Work in 

Progress, 2005). 
February 2006 32 Naples Bay SWIM Reconnaissance 

Figure 23. SFWMD Canals and Structures (data source: SFWMD, 2002 - 2004, SWFFS area data were developed 

for regional model and are subject to revision. BCB data were used in the MIKE SHE model).
February 2006 33 Naples Bay SWIM Reconnaissance 

Figure 24. Canals and sub-basins in the eastern portion of Naples Bay Basin (data sources: SFWMD, 2005).
February 2006 34 Naples Bay SWIM Reconnaissance 

 

Figure 25. Canals and sub-basins in the western portion of Naples Bay Basin (data sources: SFWMD, 2005). 
February 2006 35 Naples Bay SWIM Reconnaissance 

Based on these criteria, approximately 29% of the 163 total miles of canals in the Big Cypress Basin 

(or 47.6 miles) are located in flood control problem areas having inadequate flood control for the design 

storm events. The design storm events are the 25-year, 3-day storm event in urban areas and the 10-year, 

3-day storm event in rural areas. 

The Golden Gate Main, Orange Tree, Corkscrew, and Curry Canals all originate in the northeastern 

corner of the Naples Bay Basin (Figure 24). These canals run north-south and are located a little more 

than a mile apart. The Golden Gate Main Canal is by far the longest of the four. Originating on the south 

side of Immokalee Road southeast of Corkscrew Swamp, this canal drains an area that was historically 

mesic flatwoods. Sub-basins in this area are Golden Gate #7, Golden Gate #5, and Golden Gate #4. 

These sub-basins (particularly #7) are currently dominated by agriculture and wetlands. The vast 

majority of the almost 10,000 acres of agricultural land and rangelands in the Naples Bay Basin are found 

in these sub-basins. The District’s 2050 future land analysis projects almost all non-wetland areas in the 

sub-basins will be low or medium density residential. 

The Golden Gate Main Canal is approximately 27 miles long with an outfall near the opposite end of 

the Basin in the Gordon River, just north of the Naples Airport (Figure 25). There is a significant control 

structure located just above the canal’s outfall. Many of the other canals in the Basin drain into the 

Golden Gate Main Canal along its route in the eastern and southeastern boundaries of the Naples Bay 

Basin. As such the canal is thought to be particularly susceptible to flood capacity issues resulting from 

land use changes. The Big Cypress Basin classifies 43% of this canal as flood control problem areas. 

The Orange Tree Canal is a short canal immediately west of the Golden Gate Canal. The canal 

begins east of Immokalee Road and empties into the eastern portion of the Cypress Canal. The Orange 

Tree Canal drains the Orange Tree sub-basin, an area that was historically mesic and hydric flatwoods. 

The sub-basin currently contains a mix of low density residential, agriculture/rangelands, and wetlands. 

The 2050 land use projects this area to be predominantly low density residential uses and wetlands. 

The Corkscrew Canal is located west of the Orange Tree Canal. The Corkscrew Canal has its origins 

north of Immokalee Road near a large rock mine and the southern end of the Corkscrew Swamp. At the 

southern end of its six mile course, the canal empties into the Cypress Canal. The Corkscrew Canal 

drains one sub-basin on the north and one on the south side of Immokalee Road. The current land use in 

these areas is largely wetlands and agriculture, with some low density residential and smaller amounts of 

upland and rangeland. Future land use is projected to be almost entirely low density residential uses and 

wetlands. The Big Cypress Basin classifies 37% of this canal as flood control problem areas. 

The Curry Canal is the westernmost of the four canals in the northeastern Gordon River Basin. It is 

another short canal and drains a small sub-basin immediately south of Immokalee Road. The canal is 

named for the Curry Island, an historic vegetation feature located among the wetlands that dominate this 

portion of the Basin. The Curry sub-basin contains a large percentage of wetlands and forested areas 

along with low density residential uses, much of which is centered on the Rock Road corridor. Curry 
February 2006 36 Naples Bay SWIM Reconnaissance 

Canal has its outfall in the Cypress Canal. Current land uses and land cover are primarily low density 

residential and wetland with small amounts of upland forest, agriculture and rangeland. Future land use 

and land cover are projected to be wetland and low density residential, with a small amount of medium 

density residential. 

The Cypress Canal is an 8-mile long canal that receives flow from the Orange Tree, Corkscrew, and 

Curry Canals. The Cypress runs east-west at the same latitude as Vanderbilt Beach Road from the 

Orange Tree Canal to the intersection of Vanderbilt Beach Extension and Massey Street. Cypress Canal 

then follows a north-south course until it reaches its outfall in the Golden Gate Main Canal east of Green 

Boulevard. Cypress Canal drains two, large sub-basins, Cypress East and Cypress West. These areas 

were historically a mosaic of flatwoods and cypress. The southern portions of these basins are more 

heavily developed and primarily low density residential with some upland and wetland forests. The 

northern portions of the basins still contain large areas of wetlands, as well as natural uplands, agriculture, 

and low density residential uses. The 2050 land use projections show the basins as medium and low 

density residential uses with scattered wetlands. 

The County Road 951 (CR951) Canal follows a north-south course down the middle of the Naples 

Bay Basin (Figures 24 and 25). The canal is a little over seven miles long and was originally excavated to 

provide fill for the adjacent roadbed. Despite its original purpose, the CR951 canal now serves as a 

conveyance structure. It originates at the intersection of Immokalee Road and CR951 on the northern 

boundary of the Basin. Its outfall is where CR951 crosses the Golden Gate Main Canal just north of I-75. 

It drains two very narrow basins on the east side of CR951, 951 North and 951 South. The current 951 

South basin land-use is predominantly low density residential with some Upland Forest. Future land use 

is projected to be medium density residential. The 951 North basin is currently low density residential 

and upland forest with some wetland and agriculture. Future land use is projected to be medium and high 

density residential with some wetland and commercial land use. The Big Cypress Basin Board classifies 

35% of this canal as flood control problem areas. 

The Green Canal is a short canal that runs east-west just south of Green Boulevard. It drains the 

Green sub-basin that is dominated by the developed hub of the Golden Gate area. The canal originates 

just west of CR951 and empties into the I-75 Canal just south of Green Boulevard. Current land use is 

predominantly medium density residential with a small amount of commercial. Future land use is 

projected to be high density residential and commercial. 

The Harvey Canal is a north-south conveyance less than a mile west of CR951. The canal originates 

on the south side of Vanderbilt Beach Road and empties into the Green Canal two miles to the south. The 

Harvey Canal drains a sub-basin that was historically hydric flatwoods with smaller areas of cypress and 

mesic flatwoods. The current land use of low density residential with scattered patches of upland forest is 

enabled by drainage from area canals. Future land use within the Basin is projected to be entirely 

medium density residential. 
February 2006 37 Naples Bay SWIM Reconnaissance 

Figure 27. FWCS Threatened and Endangered Species 

(FWS). 

The I-75 Canal is a north-south conveyance that follows I-75 from roughly Immokalee Road to its 

junction and outfall with the Golden Gate Main Canal. It drains sub-basins I-75 #1, #2, and #3. The 

Airport Road Canal is located two miles west of I-75 on the eastern edge of Airport Pulling Road. This 

canal also follows a north-south course from Immokalee Road to the Golden Gate Main Canal. These 

two canals drain basins with similar land uses. Low and medium density residential uses dominate the 

current land use. Medium and high density residential uses are projected to dominate in 2050, with a 

decrease in upland forest and low density residential. 

The Lely Canal is the exception to the rule of north-south and east-west canals running along section 

and quarter section boundaries. This canal runs southwest from the Lely area to the coast and has an 

outfall in the vicinity of Dollar Bay. This drainage area of this canal can be characterized by a mixture of 

different land uses and land cover. Future land uses are projected to be increasingly medium and high 

density residential as well as commercial. Much of the residential development in this basin in fairly 

recent, but the canal predates this development. 

Haldeman Creek is a short, channelized creek that empties into Naples Bay between the Golden Gate 

Canal and Lely Canal. Haldeman Creek drains basins that contain a large proportion of residential and 

commercial land uses. 

SPECIES AND HABITAT 

The species richness index was developed by FFWCC in order to assess habitat conservation needs of 

rare and imperiled wildlife in Florida (Cox and Kautz. 2000). The index represents the number of species 

identified as having potential habitat at a given location. Potential habitat was modeled for 130 focal 

species. Index values range from 0 (representing no species) to 26 (the maximum number of species in 

one location) in the state of Florida. Within 

the Naples Bay Basin, values range from 0 to 

15 (Figure 26). Species richness is greater in 

and around the natural areas that boarder the 

study, and these areas are largely held in 

conservation. The index is a useful planning 

resource when considering habitat and 

species, though other data, both observed and 

modeled, for individual and for multiple 

species are available. 

Threatened and endangered species 

identified and mapped by the FWS (Figure 

27) indicate that several Eagle nests are 
February 2006 38 Naples Bay SWIM Reconnaissance 

Figure 26. Species Richness and Selected Species (data sources: FFWCC Species Richness Index, 2000, Collier 

County selected species, 2004).
February 2006 39 Naples Bay SWIM Reconnaissance 

present along the coast. Panthers and Red-Cockaded Woodpeckers are present in and around the 

Corkscrew Swamp and Picayune Strand, and near the northern and southern boarders in the central 

portion of the Study Area. It should be noted that not all State-listed species are included on the FWC 

map, and that data represent a wide range of dates (from 1970 to 2004, with some dates uncertain). 

Additional data for shore and wading birds (FFWCC), Least Terns (Collier County), and sea turtles 

(Collier County) are shown in Figure 26. It should also be noted that the several wading bird colonies 

shown on the map may under-represent those actually present. Sea turtle nests and false crawls are 

prolific along the beaches. The Statewide Nesting Beach Survey program (SNBS) GIS data, however, 

does not indicate that any of the three species of sea turtles surveyed are active on beaches within the 

Study Area. The loggerhead (Caretta caretta), the green turtle (Chelonia mydas), and the leatherback 

(Dermochelys coriacea), regularly nest on Florida’s beaches and are listed as either Threatened or 

Endangered under the Endangered Species Act. 

The West Indian Manatee, a marine mammal on the endangered species lists, uses Naples Bay 

habitat. According to the FFWCC GIS data (FFWCC, 2004), three manatees were observed during 

synoptic surveys between 1994 and 2001. Synoptic surveys are a tool used for estimating the size of the 

population. The two day aerial surveys cover all of the manatee's wintering habitats in Florida and 

southeast Georgia between 1976 and 2004. There were 55 manatee deaths reported within the Study Area 

between 1974 and 2004. 

Repeated anecdotal assertions indicate that seagrasses were present in the Bay prior to canal dredging 

and mangrove removal. The BCB Science Plan contains a proposal to document existing locations, and a 

project being funded by the SFWMD to document the Naples Bay historic habitat (Conservancy, in 

Progress) including GIS mapping of benthic communities. 

The use of Naples Beach by coastal water birds has been documented and reported based on over 30 

years of biweekly census data in “Coastal Water Bird Beach Utilization Naples Florida” (Below, 2004). 

The census was initiated between Doctors and Gordon Pass, then focused on two areas that are heavily 

used by birds: the structures present at 3rd Avenue North and one kilometer north of 32nd Avenue South. 

Those areas are used for roosting and feeding. 

The latest available document listing Florida’s Endangered Species, Threatened Species, and Species 

of Special Concern (FFWCC, 2004) consolidates the official state and federal species lists. The MultiSpecies Recovery Plan for South Florida was prepared by the U.S. Fish and Wildlife Service as part of the 

South Florida Ecosystem Restoration Initiative (US Fish and Wildlife Service, 1999). The Plan identifies 

the recovery needs of 68 threatened and endangered species and 23 natural communities. The plan 

includes habitat requirements and limiting factors, recovery objectives and criteria, both habitat and 

species level recovery actions needed, estimated costs of recovery implementation, and the targeted date 

of recovery for each species (USACOE and SFWMD, 2002). As part of the SWFFS effort, a SWFFS 

Species Update is being prepared. The SWFFS's Feasibility Scoping Meeting critical habitat designation 
February 2006 40 Naples Bay SWIM Reconnaissance 

Figure 28. Clam Bay mangrove die-off area 

(Turrell & Associates).

(FSM) document will include current information (status, critical habitat designation, recovery 

recommendations) on federally listed species occurring within the boundaries of the SWFFS. The 

SWFFS Species Update final draft is anticipated late 2005. (Daryl Thomas, USFWS, personal 

communication). 

Southwest Florida Coastal Conservation Corridor (SWFCCC) Plan (The Nature Conservancy, In 

Preparation) is a landscape scale conservation planning project that intends to enhance cooperative 

planning between public and private land acquisition entities. The goal is to establish a multijurisdictional partnership to identify, create, and manage a conservation corridor system from Dixie to 

Monroe County. Products of the project are to include a series of maps showing opportunities for 

landscape-scale connection along with a comprehensive GIS database and an interactive internet map 

server. Principal partners are The Nature Conservancy, US Fish & Wildlife Service, FDEP and the 

FFWCC. The project is being done in coordination with the Southwest Florida Regional Wildlife Habitat 

Plan, the Southwest Florida Feasibility Study (SWFFS), Comprehensive Everglades Restoration Plan 

(CERP), and the South Florida Ecosystem Restoration Task Force, and the Multi-species Recovery Plan/ 

Multi-Species Ecosystem Recovery Implementation Team. The plan is expected to be available on the 

Nature Conservancy website in 2005 and can be found through: 

http://nature.org/wherewework/northamerica/states/florida/ 

In 1992, a mangrove die-off was documented in Clam Bay at the northern, coastal portion of the 

Basin (Figure 28). Water quality, sediment, biological and hydrographic studies were conducted for 

Clam Bay and the Parkshore subdivision between 1975 and 1977, along with recommendation and 

evaluations of over-water structures. Findings indicated parameters within normal ranges (USEPA, 1975, 

USEPA 1977). Ongoing water quality monitoring efforts by Collier County Environmental Services and 

Pelican Bay Services District did not indicate the presence of excessive chemicals or nutrient in 

concentrations high enough to solely cause the mangrove 

mortality. Rather, the monitoring suggested that the death 

of the mangroves was attributable to excessive freshwater 

input to the system from the adjacent, developed uplands 

and inadequate drainage/tidal exchange through 

increasingly constricted channels. As a result, water 

became elevated and stagnated above the pneumatophores 

of the black mangrove for lethally long periods of time. In 

1998, one joint coastal permit was issued to Collier 

County-Pelican Bay Services Division to restore and 

manage the Clam Bay Natural Resource Protection Area 

based on the Clam Bay Restoration and Management Plan 

(CBRMP) (Brown et al., 1998) over the life of a ten year 

permit. This plan included dredging, water quality, 
February 2006 41 Naples Bay SWIM Reconnaissance 

hydrographic and biological monitoring. The Conservancy also has studies focused on the Clam Bay 

mangrove die-off. Related documents are summarized in Appendix A2. 

PUBLICLY OWNED/CONSERVATION LANDS 

Existing and proposed publicly owned land and conservation areas were investigated and mapped 

(Figure 29) using the best available data. The significant areas are described below. The Naples Bay 

Basin is surrounded by or partially contains several major conservation areas, and additional acquisitions 

are proposed. Additional smaller public/conservation lands, less than 300 acres, are proposed within the 

Basin, primarily by the Conservation Collier Land Acquisition Program, which is further described in 

Chapter 4 under Programs. Many small access and conservation easements are also present within the 

Study Area. Existing and proposed conservation lands and easements within the Basin total 3,440 acres, 

approximately 3% of the Basin. Of those lands, 2,650 acres or 2.6% are existing lands, and 790 acres, or 

0.8%, are proposed. As described in Chapter 4 under Projects, land in Northern Golden Gates Estates has 

been proposed for acquisition for a Regional Off-site Mitigation Area (ROMA) as well. 

There are 45 SFWMD Conservation Easements acquired through the regulation permitting process 

scattered throughout the Study Area. Together they total 950 acres and less than 1% of Study Area. 

Other than for Naples Municipal Airport, they are primarily associated with residential developments and 

golf courses. Three Access Easements (ingress/egress) owned by the SFWMD are located in the southern 

portion of the Basin, the largest being the Lely Canal and structure, another at the Golden Gate Canal, and 

a very small parcel along I-75 between Green Boulevard and Golden Gate Parkway. 

Corkscrew Regional Ecosystem Watershed (CREW) is a 60,000-acre project in Lee and Collier 

counties, consisting of Corkscrew Swamp Sanctuary, Corkscrew Marsh, Camp Keais Strand, Flint Pen 

Strand, and Bird Rookery Swamp. Existing (200 acres) and proposed (540 acres) portions of CREW 

extend into the northeast portion of the Basin. CREW lands are dominated by cypress forest, low pine 

flatwoods, hardwood hammocks, marshes, mixed swamps, and ponds. This system provides habitat 

which supports at least 65 species of plants and 12 species of animals listed by the state as endangered or 

threatened (USACOE and SFWMD, 2002). CREW surrounds Audubon’s Corkscrew Swamp Sanctuary 

and conveys water to it and other conservation lands. 

The Rookery Bay National Estuarine Research Reserve (RBNERR) area is 110,600 acres of primarily 

estuarine habitats including mangroves, salt marshes, estuarine bay and associated mudflats, oyster bars, 

and seagrass beds. There are some areas of freshwater marsh, cypress swamps, coastal strand, scrub, pine 

flatwoods, and cabbage palm/oak hammock. The northwestern tip of the Reserve, 1,460 acres, lies within 

the southwest tip of the Basin. RBNERR comprises 1.4% of the Naples Bay Basin. 
February 2006 42 Naples Bay SWIM Reconnaissance 

 Gordon River. Conservation Collier will partner with County Stormwater and Transportation of the Figure29. Existing and Proposed Conservation Lands and Easements (data sources: SFWMD, Conservation 

Collier, Florida Natural Areas Inventory (FNAI), 2005).
February 2006 43 Naples Bay SWIM Reconnaissance 

Conservation Collier has purchased portions of two multi-parcel projects, and solicitations for 

purchase are ongoing. The first multi-parcel project is the Red Maple Swamp Preserve (comprised of the 

entire North Golden Gate Estates Unit 53), a seasonal wetland located south of CREW lands and just west 

Study Area. In this project, 30 out of a total of 285 acres have been purchased. In the second multiparcel project, called Winchester Head (a 200-acre cypress and marsh wetland immediately east of the 

Study Area), less than 10 of the 141 acres within the project boundary have been purchased. 

Other conservation acquisition activities within the Study Area include several potential purchases 

along the Gordon River. Conservation Collier will partner with County Stormwater and Transportation 

Departments to purchase 13 acres of a 52-acre parcel on the NE corner of Goodlette-Frank Road and 

Golden Gate Parkway, where Florida Community Trust is involved in a grant partnership for the Gordon 

River Water Quality Park. Conservation Collier is seeking to purchase approximately 100 acres due 

south of the Gordon River Water Quality Park along the Gordon River to provide recreational trails and 

canoe access to the Gordon River. Farther south, also along the Gordon River, the program is in the 

process of making an offer on 49 acres which will help connect with others to create an envisioned 

Gordon River Greenway stretching from Golden Gate Parkway on the north to the Gordon River Bridge 

and U.S. 41 to the south. Property reports and maps are available on the Conservation Collier website at: 

http://www.colliergov.net/natresources/conservationcollier/index.cfm. 

AQUIFER 

The principle source of drinking water in southwest Collier County is the surficial aquifer, also 

known as the Chokoloskee Aquifer. It is recharged primarily by rainfall (Jarosewich and Wagner 1985, 

Jakob 1983). Most of this formation is underlain by the Tamiami Formation, a thin, highly permeable 

layer with the top exposed in some areas. The Hawthorne Formation, present in north Collier County, is 

absent in most of the Study Area, but may be present in the northeast corner. The Floridian Aquifer lies 

beneath the Tamiami in southwest Collier County and extends out into the coastal shelf. The top of this 

formation is about 400 ft below surface at the coast. Since the pieziometric head is about 200 feet 

throughout south Florida, recharge of this aquifer does not occur outside of the central Florida ridge 

(McCoy 1962). 

SANITARY SEWER SERVICE 

The County Sewer Service area extends slightly more than halfway across the western portion of the 

Basin (Figure 30). More information about the existing and future conditions of sanitary sewers can be 

found in Collier County Growth Management Plan Sanitary Sewer Sub-Element, included in digital 

format with this Reconnaissance Report. The Sewer Sub-Element was last amended September 2003. 
February 2006 44 Naples Bay SWIM Reconnaissance 

Figure 30. Collier County Sewer and Water Service Area (data source: Collier County, 2005).
February 2006 45 Naples Bay SWIM Reconnaissance 

4 INFORMATION REVIEW 

Over the past 35 years, substantial research, monitoring, studies, and plans have been done that 

address water quality, hydrology, and ecosystems in the area. The “Naples Bay Study”, completed in 

1979, identified problems affecting the Bay and provided a number of recommendations. Many 

organizations, both government and citizen based, have focused their efforts on studying, restoring and 

managing the system. CERP has undertaken comprehensive restoration and preservation of water 

resources in Central and South Florida. To date, however, CERP actions taken specific to the Naples Bay 

basin are limited to Program Management Plans for Feasibility Studies, compilation and evaluation of 

water quality data, and water quality strategy development by a Water Quality Sub-team. Other 

governmental entities including Collier County, the City of Naples, SFWMD, and Rookery Bay National 

Estuarine Research Reserve actively support efforts to improve the Bay, as do several non-government 

support groups. 

Summaries of data sets, studies, plans, projects and programs that are pertinent to surface water 

resource management are presented in this Chapter with some more detailed information provided in 

Appendix A. Within each section of the Chapter, the information is presented in chronologic order, with 

the most recent information first. Other sources considered for this report but not summarized here are 

included in the References Cited Section. 

Information focused on habitat and species was included in the Geographic Analysis Section. A 

summary of four canal studies completed between 1972 and 1980 is given in Appendix A4. Water 

quality data that are collected by groups such as the Conservancy of Southwest Florida and Bay Watch, 

but not analyzed by certified laboratories are not reviewed here. Those data are covered in more detailed 

reviews, such as the Tetra Tech Report, summarized below. 

The BCB Library Catalog was reviewed for inclusion of pertinent bibliographic sources. The catalog 

is in spreadsheet format, approximately 50 pages, and can be searched by key word. A compilation in 

progress, the BCB – Estero Bay Regional Research Database was searched as well 

(http://ocean.floridamarine.org/bcb). The database is a collection and documentation of data that can be 

queried on-line using a traditional database interface, or using an interactive mapping interface. A list of 

projects for a given geographic area or keyword can be retrieved, along with project details. A list of 

ecological projects and research scientists maintained by SFWMD staff (Tomma Barnes, SFWMD, 

personal communication) was also reviewed. 
February 2006 46 Naples Bay SWIM Reconnaissance 

CURRENT DATA 

Preferred Water Quality Data 

As a result of the SWFFS, the Water Quality Sub-Team was formed and the report, Compilation, 

Evaluation and Archiving of Existing Water Quality Data for Southwest Florida (Tetra Tech and Janicki, 

2004), was produced with a ‘preferred’ Access dataset containing about 2 million records. SFWMD 

identified and improved some problems with the database (Darren Rumbold, SFWMD, personal 

communication). Data gaps have been addressed and future sampling plans discussed as a cooperative 

effort among the City of Naples, Collier County, FDEP, and SFWMD staff. Additional funding sources 

and means of sampling have been sought. 

Since the Tetra Tech and Janicki report was completed in mid 2004, re-sampling of historic sites has 

been performed and new sampling sites and parameters have been added, though new data are still 

provisional. Starting January 2005, one site was added in the Bay and other sites were added near the 

mouth of the Bay. BOD has been added to all County sampling sites (Rhonda Watkins, Collier County, 

personal communication, Karen Bickford, FDEP, personal communication). Strategies and 

recommendations of the Water Quality Sub-committee are described in this report. “Evaluation of Naples 

Bay Water Quality and Hydrologic Data” (Taylor Engineering, Inc., 2005), completed June 2005, further 

evaluated the preferred Access dataset for Naples Bay. These two recently completed reports provide a 

succinct and complete evaluation of water quality monitoring in the Naples Bay Basin. 

Collier County, SFWMD, FDEP (DBHYDRO and STORET) 

Since 1998, the Collier County Pollution Control and Prevention Department has collected and 

analyzed monthly water samples in the Bay and surrounding tributaries under contract with the South 

Florida Water Management District and the Big Cypress Basin. The station locations are shown in Figure 

31. Samples are analyzed for the following parameters: 

Monthly Parameters 

Calcium Fecal Coliform pH Total Nitrogen 

Chlorophyll Total Hardness Phaeophytin Total Organic Carbon 

Color Magnesium Salinity Total Organic Nitrogen 

Diss. Inorganic Nitrogen Ammonia Secchi depth Total Coliform 

Diss. Oxygen Ammonium Total Kjeldahl Nitrogen Total Depth 

Specific Conductivity Nitrite Ortho-phosphorus Total Phosphorus 

Staff gauge Nitrate Turbidity Total Suspended Solids 

Total Diss. Solids Nitrite+Nitrate Temperature BOD (as of Jan. 2005) 

Additional Quarterly Parameters 

Alkalinity Chloride Fluoride Silicate 

Arsenic Chromium Iron Sulfate 

Cadmium Copper Lead Zinc 
February 2006 47 Naples Bay SWIM Reconnaissance 

Figure 32. FDEP Current Sampling Stations (FDEP). 

Figure 31. Current Collier County surface water monitoring 

locations (Collier County Pollution Control and Prevention Department).

FDEP collects additional data 

that are available through STORET, 

including the surface water data of 

the Integrated Water Resource 

Monitoring Network (IWRM) 

Program (Figures 32 and 33). 

Water quality monitoring conducted 

by Collier County for SFWMD are 

loaded into DBHYDRO, SFWMD's 

online environmental database, 

which stores hydrologic, 

meteorologic, hydrogeologic and 

water quality data 

(http://www.sfwmd.gov/org/ema/ 

dbhydro/index.html). 

DBHYDRO data are also 

loaded into the FDEP database, 

STORET, and are available for 

download at (http://STORET. 

DEP.STATE.FL.US/). STORET is 

adatabase administered by the 

USEPA, the acronym being derived 

from STOrage and RETreival. 

STORET is a primary data source 

used to create the National Water 

Quality Inventory Report to 

Congress (305(b) report), which 

evaluates the status of water quality 

in the nation every two years. Data 

from STORET are also used to 

determine if a water body fails 

water quality standards and requires 

the development of Total Maximum 

Daily Loads (TMDLs). Due to 

inherent time delays in collecting, 

processing and 
February 2006 48 Naples Bay SWIM Reconnaissance 

incorporating data into databases, STORET and DBHYDRO are said to be up to 1 year behind on the 

inclusion of data from the County’s water quality sampling program. Also as a result of inherent time 

delays in collecting, processing and incorporating data in databases, flow and stage data handled by the 

SFWMD are roughly one month behind in DBYHDRO (Rhonda Watkins, Collier County, personal 

communication, Andy Potts, SFWMD, personal communication). SFWMD and FDEP monitoring 

stations locations in GIS data sets are shown in Figure 34 and 35. It should be noted that not all stations 

shown on the map are currently being sampled. The locations of the sampling sites might also differ from 

those shown on the maps due to error in data collection and processing. 

FFWCC 

FFWCC has sampling locations for the phytoplankton that causes red tide near the shoreline of Study 

Area and about 5 miles offshore (Figure 35). As of May 2005, only one sample, taken at Clam Pass, 

indicated a presence of Karenia brevis (less than 1001 cells per liter, 04/25/2005). The sample locations 

offshore from Clam Pass and from the southern tip of the Study Area report up to a ‘medium’ amount of 

Figure 33. FDEP IWRM Network Sampling Locations. 
February 2006 49 Naples Bay SWIM Reconnaissance 

Figure 34. Collier County, FDEP and FFWCC Water Quality Monitoring Stations (data sources: Collier 

County, FDEP, FFWCC, 2005). 
February 2006 50 Naples Bay SWIM Reconnaissance 

Figure 35. SFWMD Monitoring Stations (data sources: SFWMD, FDEP 2005).
February 2006 51 Naples Bay SWIM Reconnaissance 

the algae (1,000,000 cells per liter) during October and November 2004. Data are available for viewing, 

interactive mapping and download at http://ocean.floridamarine.org/mrgis/viewer.htm. 

Petroleum Storage Tanks and Hazardous Waste 

Petroleum storage tank facilities within the Naples Bay Basin are regulated by the Florida Department 

of Environmental Protection due to the potential for groundwater contamination. The facilities identified 

in Figure 36 and Appendix A5, are regulated petroleum storage tank facilities, which include above 

ground storage tanks greater than 550 gallons in volume, and underground storage tanks greater than 110 

gallons in volume. Also identified are petroleum storage tank facilities with confirmed discharges. These 

confirmed discharges may be caused by leaks or corrosion in the tank system, equipment failure, and 

operator error (i.e. overfilling of tank). Cleanup of contamination is required to be completed by the 

property owner under the supervision of FDEP. 

Hazardous waste generators within the Naples Bay Basin are regulated by the Florida Department of 

Environmental Protection due to the potential threat they pose to human health and natural resources. 

The facilities identified in Figure 36 and Appendix A5 include small quantity generators, conditionally 

exempt small quantity generators of hazardous waste, and non-handlers (used oil generator). The 

designation of small quantity generator includes facilities that generate between 100 kg – 1,000 kg of 

hazardous waste per month. Conditionally exempt small quantity generators of hazardous waste generate 

up to 100 kg of hazardous waste per month or less than 1 kg of acute hazardous waste. Acute hazardous 

wastes are substances that have been found to pose significant, irreversible harm to human health, such as 

arsenic and cyanide compounds. All small quantity and conditionally exempt small quantity generators 

of hazardous waste, as well as non-handlers (used oil generating facilities) are required to ensure proper 

disposal of their wastes through pick up by a licensed hauler for its eventual proper disposal or storage. 

The Basin has no large quantity generators, nor any treatment, disposal, or storage sites. 

Wastewater 

Wastewater generating facilities within the Basin are permitted by the FDEP. These facilities include 

domestic wastewater treatment facilities and industrial wastewater facilities (Figure 37 and Appendix 

A5). A number of these facilities are required to obtain a National Pollution Discharge Elimination 

System (NPDES) permit, administered through the FDEP, while some are not and are regulated solely 

under Florida Statutes. 

The domestic wastewater treatment plants generate secondarily treated wastewater that may be 

permitted to be disposed of in many ways including: surface water discharge; deep well injection; re-use 

(treated to a higher standard); intermittent surface water discharge; or a combination of these. 

Intermittent surface water discharge generally means the wastewater is contained within an isolated pond 
February 2006 52 Naples Bay SWIM Reconnaissance 

Figure 36. Petroleum Storage Tanks and Hazardous Waste Generators (data source: FDEP, Petroleum 

Contamination (PCT) and Statewide Coverage for Compliance and Enforcement Tracking of Hazardous Waste (CHAZ), 

August, 2005). 
February 2006 53 Naples Bay SWIM Reconnaissance 

Figure 37. Wasterwater Facilities (data source: FDEP, Statewide Coverage of Wastewater Facility Regulation 

(WAFR), August 2005).
February 2006 54 Naples Bay SWIM Reconnaissance 

and only reaches surface waters of the state through ground water seepage and transmission, or during a 

significant storm event. 

The industrial wastewater permits in the Study Area are for facilities such as concrete batch plant, 

reverse osmosis plants, an agricultural processing operation (tomatoes), and primarily discharge to 

groundwater through percolation ponds or deep well injection. Other types of discharge that occur to a 

lesser extent are: surface water discharge, and re-use. The wastewater discharged from concrete batch 

plants have elevated total suspended solids (TSS) generated from water runoff within the site. The 

wastewater discharged from reverse osmosis plants is high in total dissolved solids (TDS). 

The main contributor of secondarily treated wastewater to surface waters in the Study Area is the City 

of Naples Wastewater Treatment Plant, which is permitted to discharge approximately 2.4 mgd (annual 

average daily flow) to the Gordon River, with the remainder of its wastewater being disposed of through 

re-use. 

The Department of Environmental Protection through agreements with the Environmental Protection 

Agency, is working toward eliminating as many surface water discharges as possible, and has made 

considerable progress with this in the past several years. 

STUDIES 

Coastal Bays and Barrier Islands Ecological Conceptual Model 

Thomas, D. and D. Rumbold,. Unpublished. Coastal Bays and Barrier Islands Ecological 

Conceptual Model, US Fish and Wildlife Service. Vero Beach, Florida. Unpublished working 

paper. 

While this draft report is for planning purposes only and is not to be cited or quoted, it is being 

referred to here with permission from its authors. The modeling effort is being lead by Daryl Thomas, 

USFWS, and Darren Rumbold, SFWMD. The conceptual model includes Naples Bay, Estero Bay, and 

Rookery Bay. Baseline conditions are described, covering water quality and parameters of concern, as 

are habitat alteration and loss, and human use. It also addresses the following: 

• External drivers: climatic cycles and meteorological events, sea level rise, water management, 

urban, industrial and agricultural development 

• Ecological stressors/chemical or physical changes: altered hydrology and freshwater inflow, 

changes in water quality and increased contaminants, toxicants 

• Ecological attributes/biological indicators: community structure and function of algal bloom, 

benthic, wading and shore birds, fisheries, submerged aquatic vegetation, bivalve, mangroves, as 

well as the manatee population abundance, distribution, and health 

• Ecological effects/response: mangroves, manatees, fisheries, oysters, SAV and plankton, water 

quality 

• Hydrologic performance measures: adopted from the SWFFS

• Ecological performance measures: adopted from the SWFFS 
February 2006 55 Naples Bay SWIM Reconnaissance 

• Water quality performance measures: evaluation measures and assessment measurers are 

currently being developed by the SWFFS Water Quality Sub-team (see SWFFS Water Quality 

Strategy Document in Modeling and Plans section). 

Evaluation of Naples Bay Water Quality and Hydrologic Data. 

Taylor Engineering, Inc. 2005. Evaluation of Naples Bay Water Quality and Hydrologic 

Data. Prepared for South Florida Water Management District. Fort Myers, FL. 

Taylor Engineering used the Southwest Florida Feasibility Study ACCESS database framework to 

compile water quality data for Naples Bay and adjacent tributaries (Lely Canal, Haldeman Creek, Rock 

Creek, Gordon River, and Golden Gate Canal). Data were compiled from 1957 to 2003 for 150 of the 

155 stations representing several locations with the Naples Bay Basin and the Gulf of Mexico. Most of 

the samples were taken after 1985, though the data record became more consistent after 1999. 

Water quality conditions of concern within the Naples Bay Basin included both chemical and 

biological parameters. Dissolved oxygen, nitrogen, phosphorus, copper, iron, lead, and zinc exceeded 

state water quality standards in more than 10% of the sample sets and nutrient parameters also frequently 

exceeded nutrient criteria defined for Class III waters. Chlorophyll-a concentrations and fecal coliform 

counts were often elevated relative to the state or regional estuary criteria. Lower Naples Bay is 

occasionally less saline than normal, and dissolved oxygen concentrations have decreased slightly from 

1957 to 2003. Nitrogen has decreased since 1990. Upper Naples Bay did not exhibit the same change in 

nitrogen concentrations but total phosphorus has decreased since 1990. Dissolved oxygen standards were 

often not met. The less frequently sampled tributaries provide less data for examination. 

This study also had a goal of assessing the quality of data and to determine their utility in calibrating a 

water quality and hydrodynamic model for Naples Bay. The study concludes that existing data would 

allow limited model calibration, but an intensive calibration effort would require collection of more 

complete data. 

Compilation, Evaluation, and Archiving of Existing Water Quality Data for Southwest Florida. 

Tetra Tech, Inc. and Janicki Environmental, Inc. 2004. Compilation, Evaluation, and 

Archiving of Existing Water Quality Data for Southwest Florida. Department of the Army, 

Jacksonville District Corps of Engineers. Jacksonville, Florida. Contract No. DACW 17-02-

D-0009. 

This report is an extensive listing of water quality data available as of early 2004 throughout the 

entire Southwest Florida region. Each set of data is evaluated for quality and details about the sampling 

frequency and parameters tested are provided. The location of the data is also provided, with a large 

percentage in the DBHYDRO database. The data were used to identify areas for potential concern and 

gaps in important information. Three basins from the Tetra Tech study are incorporated either completely 

or partially in the Naples Bay Study Area: Basins 284, 302, and 306 (Figure 38). 
February 2006 56 Naples Bay SWIM Reconnaissance 

The term ‘verified concern’ was used to indicate that state standards were not being met, and the 

number of times a measure exceeded limits was in excess of the allowable occurrences. The term 

‘potential concern’ meant that the number of times a measure exceeded limits was close to the allowable 

occurrences. Basin 284 is identified as having waters of verified concern in the following areas: 

conductance, dissolved oxygen, fecal coliforms, excess iron and nutrients, total coliforms and unionized 

ammonium. Basin 304 is identified as having waters of verified concern in the following areas: fecal 

coliforms, excess nutrients and total coliforms. Basin 306 is identified as having waters of verified 

concern in the following areas: conductance, dissolved oxygen, fecal coliforms, excess iron and total 

coliforms and is identified as having waters of potential concern related to unionized ammonium. 

Data gaps in water quality parameters have also been identified in these three basins. Areas with 

insufficient data for these basins as defined by the Tetra Tech study are conductance, dissolved oxygen, 

fecal coliform, iron, total coliforms and unionized ammonium. Specifically, Basin 284 has no recorded 

data for mercury. Basin 304 has no recorded data for endrin, antimony, or thallium. Basin 306 has no 

Figure 38 Basins from the Tetra Tech Study (Tetra Tech and Janicki, 2004). 
February 2006 57 Naples Bay SWIM Reconnaissance 

Figure 39. FIU Sediment contaminant 

sample sites for Collier County in 2001-2002 

(FIU website).

data for mirex, radioactivity, bromoform, methylene chloride, carbon tetrachloride, flourene, 

hexachlorobutadiene, PCPs or trichloroethylene. 

There are 23 monitoring efforts included in the Tetra Tech study that have at least one sampling site 

within the Naples Bay Basin or the near offshore waters. Four additional monitoring efforts that pertain 

to the area were not included because either 1) the source is an unverified lab or 2) data were only 

available in hard copy. A summary of these monitoring efforts, including sampling parameters, dates and 

location, is presented in Appendix A6. 

Effects Of Increased Urban And Agricultural Landuse On The Anthropogenic Loading To 

Southwest Florida Estuaries 

Gardinali, P., Y. Cai, R. Jaffe and J. Boyer. 2002. Effects of Increased Urban And 

Agricultural Landuse On The Anthropogenic Loading To Southwest Florida Estuaries. Final 

Report Prepared for Environmental Services Division, Pollution Control Department, Collier 

County, Florida Grant # 579901900. SERC TECHNICAL REPORT T-191 Revision 1 

The purpose of this study was to assess 104 common organic contaminants and metals in surficial 

sediments along the coast of Collier County (see Appendix A7 for complete list). Eight sites were 

sampled in the Naples Bay Basin. Testing was conducted twice – May-June 2001 and December 2002. 

Sample site’s (Figure 39) were chosen from low energy depositional areas with a high accumulation of 

fine particles so that low concentration levels would still be possible to detect using protocols from 

NOAA’s Status and Trends Program as described in NOAA Technical Memorandum 

NOS/ORCA/CMBAD 130 (Lauenstein and Cantillo, 

1998). Results from this test were compared to testing 

completed by Grabe in the early 90s (1996, 1993, 1990). 

The Naples Bay station near the US-41 Bridge 

(CC04) had PAH concentrations exceeding more than 

half of the Threshold Effects Levels (TEL) for individual 

PAH groups present. The most likely source for this sites 

PAH loading was determined to be from vehicular and 

boat traffic. Five of the sample sites exceeded TELs for 

several other contaminants: Naples Bay/Gordon River at 

the US-41 Bridge (CC04), just north of the bridge 

(CCX04), Wiggins Pass (CC05), mid Naples Bay 

(CCX06) and the north end of Keewaydin Island 

(CC465). Specific contaminants for these sites are 

presented in Appendix A7. 

A more intensive site specific survey was 

recommended for Naples Bay and the Gordon River area 
February 2006 58 Naples Bay SWIM Reconnaissance 

and proposed locations for testing were provided. Additional details about contents for this report are 

listed in Appendix A7. 

Effects of Water Control Structures on Estuaries. 

Savarese, M., L.P. Tedeso, M.S. Shirley, G.Filippelli, S.M. Bush, H.E. Stoffel. 2002. 

Restoring Estuarine Habitat Quality: Effects of Alternative Types of Water Control Structures 

on Freshwater Inflow, the Distribution of Non-point Source Pollutants, and the Dispersal of 

Non-Indigenous Species. National Oceanographic and Atmospheric Administration. 

Washington, D.C. 

The purpose of the study was to investigate the relative influences that three different weir designs 

and water release practices have upon estuarine habitats. Three Collier County systems were studied; the 

Faka-Union, Henderson Creek, and the Cocohatchee River, with the unmanaged Blackwater River used 

as a control comparison. Estuarine habitat quality upstream and downstream from each water control 

structure was evaluated by 1) monitoring sedimentological changes; 2) measuring the concentration of 

trace, minor, and major metal and organochlorine contaminates in sediments; 3) estimating the abundance 

and size distribution of salinity-sensitive macroinvertebrates; 4) estimating the abundance of exotic fish; 

and 5) comparing water quality (principally salinity, dissolved oxygen, and primary productivity as 

measured by chlorophyll concentration). Methods used and resulting data are presented in detail. It was 

concluded that it is the “simple design and lack of dynamic control of water release that is potentially 

detrimental to estuarine health”. The timing and rate of salinity change should be controlled such that 

“pulses of freshwater are avoided” and biological organisms are able to accommodate the change. 

Results will influence design modifications for the fixed-crest weir retrofit planned at the headwaters of 

Henderson Creek to improve the timing and quantity of freshwater to Rookery Bay. Long term 

monitoring is planned by the Reserve for design evaluation. This study provides input for designing 

modifications to existing canal control structures or new canal control structures throughout the Naples 

Bay Basin. 

Environmental Impact Statement On Improving the Regulatory Process in Southwest Florida, 

Lee and Collier Counties, Florida. 

U.S. Army Corps of Engineers, U.S. Fish and Wildlife Service and U.S. Environmental 

Protection Agency, 2000. Environmental Impact Statement on Improving the Regulatory 

Process in Southwest Florida, Lee and Collier Counties, Florida. USACOE. Jacksonville, 

Florida. Revised 2005. 

This EIS for Southwest Florida was primarily prepared to propose new procedures for permitting 

wetland impacts. These procedures were designed to provide a more holistic approach to permitting, 

reviewing all of the natural resources in a watershed with specific criteria dependent upon overall 

condition. Ecological parameters such as species management and landscape configuration were the 

primary focus, but water quality was also considered. Early data collected in USEPA and FDEP studies 

were analyzed for the entire area, and the areas relevant to the Naples Bay Study Area are summarized 

below. 
February 2006 59 Naples Bay SWIM Reconnaissance 

Historical STORET water quality data from 1980-1989 was used to summarize conditions for the 

Golden Gate Canal. Values and interpretations in the EIS are listed below. 

• Relatively low turbidity (3.5-4.3 NTUs) 

• Low TSS (2-3 mg/L) 

• Higher color content than average (50-99 PCUs) 

• Neutral pH 

• Low to moderate levels of DO (4.8-6.0 mg/L) 

• Conductivity higher than average (572-650 micromhos) 

• BOD exceeded State standards ( 2.4 mg/L at one canal sample location) 

• Chlorophyll a higher than average (19 mg/L) 

• Fecal coliform bacteria lower than average (55 MPN/100 ml) 

• TN and TP lower than average ( 0.81-1.07 and 0.02- 0.03 mg/L respectively) 

• WQI ranged from 36 to 40, an indication of “good” water quality 

Another compilation of water quality data from all available organizations within the Study Area was 

completed and WQIs were calculated by decade (1970-1979, 1980-1989, and 1990-1998) and 

approximate 55.5, 59.4, and 60.0, respectively for the Golden Gates Canal Basin indicating an increasing 

degradation in water quality. DO, BOD and fecal coliform were determined to be the cause of the 

degradation. 

STORET data from 1989 was also used to describe water quality for Naples Bay. 

• Near average turbidity (3.6-4.5 NTU/NTUs) 

• Slightly better than average color (40-80) 

• Low DO observed at two sample locations (4.5 to 6.0 mg/L) 

• Low Chlorophyll a, (6-7 mg/L) 

• TN exceeded screening levels (1.31 mg/L) 

• TP exceeded screening levels (0.10 mg/L) 

Very little historical or current water-quality data were available for the Lely Area, formerly known 

as Water Management District 6 Basin; however, an appendix in the report provides a summary of the 

water quality from the STORET database by decade. No overall summary was included for this basin, 

but records indicate low DO (average 5.1 mg/L), BOD exceeding screening level in 1990-1998 summary 

(3.56 mg/L), and fecal coliforms exceeding screening levels since 1980 (average of 710 MPN/100 ml). 

The majority of this EIS dealt with ecological issues of concern, and is therefore more fully summarized 

in Section 6 of this reconnaissance report. Details for relevant information can be found in Appendix A8. 

Five future landscapes (called “Ensembles”) were created that suggested different locations of 

development and different criteria for the permitting of developments and were used to propose an 

alternative procedure for reviewing wetland permits. The EIS proposed a set of standardized natural 

resource criteria be used in reviewing permit applications in Southwest Florida, called the Permit Review 

Criteria (Appendix H of the EIS). Anticipated future uses where a project may have a high potential for 

adverse effect were shown on the companion Natural Resources Overlay Map. Each application would 

then be evaluated using the criteria and evaluations suggested in the EIS applicable to the important 

resources found in that area. 
February 2006 60 Naples Bay SWIM Reconnaissance 

The sub-area pertinent to the Naples Bay Study Area is included in “Zoom C” defined to the west by 

the Gulf of Mexico and to the east by the Faka-Union Canal, Miller Boulevard, Winchester Strand, and 

Big Corkscrew Island. 

The Corps determined that seventeen listed fauna occurred in the Study Area that could be most 

affected by the proposed new procedures for permitting wetland impacts, although there were 23 species 

in Southwest Florida on the USFWS list and 45 on the FFWCC list. These species included the American 

crocodile, Eastern indigo snake, Florida scrub-jay, bald eagle, wood stork, red-cockaded woodpecker, 

piping plover, Audubon’s crested caracara, Everglades snail kite, Florida panther, West Indian manatee, 

and the Loggerhead, Hawksbill, Green, Leatherback, and Kemp's Ridley Sea Turtles. 

An Integrated Surface Water Quality Monitoring Program for the South Florida Coastal 

Waters 

Jones. R. and J. Boyer. 2000. An Integrated Surface Water Quality Monitoring Program for 

the South Florida Coastal Waters. Southeast Environmental Research Center, Florida 

International University. Miami, Florida. 

The Integrated Surface Water Quality Monitoring Program is a long term annual water quality 

(nutrient) sampling program with a grid of sites throughout coastal waters in south Florida. There are two 

sites in the Naples Bay Study Area: one in Naples Bay at Gordon Pass (Site 464) and one in the Gulf of 

Mexico just west of Gordon Pass (Site 465). These sites have been sampled since 1999 and annual 

reports issued since 2000. Data and annual reports through 2004 are available at 

http://serc.fiu.edu/wqmnetwork/SFWMD-CD/index.htm. 

This program monitors 12 components monthly: salinity, temperature, dissolved oxygen, ammonium, 

nitrate, total phosphorus, soluble reactive phosphate, chlorophyll a, alkaline phosphatase, total organic 

carbon, total organic nitrogen and turbidity. Summary reports combine the results from both Naples sites, 

but the raw data are also available for each individual site (Figures 40 and 41). Details for the 2000 report 

and the website are provided in Appendix A9. 

Figure 40. Salinity graph for data available for one of the sampling sites within the Naples Bay Study Area 

Site 464 to the east of Gordon Pass (FIU website).
February 2006 61 Naples Bay SWIM Reconnaissance 

Figure 41. Dissolved oxygen graph for data available for one of the sampling sites within the Naples Bay 

Study Area – Site 464 to the east of Gordon Pass (FIU website). 

Data from this study show no statistically significant trends in dissolved oxygen or nutrient 

concentrations within the water column for the two sites within Naples Bay between 1999 and 2005. 

However, both sites exhibit a small decline in DO, almost no change in nitrogen, a decline in TP and high 

seasonal variability in chlorophyll concentrations. 

Big Cypress Basin Water Quality Monitoring Report: 1979 – 1988 

Grabe, S. 1989. Big Cypress Basin Water Quality Monitoring Network Report: 1979 – 1988. 

Big Cypress Basin Board South Florida Water Management District. West Palm Beach, 

Florida. 

This study presents water quality monitoring completed between the Naples Bay Study and work 

included in the Tetra Tech compilation. It is specific to Collier County and has four sites of interest to the 

Naples Bay Study Area: Gordon River above the Golden Gate Canal (GGC), GGC at Airport-Pulling 

Road, GGC at CR951, and the upper Lely Canal (Table 5). Parameters evaluated include nutrients and 

bacteria (monthly) and metals (biannually). The report focuses on statistical analysis of variance 

between overall annual averages for the entire area sampled. The report’s appendix provides data by 

station, however, it is averaged over the entire sampling period (January 1979 – September 1988), and 

therefore neither trends nor seasonal variance can be reviewed. A brief summary of results relevant to the 

Naples Bay area is provided in Table 5. 
February 2006 62 Naples Bay SWIM Reconnaissance 

Table 5. Brief summary of water quality data for four stations, means for 1979-1988. 

Naples Bay Study 

Simpson, B., R. Aaron, J. Betz, D. Hicks. J. van der Kreeke, B. Yokel, 1979. The Naples Bay 

Study. The Collier County Conservancy. Naples, Florida. 

This report presents detailed field studies evaluating the condition of Naples Bay and the effect of the 

residential canals connected to the Bay. Most of the sampling spanned a year between November 1976 

and November 1977 with some follow-up bacterial work from September 1977 through February 1978. 

This body of work summarized: legislation; the currents and flows in both the Bay and canals; 

construction details for residential canals; bacterial, physical and chemical conditions in water 

Parameter measured GGC at AirportPulling GGC at CR951 Gordon River Lely Canal 

Temp, C 24.9 25.1 24.0 26.1 

DO, mg/l 5.1 4.6 3.0 6.6 

Conductivity, umhos/cm 572.2 547.8 1957.5 1389.7 

pH 7.4 7.4 7.4 7.6 

TKN, mg/l 1.1 1.0 1.2 1.1 

TP, mg/l 0.03 0.02 0.07 0.03 

Turbidity, NTU 4.4 4.7 3.5 3.7 

Fe, mg/l 0.78 1.03 0.18 0.46 

TSS, mg/l 3.6 6.7 4.9 4.3 

NO3, mg/l 0.07 0.04 0.11 0.02 

NO2, mg/l 0.007 0.005 0.010 0.005 

NH4, mg/l 0.05 0.04 0.07 0.04 

OPO4, mg/l 0.011 0.009 0.033 0.005 

Cl, mg/l 39.1 26.0 638.0 611.6 

SO4, mg/l 35.0 31.9 139.3 115.8 

Color 84.9 98.6 57.2 49.1 

Ca, mg/l 102.7 99.8 99.7 104.5 

Mg, mg/l 4.2 3.4 19.5 18.1 

Na, mg/l 20.3 12.4 150.7 125.7 

K, mg/l 1.2 0.7 6.9 4.5 

As, ug/l 7.2 6.6 11.2 8.1 

Cd, ug/l 0.70 0.61 0.45 1.65 

Cu, ug/l 4.8 2.3 4.0 3.4 

Hg, ug/l 0.81 0.76 0.91 0.87 

Pb, ug/l 2.6 3.3 3.4 4.3 

Zn, ug/l 49.2 45.8 33.1 23.2 

CaCO3, alk, mg/l 219.1 223.3 206.7 206.9 

Chl a, ug/l 3.7 5.2 2.4 17.4 

Fecal, max, #/100 ml 28 16 205 219 

Strep, max, #/100 ml 10900 2880 370 64 

Total coliform, max, 

#/100 ml 

10 26 62 18 
February 2006 63 Naples Bay SWIM Reconnaissance 

Figure 42. An example of water quality data 

presented graphically in the Naples Bay Study 

(Simpson et al. 1979). 

and sediment; and the benthic, midwater and surface 

fauna present. Methods are well documented and 

results, including statistical analysis, are extensive, 

presented in both tabular and graphical formats 

(Figure 42). 

A total of 24 sites were chosen spanning from 

Gordon Pass at the southern boundary up to the 

Golden Gate Canal Dam at the northern boundary. 

Two additional sites in Dollar Bay were chosen as 

reference sites. Twelve of the locations are in 

residential canals, one is in Gordon Pass, four are in 

Naples Bay, three are in Haldeman Creek, two are in 

Rock Creek, one is in the Gordon River and the last is 

at the Golden Gate Dam. In addition, a schematic 

drawing of the waste water collection and drainage 

system in 1977 is provided in Appendix F of the 

Naples Bay Study. 

A legal analysis of federal, state and local 

regulations related to water quality, construction, 

ownership and management, and permitting is 

included, although much of this legislation has been 

modified since. The study concluded that the canals in 

Naples Bay were constructed on highly permeable soil 

without lining and using drag lines and suction, two of 

them deep enough to breach the shallow aquifer. A silting study was not done; a study on similar canal in 

Marco Island was used as reference (Wanless, 1994). 

Street runoff and storm water drainage were main nitrogen sources, while the Naples sewage 

treatment facility was identified as the primary phosphorus source. Freshwater drainage from Golden 

Gate was considered a low nutrient runoff input and acted as a diluting agent during otherwise high 

nutrient input periods, curbing algal bloom persistence in Naples Bay. However, Golden Gate runoff was 

the primary source of organic matter loading. 

Overall respiration was greater than productivity in Naples Bay throughout the year, except April and 

May. This coincided with the driest part of the sample year and periods of only slight salinity 

stratification. In general dissolved oxygen less than 4 ppm occurred for prolonged periods in the deadend canals. Low DO occurred in the Bay and river during periods of high freshwater input leading to 

severe salinity stratification. Respiration was about 30% greater in canals than the Bay, overall. 
February 2006 64 Naples Bay SWIM Reconnaissance 

In the upper Study Area near the outfall from the sewage treatment plants, 35 to 65% of collected 

samples exceeded state fecal coliform standards. Urban runoff was the main cause of bacteria in the 

lower reaches with fewer exceedance violations than the upper reaches. Mean fecal coliform values at 5 

stations tested prior to this study (1970) were significantly higher in the 1977 testing in this study, as 

much as 10 times higher at three sites. Three of the sampling sites did not meet the body contact limit 

during any of the eight sampling times, three sites met the limit once, and only one of the sites met the 

limit for six out of eight samples. The Naples Land Yacht Harbor was the most polluted with coliform. 

Excess freshwater discharge eliminated or displaced a high percentage of typical fauna communities 

from June to October. Because of this, Gordon River exhibited lower catch and occurrence of recurrent 

benthic groups and animal diversity than the control area in Dollar Bay. The Naples Bay canals had 

lower diversity than Naples Bay but slightly higher catch results, but were still below Dollar Bay results 

for the same measures. Loss of benthic species in the canals appeared to be due to salinity stratification 

and reduced flushing leading to low DO in the deeper portions of the canals. 

The graphs in Figure 42 represent typical graphical presentations of data in the report. Details about 

the format of the report and the location of different data are presented in Appendix A10. 

The study demonstrated that the main source of freshwater in the system was from the Golden Gate 

Canal with as much as 1500 cfs during September, 1977, while the combined contributions of Halderman 

Creek, Rock Creek and Gordon River were estimated to be 100 cfs. Dye studies were conducted to 

determine the flushing times in eight canals typical of other canals in the area. A hydrography model for 

Naples Bay was simulated with tidal ranges and current magnitudes accurately predicted, but with a 30 to 

60 minute time lag in flooding results. In addition, a schematic drawing of the waste water collection and 

drainage system in 1977 is provided in Appendix F of The Naples Bay Study. Details about the format of 

the report and the location of different data are presented in Appendix A10. 

MODELING AND PLANS 

SWFFS Water Quality Strategy Document 

SWFFS. 2003. SWFFS Water Quality Strategy Document. Southwest Florida Feasibility 

Study Water Quality Sub-team. USACE, Jacksonville, Florida. 

Within the context of the Comprehensive Integrated Water Quality Feasibility Study, (CIWQFS), 

objectives were developed by the WQ Sub-team to ensure that the SWFFS fulfills its role in restoring 

water quality. This plan outlines recommendations made by the Southwest Florida Feasibility Study 

Water Quality (WQ) Sub-team as a basis for further discussion of water quality guidelines for alternatives 

evaluation. Given the limited information available, a process for developing a stratified or tiered 

approach for evaluation of the incremental benefits and costs in comparing alternatives was developed. 

Below is a much simplified version of this process which is subject to re-evaluation: 
February 2006 65 Naples Bay SWIM Reconnaissance 

• Compile all available WQ data into a single preferred data set (this was achieved through the 

Tetra-Tech report and its associated Access dataset) 

• If needed for alternatives analysis, formulate a plan with the goal of achieving the necessary level 

of WQ 

• Where a proposed alternative has a hydrologic focus: 

o Assess alternative for potential adverse WQ impacts 

o Identify and quantify possible WQ improvements, including credits to Environmental Quality 

(EQ) account 

o Optimize the proposed alternative to take full advantage of opportunities for WQ 

improvement 

o Develop a multipurpose alternative that achieves WQ restoration targets 

• Review other WQ initiatives within the Study Area (e.g., CERP Projects such as C43 Basin 

Storage Reservoir (BSR) and ASR Pilot; TMDLs; SWIM Plans) to assess consistency or conflict. 

To this end, the Sub-team is currently reviewing regional plans and studies for findings and 

recommendations on WQ needs. 

Two sets of performance measures were developed; 1) assessment measures, used for real responses 

and 2) evaluation measures, which predict the performance of a given alternative (Tables 6 and 7). This 

document focuses on the rationale for selecting evaluation measures and the development of water quality 

goals. The use of evaluation measures will be constrained by the availability of modeling tools, including 

data. 

Table 6. Assessment WQ Performance Measures for SWFFS. 

Assessment Performance Measure Target

Dissolved Oxygen (DO) Project/indicator region specific 

Specific Conductance Project/indicator region specific 

Salinity Project/indicator region specific 

Turbidity/ TSS / Color Maintain or reduce to levels that support healthy flora and fauna. 

Photosynthetically Active radiation (PAR) / 

secchi disc depth 

Maintain or increase to levels that support healthy flora and 

fauna. 

Chlorophyll a (Chl a) Maintain or reduce to levels that support healthy flora and fauna. 

Total Nitrogen / Ammonia Nitrogen / Total 

Kjeldahl Nitrogen / Nitrate / Nitrite / Dissolved 

inorganic nitrogen 

Maintain or reduce loads and concentrations to support healthy 

flora and fauna. 

Total Phosphorus / Orthophosphate/soluble 

reactive phosphorus 

Maintain or reduce loads and concentrations to support healthy 

flora and fauna. 

Chloride Project/indicator region specific 

Sulfate Project/indicator region specific 

Silica Project/indicator region specific 

Pesticides Project/indicator region specific 

Trace Metals Project/indicator region specific 

The performance measures were developed through WQ Sub-team meetings, review of others’ 

performance measure-related information, and previous assessments within the study boundary. They are 

scientifically based and the result of applying research findings, literature information, and best 

professional judgment. Atmospheric loading and metals are intended to be included as well. Salinity as a 

restoration target and ecological assessment performance measures (secondary response variables such as 
February 2006 66 Naples Bay SWIM Reconnaissance 

SAV and fish) will be discussed in the SWFFS. An evaluation protocol that recognized the uniqueness 

and diversity of the study was culled from multiple guidelines and approaches. It addresses: 

concentrations within water quality treatment areas, concentrations within receiving waters, and 

downstream loading to “waters to be restored”, and concentrations in ‘waters to be restored”. 

Given that SWIM plans and TMDLs have not been established within the Study Area, if pollutant 

load reduction targets follow the FDEP load reduction and abatement assessment for the C-43 basin are 

deemed appropriate by the Sub-team, they may be adopted. Other tools that may be used to set load 

reduction targets are the Estero Water Quality model (DHI under contract to Lee County) and other 

regional plans and studies. 

 Table 7. SWFFS WQ Sub-Team Evaluation Performance Measures.

Evaluation Performance Measures

Dissolved Oxygen (DO) 

Salinity (PSU, see hydrologic targets) 

Turbidity / TSS 

Photosynthetically Active radiation (PAR) / Color 

Chlorophyll a (Chl-a) 

Total Nitrogen (TN) 

Dissolved inorganic nitrogen (DIN) 

Soluble Reactive Phosphorus (SRP) 

Total Phosphorus (TP) 

The type of model used to forecast a systems response is considered. Pending the development of 

TMDLs, the Sub-team recommends alternatives evaluation be based, in part, on the reduction in annual 

nutrient loads as a percentage of current loading. The debate over load or concentration as a management 

objective is described. 

It is recommended that an evaluation measure be developed for specific waterbody types in “waters to 

be restored” that addresses target concentrations for a typical dry season. The frequency, duration, and 

magnitude that a constituent exceeds target concentrations should be minimized. 

City of Naples Basin V Stormwater System Improvement Plan Phase I: Basin Assessment and 

Conceptual Improvement Plan 

Camp, Dresser and McKee. 2004. Basin V Stormwater System Improvement Plan Phase I: 

Basin Assessment and Conceptual Improvement Plan. Draft Interim Report. City of Naples. 

Naples, Florida. 

This report is the first of three phases in an effort to document the current Basin V storm water 

system, recommend alternatives and provide design for these alternatives. The second and third phases 

(preliminary and final designs) were not authorized at the time of this draft. The Study Area was 

approximately bounded by Goodlette-Frank Road to the east, US 41 to the west, Ridge Street to the north 

and 6th Avenue North to the south. The first phase presented in this report included data compilation and 

evaluation using data provided by the City of Naples, and resulted in maps and identification of additional 

surveys required for complete assessment. Water quantity models were also simulated, similar to models 
February 2006 67 Naples Bay SWIM Reconnaissance 

from the Gordon River Basin Extension Modeling (Wilson Miller, 2001) and using the same modeling 

parameters, but further delineated into a larger number of smaller hydrologic units and with additional 

junction nodes and conduits. The model was calibrated for four significant rain events: late September 

2003, Tropical Storm Floyd in September 1999, early October 1995, and Tropical Storm Jerry in August 

1995. 

Overall, the model was determined to provide a reasonable match to actual events with predicted peak 

stages within 0.1 ft across the entire basin, and simulation results were used to determine the Level of 

Service provided for all units and junctions in the modeled area. Level of Surface (LOS) was divided into 

four classes defined by amount of flooding protection with A as the highest level of protection (no 

flooding in roads, yards or buildings) and D as the lowest level of protection (extensive road and building 

flooding predicted). For a 5 year/24-hr event, 64% of the Basin received Class A protection and 10% 

received Class D LOS. Results for all junction points are listed in Table 5-1 of the CDM draft. The 

Existing System LOS Evaluation-Comparison to Reported Flooding Problems (Table 5-3, CDM draft) 

and other details of this report are in Appendix A11. 

The Southwest Florida Feasibility Study (SWFFS) 

U.S. Army Corps of Engineers and South Florida Water Management District, 2002. Central 

and Southern Florida Project Management Plan: Southwest Florida Feasibility Study. 

USACOE. Jacksonville, Florida. 

The SWFFS is one of a series of feasibility studies recommended in the Comprehensive Everglades 

Restoration Plan (CERP). The project boundary corresponds to the SFWMD Lower West Coast Water 

Supply Plan (LWCWSP) planning area. This includes most of Collier County, including Naples and 

Golden Gates Estates. The Project Management Plan (PMP) for the SWFFS is complete. Preliminary 

alternatives have been formulated and analytical methods and tools have been determined. 

“The purpose of the study is to determine the feasibility of making structural, non-structural, and 

operational modifications and improvements in the region in the interest of environmental quality, water 

supply, and other purposes. The SWFFS will develop a comprehensive regional plan of action to address 

the health of aquatic and upland ecosystems; the quantity, quality, timing, and distribution of water flows; 

agricultural, environmental, and urban water supply; the sustainability of economic and natural resources; 

flood protection; fish and wildlife; biological diversity; and natural habitat.” (USACE and SFWMD, 

2002) 

An inventory of public concerns, developed during several public workshops is listed in the PMP. 

Planning objectives include: 

• Conserve and protect water resources to ensure sustainability of economic and natural resources. 

• Ensure availability of ground and surface water supplies for agricultural, environmental, and 

urban uses. 

• Improve and protect quality, heterogeneity, and natural biodiversity in freshwater, upland, 

estuarine, and marine ecosystems. 
February 2006 68 Naples Bay SWIM Reconnaissance 

• Improve quantity, quality, timing, and distribution of freshwater flows to estuaries and wetlands. 

• Protect and improve water quality conditions within the Study Area. 

• Protect and recover listed species. 

• Reduce flood damages within the Study Area. 

A brief description of the general types of structural and non-structural features that may be used to 

formulate alternatives is given. They are: 

• Surface water storage 

• Improve Water Deliveries to Estuaries 

• Aquifer Storage and Recovery 

• Stormwater Treatment Areas 

• Reestablish Sheetflow 

• Reuse Wastewater 

• Conservation 

• Land Acquisition 

• Rehydration of Wetlands 

• Operational Measures 

Big Cypress Basin Integrated Hydrologic-Hydraulic Model 

DHI Inc. 2002. Big Cypress Basin Integrated Hydrologic-Hydraulic Model. South Florida 

Water Management District. West Palm Beach, Florida. 

This BCB project explored the value of an integrated MIKE SHE/MIKE11 model for the western Big 

Cypress Basin for assessment of the impact of various water management strategies on flood dynamics, 

wetland hydro-periods and water supply. The primary objective was to model flood levels, peak flows 

and wetland hydro-period. The main scenario was the model of the hydrologic restoration of the Southern 

Golden Gates Estates wetland, which is peripheral to the Naples Bay Study Area. However, two other 

water management scenarios were tested that either directly or indirectly affect Naples Bay: a canal 

extension from Golden Gate Main to Henderson Creek with the intention of diverting water to Henderson 

Creek and flow diversion from Corkscrew Canal to Golden Gate Main. 

The Big Cypress Basin model was determined capable of simulating historic records of water levels 

and flows in the BCB watershed from 1990-1995 within predefined target criteria. However, the scenario 

related to diversion of GGC wet season flow to Henderson Creek showed that the new channel with 

chosen channel and structure geometry would not have the intended effect. Diversion from Corkscrew 

Canal to Golden Gate Main resulted in considerably increased flow. Since Golden Gate Canal water is 

now drained into Naples Bay, this diversion without the Henderson Creek diversion working properly 

would result in additional excess freshwater input to Naples Bay. Details of this report are summarized in 

Appendix A12. 
February 2006 69 Naples Bay SWIM Reconnaissance 

Five Year Plan -- 2002-2006 For The Big Cypress Basin of The South Florida Water 

Management District 

BCB-SFWMD. 2002. Five Year Plan -- 2002-2006 For The Big Cypress Basin of The South 

Florida Water Management District. Big Cypress Basin Board South Florida Water 

Management District. West Palm Beach, Florida. 

This report provides details related to the canals and control structures considered to be under the 

control of the BCB in an agreement with Collier County extending through 2011. Information about 

proposed capital improvements and projects related to improved data acquisition is provided in tables on 

pages 18, 22, 23 and 51 with maps of locations on pages 15 and 52. Sites of interest to the Naples Bay 

Study Area include modernization of the meteorological station at The Conservancy and the surface water 

hydrological data stations on the Golden Gate Canal, Haldeman Creek, Corkscrew Canal, Cypress Canal, 

Gordon River and the I-75 canal. A meta-database of research and monitoring activities at these sites is 

publicly accessible at: http://library.fgcu.edu/big_cypress. Most of these stations should already be in 

place. 

Capital improvements relevant to Naples Bay include a retrofit to Golden Gate #1 and Airport Road 

South weirs and improvements to Corkscrew and Golden Gate canals. The Plan has considered one water 

management strategy to divert a portion of the peak flows from the Golden Gate Canal to the Henderson 

Creek Canal. The implementation of this plan will involve construction of a diversion channel that will 

convey flow from the Golden Gate Main Canal segment east of CR 951 through a culvert under I-75, 

southward to the Henderson Creek Canal. The Corkscrew Canal and its side ditches including the Curry 

Canal comprise a network of poorly drained canals that provide an interbasin transfer of water from the 

Corkscrew-Cocohatchee Basin to Golden Gate Canal Basin. In FY02, additional drainage improvement 

work, including replacement of six culverts, was coordinated with Collier County. This drainage network 

currently affects Naples Bay through drainage of the Golden Gate Canal (GGC). However, with 

completion of the extension between the GGC and the CR951 canal, much of this extra water will be 

diverted to Henderson Creek. Much of this work should have already started, with completion after 2006. 

The diversion of water may decrease the effective size of the Naples Bay Basin. The management plan 

also proposes the development of a hydrodynamic and water quality model for the estuary to track the 

impact of changes in freshwater and nutrient loads on the estuary. 

BCB Region Science Plan 

Rookery Bay National Estuarine Research Reserve and Florida Department of Environmental 

Protection. 2002. Region Science Plan: Big Cypress Basin - Estero Bay, Southwest Florida. 

Rookery Bay National Estuarine Research Reserve. Naples, Florida. 

The Region Science Plan for Big Cypress Basin Southwest Florida is a compendium of individual 

project recommendations for studies, monitoring or improvements related to biodiversity, water quality 

and hydrogeology and recommended efforts to improve information management. These projects were 

submitted by several state and federal agencies in an effort to identify data gaps and to prioritize funding 

needs with individual forms supplying an estimated cost, problem statement and project synopsis. The 
February 2006 70 Naples Bay SWIM Reconnaissance 

report is still in draft form. Most of the suggestions were generic to the entire BCB region, but several 

applied to the Naples Bay Study Area. These projects are summarized in Table 8 and represent potential 

data gaps or opportunities for future work. Some of these projects have already been implemented. 

Notes from the initial effort in 1997 are also included in this report (BCB Science Plan: Issues 

Characterization Workshop) but are not summarized here. 

Table 8. Projects from the Region Science Plan for BCB Southwest Florida of potential relevance to Naples 

Bay SWIM plan. 

Project category and title Project 

number 

Biodiversity: BCB region land acquisition map; Impacts of canal/lake management activities on 

fish and wildlife in the BCB; Review of cumulative and secondary impacts in the BCB; BMPs for 

fish and wildlife conservation on agricultural operations 

1, 5, 7, 8, 21 

Water quality: Evaluation of regional historical water quality data; minimum flow requirements for 

estuaries in the BCB; Regional groundwater constituent survey; Ambient stormwater monitoring 

and evaluation; Bioassays to assess impact of agricultural chemicals in freshwater habitats 

31, 32, 33, 

34, 35, 38 

Hydrogeology: Development of BCB region/subregion water budget 42, 43, 44, 

45, 49, 53, 

50, 52 

Information management: Summary reports on state of the BCB region; GIS map component from 

the BCB Database; BCB Water Quality Monitoring Consortium 

57, 58, 59, 

60 

Gordon River Extension Basin Study, Phase IV 

Wilson Miller and Camp, Dresser & McKee. 2001. Gordon River Extension Basin Study, 

Phase IV, Preliminary Technical Memorandum. Collier County Stormwater Management 

Department. Naples, Florida. 

The goal of this modeling study was to identify regional alternatives to improve flood protection, 

surface water quality and groundwater recharge. This report covers Phase IV of a seven phase project. 

Phases I through III covered data collection in existing drainage along main channels. Phase IV modeled 

existing conditions and three alternatives, and includes extensive detail about water quality and 

hydrology, existing and modeled results. Two storm events were modeled: 25 and 100 year events, both 

for 72 hours (Figure 43). 

The area covered in the modeling was divided into eight reaches beginning at the northwest corner of 

Pine Ridge Industrial Park and ending at the tidal outfall of the Gordon River. The reaches also include 

the Goodlette-Frank road ditch, and tributaries through and next to four golf courses. The graphics on the 

following pages illustrate the eight reaches modeled, and the problem areas identified for a 25 year, 3 day 

event (Figure 44). 

The water quality component used a model developed for USEPA (EPA-841-R-92-002) based on 

concentrations typical for the aggregated land use categories and evaluated 12 pollutants: BOD5, COD, 

TSS, TDS, TP DP, TKN, NO2+NO3, Pb, Cu, Zn and Cd. There is no attempt to compare water quality 

model results to actual data, and comparisons to established PELs and TELs are not offered. Predicted 

pollutant loads are provided for each reach evaluated. 
February 2006 71 Naples Bay SWIM Reconnaissance 

The water quantity component of the simulation used EPA models RUNOFF and EXTRAN for 

hydraulic components and typical infiltration and overland flow equations for sheet flow. An extensive 

inventory of channel parameters and hydrological properties for the hydrological units modeled was 

presented. Further, a summary of tidal stillwater elevations was provided along with a review of a 1986 

FEMA flood insurance study and a listing of identified flood areas as of May 2001. 

Model results were a reasonable match in 9 out of 12 locations and for overall timing. Simulation of 

a 25 year, 3 day design storm event identified 13 areas of flooding and a 100 year, 3 day storm event 

found three additional areas of flooding. A more detailed summary of this report’s water quantity 

contents is listed in Appendix A13. 

Big Cypress Basin Watershed Management Plan: Hydrologic Hydraulic Assessment for 

Golden Gate Canal Watershed Improvements Phase I – Retrofit of Golden Gate Canal 

Weir Number 1 

BCB-SFWMD. 2001. Big Cypress Basin Watershed Management Plan: Hydrologic Hydraulic 

Assessment for Golden Gate Canal Watershed Improvements Phase I – Retrofit of Golden 

Gate Canal Weir Number 1. Big Cypress Basin Board South Florida Water Management 

District. West Palm Beach, Florida. 

Between 1985 and 2001, BCB modified ten water control structures in the Golden Gate Main Canal 

for better management of water supply. Despite these modifications, excessive freshwater was still being 

discharged into Naples Bay. This report provides recommendations for installation of an automated, 

gated spillway with three hinged crest gates. Differences in operating protocols are provided in Table 3 

on page 24 of the plan with modeled results of peak flows on pages 27 through 33. This capital 

improvement is included in the BCB five year management plan covered in the Five Year Plan (BCBSFWMD, 2002). 

Big Cypress Basin Watershed Management Plan, Flood Control Element 

BCB-SFWMD. 2000. Big Cypress Basin Watershed Management Plan, Flood Control 

Element. 06/25/01 Draft. Big Cypress Basin Board South Florida Water Management 

District. West Palm Beach, Florida. 

This study presents simulations of design storms to identify flood problems and assesses alternatives 

for development of a regional plan addressing flooding, water supply and environmental impacts. 

Simulation showed that 11.8 miles out of 27 miles of the Golden Gate Canal and 2.5 of 7.2 miles of the 

CR951 canal were considered flood control problems, and one alternative for management was to divert 

aportion of the Golden Gate Canal (GGC) flow into the Henderson Creek basin (Figure 45). Other 

alternatives also considered were channel and structural modifications to the canal west of CR951 and to 

CR951 Canal and aquifer storage and recovery (ASR) of GGC wet season overflow. Diversion of 

Corkscrew Canal flows into the GGC was considered but not recommended. 
February 2006 72 Naples Bay SWIM Reconnaissance 

Figure 43. Map of eight reaches included in stormwater modeling in the Gordon River Basin Extension.
February 2006 73 Naples Bay SWIM Reconnaissance 

44. Map of 25-year, 3 day storm event problem areas in the Gordon River Basin. 
February 2006 74 Naples Bay SWIM Reconnaissance 

Figure 45. Big Cypress Basin retrofit examples 

(BCB-SFWMD, 2000).

The RUNOFF block of the SWMM model 

was used to simulate the rainfall-runoff and the 

upper zone ground water processes, and the 

interaction between ground and surface water for 

eight basins, including two in the Naples Bay 

Study Area – District 6 and Golden Gate Canal. 

Three design storms (25, 50, and 100-year 3-day) 

were selected for the simulation. Details of this 

report are summarized in Appendix A14. 

South Lee County Watershed Plan 

Johnson Engineering. 1999. South Lee County Watershed Plan. South Florida Water 

Management District. West Palm Beach, Florida. 

Though not within the Study Area, the South Lee County Watershed Plan includes the Corkscrew 

Watershed, adjacent to the Naples Bay Basin. There is potential for water exchange in northeastern 

Naples Bay Basin through the Corkscrew Canal. This connection was greater prior to Immokalee Road 

and its canals, and should decrease more in the future when levees are repaired through other BCB 

projects. 

“[The report] addresses flooding problems associated with development in southern Lee and 

northern Collier counties. Flooding of the residential areas in both the Imperial and the 

Cocohatchee watersheds occurred once in 1992, twice in 1995, and to a lesser degree in each 

subsequent year, with 1999 having the greatest impact to the residential area since 1995. Due to 

the relatively flat terrain, the slightest deviation in surface elevation is enough to shift runoff. 

Because of man-made alterations such as ditches, dikes, U.S. Interstate 75, and farm roads, 

historic delineations of the various contributing areas have been significantly altered. As 

sheetflow meanders southwest, it is collected by a series of natural and man-made channels 

converging into several main rivers and creeks: the Estero River, Halfway Creek, Spring Creek, 

Imperial River, Cocohatchee River, Corkscrew Canal, and Camp Keais Strand. 

As a part of the study, a hydrologic/hydraulic model, an ecological assessment, and problem 

identification and evaluation of existing hydrologic-hydraulic conditions in the Estero Bay 

Watershed were completed. As a result of the analysis performed for the South Lee County 

Watershed Plan it was determined that sheetflow has been substantially altered and cumulative 

effects of seemingly small hydrologic diversions have changed the direction of flow from basin 

to basin within the watershed. Lowlying areas in the southwestern portion of Lee County are 
February 2006 75 Naples Bay SWIM Reconnaissance 

now subject to inundation from stormwater runoff generated miles away. The plan identifies 

flow way restoration and improvements that can be made to protect the capacity of historic 

outfalls within the watershed.” 

USACOE and SFWMD (2002) 

Central and Southern Florida Project Comprehensive Review Study Final Integrated 

Feasibility Report and Programmatic Environmental Impact Statement (PEIS) 

U.S. Army Corps of Engineers and South Florida Water Management District, 1999. Central 

and Southern Florida Project Comprehensive Review Study: Final Integrated Feasibility 

Report and Programmatic Environmental Impact Statement. USACOE. Jacksonville, Florida. 

 “This report recommends a comprehensive plan for the restoration, protection, and preservation 

of the water resources of central and southern Florida, including the Everglades. It identifies 

and discusses the plan’s proposed project features [over 60], its beneficial effects and potential 

impacts on existing resources.” 

However, water resources problems and opportunities in southwest Florida were determined to 

require studies beyond the scope of The Central and Southern Florida Project Comprehensive Review 

Study, also know as the “Restudy”. Therefore, a feasibility study for Southwest Florida was 

recommended to investigate the region’s hydrologic and ecological restoration needs. The Restudy only 

assessed water resource issues in southwest Florida as they relate to the Caloosahatchee Basin. Other 

watersheds in southwest Florida have not been studied in a comprehensive fashion. 

City of Naples Basin VI Assessment Report 

Camp, Dresser and McKee. 1998. Basin VI Assessment Report. City of Naples. Naples, 

Florida. 

Assessment of sub-basins within Basin VI was completed using models similar to the Basin V 

Stormwater System Improvement Plan Phase I: Basin Assessment and Conceptual Improvement Plan 

(CDM draft, 2004). Basin VI, the Central Avenue – 10th Street drainage basin, was identified in the City 

of Naples Stormwater Management Plan (1996) as a major drainage problem area. Five alternatives were 

evaluated: one to maintain existing system except relocating and upgrading the pump station, and the 

other four with different levels of service provided by replacing or paralleling undersized pipes. A range 

of costs is offered for each alternative. The alternative offering a 10-year, 24-hour level of service was 

recommended as the most cost effective. Other recommendations include improved topographical 

mapping, flow monitors and recording rain gauges, replacing poorly built custom inlets with standardized 

FDOT inlets and restricting the placement of loose yard waste at the curb for pickup. 
February 2006 76 Naples Bay SWIM Reconnaissance 

City of Naples Interim Basin III Design Development Report 

Camp, Dresser and McKee. 2001. Interim Basin III Design Development Report. City of 

Naples. Naples, Florida. 

Modeling of Basin III was completed with the same objectives and background as Basin VI. Basin 

III drainage problems were identified on 5th Avenue South and 9th and 10th Streets from 5th Avenue to 

10th Avenue South. Four alternatives were evaluated: returning existing system to design capacity 

through maintenance; improve pipes and pumping capacity; improve piping but not pumping; even larger 

pipes and pump. The improved piping with no increase in pumping capacity is recommended as the most 

cost effective and involves no change in peak discharge or total volume discharge into Naples Bay. 

City of Naples Stormwater Management Program - Phase 1 Master Plan Draft Report 

City of Naples Engineering Division 1996. Stormwater Management Program - Phase 1 

Master Plan Draft Report. City of Naples. Naples, Florida. 

The purpose of this report was to recommend a financially feasible stormwater management plan for 

the City of Naples following a 100-yr storm event in August 1995 that flooded virtually all sections of the 

city. Previously, in February 1980 and October 1990, drainage studies were completed making 

recommendations for capital improvements, some of which were partially implemented, and development 

of a stormwater utility which in 1996 was generating $859,000 per year. The objective of the study was 

to address both quantity and quality of surface water in the City and the approach recommended is to 

upgrade existing deficient areas to a reasonable level of service while implementing quality control during 

all future construction projects, both public and private. 

This report summarizes the 1980 study by stating that some of the $5,000,000 in drainage 

improvements were implemented but that recommendations for lake monitoring had not been 

implemented and that control of aquatic weeds was implemented in limited fashion. The 1990 study 

included an inventory of existing stormwater facilities and the data from this report was the basis of this 

1996 study using modeling techniques recommended in the 1990 report. The 1995 storm event was 

summarized as a worst case scenario with complete saturation from recent rain events and exceptionally 

high tides coinciding with a 100-yr rain event. The report points out that despite extensive flooding 

throughout the city, all of the water had drained within six hours following recession of the high tide and 

that in fact the system with a few exceptions was effective, but limited, in terms of level of service for a 

major storm event. Water quantity problems encountered in the 1995 storm event are characterized in 

Chapter 4 by location with details concerning cause and status of fixes and monitoring at the time of the 

report. Characterization of water quality issues is narrative without specific data. Recommendations 

focus on use of retention ponds. Stormwater problems throughout the community were identified and 

characterized as follows: 

Back-up of major systems caused severe flooding and property damage 

Deterioration and physical failure of existing facilities caused depression or roadway failure 

Saturated sub-bases caused deterioration of roadway 

Under-design and lack of drainage facilities caused local street flooding 
February 2006 77 Naples Bay SWIM Reconnaissance 

Shoreline outfalls failed or were blocked from Naples Beach to 3rd Avenue South. 

Swale deterioration caused local flooding 

Perched water tables saturated swales 

Clogged storm lines reduced capacity 

In describing the existing drainage system, the report states that 50% of residential and commercial 

areas have swales or ditches and the other 50% are served by a network of gravity sewers with pipes 

ranging from 8 to 72 inches and some elliptical pipes and box culverts. However, most of the pipe was 

25 to 30 years old and corroded and swales have in many cases been altered through siltation, landscaping 

and plant growth. There were 25 lakes considered part of the City’s drainage e system with three more 

that were not connected to the storm sewer system. It was recommended that modifications to these lakes 

be evaluated for further retention area. Twelve basins were identified and boundaries are defined with 

pictures of the drainage facilities in 1996. Models to determine level of service were simulated for five 

different design storms with results summarized by conduit number. 

The following 23 recommendations were made. Six are general recommendations, 8 relate to water 

quantity, and 9 relate to water quality. The projected probable cost in 1996 dollars was $10,140,000. 

Costs are itemized by capital projects and an analysis of revenue and annualized costs is provided. 

General 

1. Adopt a Mater Plan and its implementation program which address both water quality and water 

quantity. 

2. Adopt a target level of service – Goal. 

3. Implement a long term Capital Improvement Projects Program to construct the remedial facilities 

needed to meet adopted level of service – Goal. 

4. Monitor and integrate Federal, State and local regulatory requirements into the stormwater 

program. 

5. Develop a Public Information Program to develop citizen support for stormwater management. 

6. Develop and adopt appropriate ordinances requiring stormwater management on all new 

construction, expansions and reconstruction to whatever degree possible. 

Water Quantity 

7. Encourage and pursue inter-governmental cooperation with Collier County and the SFWMD to 

authorize and implement the Gordon River Drainage Basin Study including water quantity 

impacts on the eastern edge of the City for those watersheds that drain to the Goodlette-Frank 

Road drainage canal. 

8. Pursue intergovernmental cooperation with Collier County relative to maintaining existing and 

developing new outfalls to the Gordon River from the Goodlette-Frank Road ditch to offset 

diversion of water from the northern section of Goodlette-Frank Road. 

9. Develop a strong public information program to inform the public and encourage citizen support 

of a stormwater quantity program with particular emphasis on stormwater retention in swales, 

lakes or other areas yet to be determined. 

10. Develop a comprehensive program of major system inspection and maintenance, particularly in 

areas of landscaped easements to maintain designed capacity of existing systems 

11. Implement comprehensive program of rehabilitation of existing systems including replacement of 

corrugated metal pipe during opportune circumstances (resurfacing projects, etc.) 

12. Implement a City wide swale restoration program as it relates to providing drainage on streets 

with no curb and gutter 

13. Develop and implement a program of lake evaluation to determine feasibility of expanding 

capacity for storage and improvement of water quality 
February 2006 78 Naples Bay SWIM Reconnaissance 

14. On a prioritized basis, model major drainage basins to determine: 

o Overall system deficiency 

o Sport deficiencies within the system that can be feasibly improved 

o Utilization of lake systems in the drainage basin 

o Opportunity to provide additional retention via available open space or swale system 

improvement 

Water Quality 

15. Develop public information programs to inform public and encourage citizen support of 

Stormwater Quality Management Program 

16. Encourage and pursue inter-governmental cooperation for the implementation of a Gordon River 

extension study, including aspects of water quality, impact on the eastern edge of the City of 

Naples, and the pollutant impacts on Naples Bay. 

17. Implement ordinances requiring stormwater management for all new construction including 

single family homes and to establish a threshold based on the percentage of remodeling of 

existing structures. 

18. Continue the water quality monitoring program, instituted in 1993, for Moorings Bay, Naples 

Bay, Gordon River, and the City’s lake system to establish a base line to measure stormwater 

related pollution and to determine if solutions are effective. 

19. Conduct studies to determine feasibility of increasing retention capacities of lakes serving the 

stormwater management system 

20. Adapt a policy of encouraging water retention on all public works projects including evaluation 

of open areas for acceptable water retention 

21. Develop a program of swale restoration throughout the community including designed inlet 

thresholds to accommodate limited ponding 

22. Adopt engineering design policies encouraging exfiltration systems as part of stormwater 

facilities 

23. Fund and implement a lake and bay quality program including pollution loading and vegetative 

aquatic growth 

Gordon River Watershed Study. 

CH2MHill. 1980. The Gordon River Watershed Study. Big Cypress Basin Board South 

Florida Water Management District. West Palm Beach, Florida. Project No. NA11977.D0. 

The project is limited to the scope of services for Phase I of the Gordon River Watershed Study, the 

study of existing conditions. Included is a summary of the hydrology of 25 and 100-year rainfall events. 

Twenty-five and 100-year flood plains and water surface profiles were determined, as were the economic 

impacts of flooding on existing and potential development. The Study Area follows roughly the current 

sub-basins referred to as Gordon River North, Gordon River Central, Gordon River South and Airport 

South, though is it bounded on its east portion by Airport Road and the Golden Gate Canals. 
February 2006 79 Naples Bay SWIM Reconnaissance 

PROJECTS 

Collier County Capital Improvement Projects 

Projects for the Collier County stormwater fiscal years 2004 -2005, 2005-2006, and 2006-2007 that 

are within the study and provide a water quality benefit are listed in Table 9 and shown in Figure 46. 

Table 9. Collier County Stormwater Management projects within the Study Area for fiscal years 2004-2005, 

2005-2006, and 2006-2007 (http://www.co.collier.fl.us/stormwater/capImprovement _pages/current.html). 

SFWMD Sub-basin 

Name 

County 

ID County Fiscal Year County Project Name 

Santa Barbara 515012 05-06 and 06-07 Australian Pine Removal 

Gordon River Central 510056 04-05 and 05-06 Westlake Outfall Improvements 

Gordon River Central 510054 04-05 and 05-06 Twin Lakes Inner-connect 

Gordon River Central 510055 04-05 and 05-06 Goodlette Frank Culvert Improvement 

Gordon River Central 510053 04-05 and 05-06 Gordon River Water Quality Park 

Rock Creek 514092 04-05 and 05-06 North Road Culvert Improvements-Rock Creek 

Lely North 511072 04-05 and 05-06 Avalon School Ditch Improvements 

Lower Haldeman Creek 518032 04-05 and 05-06 Gateway Triangle Drainage Improvements 

Lely N 511012 04-05, 05-06, 06-07 Lely Area Stormwater Improvement Project 

County-wide 510012 04-05 and 05-06 Stormwater Master Plan Update 

City of Naples Ten Year Stormwater Funding Plan 

The following 16 projects are listed on the BCB Ten-Year Grant Funding Plan for Selected 

Stormwater Management Projects, submitted to the BCB May 2005 by The City of Naples Public Works 

Department. Projects total $41,435,000 and include management plans, control measures, maintenance, 

improvements, reconstruction, removals, asset management, and public education. 

• Street Sweeper for NPDES Phase II Water Quality Control Measure 

• Stormwater Drainage Basin III Water Quality & Flood Mitigation Improvements 

• Stormwater Drainage Basin V Water Quality & Flood Mitigation Improvements 

• Stormwater Drainage Basin VI Water Quality & Flood Mitigation Improvements 

• Naples Bay Basin Management Plan (Phase I Prelim. Eng'rg. & Environmental) 

• Beach Management Plan For Removal of Ten Stormwater Outfalls (Prelim. Eng'rg.) 

• Lake Water Quality Management Plan (Phase I Prelim. Eng'rg. & Environmental) 

• NPDES Phase II Stormwater Public Education & Public Outreach Control Measure 

• Royal Harbor Water Quality (Elimination of Point Discharge Concrete Swale Outfalls) 

• Water Quality Swale & Stormwater Drainage Facility Reconstruction 

• Outfall Storm Drain Pipe Inspection, Cleaning, Lining & Replacement 

• Citywide Storm Sewer System Repair & Maintenance Program 

• Stormwater Drainage Inventory, Inspection & Evaluation (Asset Management) 

• Citywide Stormwater Master Plan (12 Basins Excluding Basins III, V and VI) 

• Vacuum Truck For Stormwater System Maintenance 

• Reconstruct Drainage Inlets (Safety, Capacity & Water Quality Inserts) 
February 2006 80 Naples Bay SWIM Reconnaissance 

Figure 46. Collier County Stormwater Division capital improvement projects (Collier County).
February 2006 81 Naples Bay SWIM Reconnaissance 

Figure 47. Gordon River Water Quality Park Conceptual Master Plan. 

Golden Gate Canal/Henderson Creek Water Transfer 

A BCB project to transfer water from the Golden Gate Canal into Henderson Creek is in progress and 

expected to be complete in 2007. The diversion will reduce flow from Naples Bay to Rookery Bay. It is 

described in further detail in the Modeling and Plans section above. 

Gordon River Water Quality Park 

The Gordon River Water Quality Park Project (Figure 47) is a 50 acre natural water quality treatment 

facility designed to provide flooding relief and tertiary treatment of stormwater runoff from the Gordon 

River Extension Basin. The proposed passive park site is on the northeast corner of Goodlette-Frank 

Road and Golden Gate Parkway. The constructed, interconnected, multi-depth ponds, polishing marshes, 

and wetlands will serve as a filtration system while the trails, fishing piers, educational facilities, 

landscaping and hardscaping will benefit park users. The Collier County website states that this facility 

will allow the County the potential option of a future Aquifer Storage and Recovery System (ASR) within 

the park for landscape irrigation use. 
February 2006 82 Naples Bay SWIM Reconnaissance 

Figure 48. Lely Area Stormwater Improvement Project (Collier County 

website).

Lely Area Stormwater Improvement Project (LASIP) 

The southwest corner of 

the LASIP project is within 

the Study Area (Figure 48). 

The project boundary includes 

most of the Lely North subbasin, referred to as the Lely 

Canal Basin on county maps, 

as well as the Lely Manor 

Basin, which is outside of the 

Naples Bay Basin. “The 

proposed Lely Area 

Stormwater Improvement 

Project consists of 

improvements to an existing 

drainage system for an 

11,100± acre East Naples 

area, which formed the major 

portions of the former Water Management District 6 area. The project area currently has two (2) outfall 

systems consisting of the Lely Main Canal and a system of farm ditches and dikes associated with 

portions of the easterly half of the project, which drains the Lely Manor area. The project area is 

therefore divided into two (2) basins. The westerly most basin is known as the Lely Canal Basin and the 

easterly most basin is known as the Lely Manor Basin. The Lely Area currently has some water 

management improvements implemented; it generally suffers from the lack of a comprehensive outfall 

system and design. 

Land use within the Basin consists of a combination of modern developments that have improved 

water management systems consistent with current design requirements and best management practices as 

well as older existing neighborhoods that were developed before water management systems were 

required. The latter areas provide little if any water quality improvements for stormwater runoff. 

The purpose of the project is to lower the flood elevations and to reduce the duration of peak stages 

while providing as much water quality improvement and groundwater recharge as possible. Careful 

design of the project has avoided wetland impacts where possible and minimized unavoidable wetland 

impacts to the maximum extent practicable, while still meeting the overall project purpose. The project 

will undertake the following construction activities: 

• Widen and deepen existing canals. 

• Construct new channels. 

• Construct new control structures and culvert systems. 

• Improve several existing control structures. 
February 2006 83 Naples Bay SWIM Reconnaissance 

• Install new flood control gates. 

• Construct spreader lakes and berms at outfalls. 

• Construct a pump station to rehydrate existing wetlands. 

An ERP from the SFWMD was issued on October 14, 2004. (Gerald Kurtz , Collier County personal 

communication). The Collier County Stormwater Department received approval from the USACE for the 

associated dredge and fill activities. Total estimated construction costs are approximately $45,000,000. 

Construction is planned to commence in January 2006, with one phase to be completed each year for six 

or seven years. 

Westlake Outfall Improvements and the Twin Lakes Interconnect 

These projects will consist of conveyance pipes and water control structures that will connect 

stormwater lakes in the Westlake and Twin Lakes subdivisions in the Gordon River basin to the 

Goodlette-Frank Canal. SFWMD expects these projects to result in tangible improvements to flood 

mitigation and stormwater quality in the Gordon River basin. In support of the Naples Bay Watershed 

Initiative, an agreement was written April 2005 to provide state appropriated funding support from the 

SFWMD to Collier County. 

Gordon River Greenway 

The Southwest Florida Land Preservation Trust is working with support from the Collier County 

Commissioners and the Naples City Council to fulfill their mission to facilitate public and private interest 

and involvement in creating and preserving a Gordon River Greenway for public use, recreation, water 

resource protection and habitat preservation. The Greenway is a continuous public right-of-way along the 

Gordon River with both a bikeway and walking path that will stretch from the Golden Gate Parkway to 

US 41 South. It will include two bridges, and will connect other parks, including the Gordon River Water 

Quality Park, trails, and the Naples Bay waterfront. A section on the Naples Airport property is complete, 

and work is in progress to obtain easements to construct other sections. A master planning process for the 

Greenway has been started. 

Northern Golden Gates Estates Regional Offsite Mitigation Area (ROMA) 

“A ROMA is intended to provide a low-cost mechanism for landowners to compensate for 

permitted wetland impacts resulting from residential construction. The ROMA for North 

Golden Gate Estates was proposed by the Collier Soil and Water Conservation District 

(CSWCD) and is in the initial review stages by the Florida Department of Environmental 

Protection (FDEP). If approved, the ROMA will include a legal agreement or memorandum of 

agreement (MOA), between the FDEP and the CSWCD, which will then be allowed to acquire 

land or conservation easements from willing sellers only in North Golden Gate Estates to 

restore wetlands”. 

 FDEP Website 
February 2006 84 Naples Bay SWIM Reconnaissance 

The proposed plan involves the acquisition of lots or conservation easements on lots concentrated in 

the platted area of North Golden Gate Estates, north of I-75 and south of 10th Avenue. Once an 

appreciable portion of property is acquired, then an enhancement plan would be initiated. Enhancement is 

proposed through exotic species eradication and long-term management. It is also hoped that the 

hydrology could be improved by adding culverts. The MOA and Mitigation Plan are available on the 

internet (http://www.dep.state.fl.us/south/ERP/Golden%20Gate%20ROMA.htm). 

Beach Re-nourishment 

Several major City/County beach re-nourishment projects are to begin November 2005 and be 

completed early 2006. Approximately 625,000 cubic yards of sand are planned for re-nourishment of 

Naples Beach, Vanderbilt Beach and Parkshore. No direct impacts to existing Bay, marsh or estuary are 

anticipated. FDEP permit requirements include one acre of artificial reef to offset potential impacts of 

beach re-nourishment activities to benthic hard bottom habitat. (Gary McAlpin, Collier County, personal 

communication). 

Transportation 

The 2004/2005 – 2008/2009 Collier County Transportation Improvement Program (TIP) (available at 

http://www.colliermpo.com) includes prioritized, financially feasible projects for all modes of travel. 

Projects identified in the TIP are consistent with the Metropolitan Planning Organization’s (MPO) 2025 

Long Range Transportation Plan as well as other organizations’ plans. 

Figure 49 provides an overview of project locations, types, and the FDOT project number and year. 

Project phases that receive funding become part of the FDOT’s Five-Year Work Program (Figure 50). 

The Tentative Work Program was adopted July 1, 2005. Major construction projects listed in the 

District One Tentative Work Program FY 2005/06 – 2009/2010 for the Study Area and their FDOT 

project numbers follow: 

175 From Golden Gate Parkway to S of Bonita Bch. Rd. Add lanes and reconstruct. 4063133 FY10 

175 Overpass at Immokalee Rd. New Road Construction. 4189371 FY09 

SR 84 (Davis Boulevard) from Santa Barbara Blvd. to CR 951. Add lanes and reconstruct. 1954162 

FY10 

There is potential for stormwater treatment within the Study Area through Joint Use Stormwater 

Management Agreements with FDOT. Joint use agreements have been made between FDOT and Collier 

and Lee Counties. 
February 2006 85 Naples Bay SWIM Reconnaissance 

Figure 49. Collier County Transportation Improvement Program.
February 2006 86 Naples Bay SWIM Reconnaissance 

Figure 50. Collier County Five Year Work Program.
February 2006 87 Naples Bay SWIM Reconnaissance 

PROGRAMS 

Background 

Many programs or organizations have set out to improve the conditions of Naples Bay. The 

following summary was taken from Bauer (2003). 

1988 - The Naples Bay Task Force was established by Area Chamber of Commerce, resulting in the 

Bay Management Organization, which provided the Naples these recommendations in 1990: 

• Carrying out a hydrographic study of Naples Bay (how much water goes where), 

• Establishing a stormwater utility, 

• Expanding the dredging and maintenance of residential canals, 

• Replacing vertical seawalls with rip rap, 

• Developing a Golden Gate Basin Management Plan, and 

• Improving stormwater management through source control BMPs. 

1997 - The Naples City Council established the Naples Project Committee, with the following 

recommendations. 

• Marine vessels be better controlled and 

• Water quality be improved by 

o removing debris, 

o aerating canals, 

o preparing a bathymetric chart of the Bay, 

o restoring mangroves, 

o creating artificial habitats in the Bay, 

o connecting dead end canals, 

o implementing a stormwater master plan, and 

o educating citizens. 

Recommendations made by these groups that have been carried out: 

• The Golden Gate discharge rate has been slowed by improvements in the canal system 

• The wastewater treatment plant has been upgraded to tertiary treatment capabilities 

• Former package and septic systems have been connected to a central sewer system 

• Stormwater management is ongoing 

• Depth changes in some canals have been corrected 

• Vessel speed controls are in place 

• All septic tanks in Naples proper have been eliminated

2002 - City, state, and local governments, environmental groups and the private sector came together 

unofficially and identified: 

• Stratification of the water column in the Bay proper and in canals is affecting oxygen levels, 

salinity, and the movement of food for aquatic organisms. 

• Stormwater runoff is still negatively impacting the Bay, and 

• Loss of intertidal habitat has occurred due to changes in the shoreline (mangroves, sea grasses, 

oyster reefs) 
February 2006 88 Naples Bay SWIM Reconnaissance 

Shortly thereafter the SFWMD sought funding to implement the following projects, listed in priority 

order assigned by group above. 

1. Mapping and Modeling of Naples Bay to determine where and how fresh water flows through the 

Bay combined with a new proposal to identify areas most impacted by fresh/salt water 

stratification. 

2. Development of a Gordon River Basin Stormwater Management Master Plan to determine where 

structures and other practices should occur. 

3. Modification of Golden Gate Canal Weir #2. 

4. Modification of I-75 Canal Weir #1. 

5. Documentation of the historic distribution of submerged aquatic vegetation, oyster reefs, and 

mangroves, followed by restoration of the habitats in these locations. 

6. Development of a Gateway Triangle Stormwater Management Plan. 

2003 - RBNERR held a Coastal Management Training Workshop for Collier County officials. The 

Collier County BCC passed a resolution requesting SWIM designation; the Naples City Council passes 

similar resolution. RBNERR, FDEP, and NOAA partnerships established to provide support. 

Non-governmental organizations that have established public support and funding for the Naples Bay 

area: 

• Conservancy of Southwest Florida 

• Southwest Florida Watershed Council 

• BCB Coordination Team 

• Collier Audubon Society 

NPDES (MS4) Municipal Separate Storm Sewer System Permits 

In October 2000, EPA authorized the Florida Department of Environmental Protection (FDEP) to 

implement the NPDES stormwater permitting program in the State of Florida. The NPDES stormwater 

program regulates point source discharges of stormwater into surface waters of the State of Florida from 

certain municipal, industrial and construction activities. A municipal separate storm sewer system (MS4) 

is a publicly-owned conveyance or system of conveyances (i.e., ditches, curbs, catch basins, underground 

pipes, etc.) that is designed for the discharge of stormwater to surface waters of the State. Under Phase II, 

the program regulates discharges from certain MS4s not regulated under Phase I, and that meet 

designation criteria set forth in Chapter 62-624, F.A.C. Regulated MS4 operators must obtain an NPDES 

stormwater permit and implement a comprehensive stormwater management program to reduce the 

contamination of stormwater runoff and prohibit illicit discharges to the MS4. (FDEP website, 

http://www.dep.state.fl.us/water/stormwater/npdes/MS4_5.htm) 

Collier County received an NPDES Phase II Stormwater Permit for its stormwater collection system 

July 28, 2003. Conditions of the permit require the County to have a stormwater quality program that 

reasonably attempts to prevent pollution from entering the stormwater collection system. The City of 

Naples and the Pelican Marsh Community Development District (CDD) were also required to obtain 
February 2006 89 Naples Bay SWIM Reconnaissance 

Figure 51. Post-development discharge areas (Collier County). 

NPDES MS4 permits in 2003. Copies of the County and City MS4 permits are in Appendix A15 and 

A16. 

Collier County Stormwater Management Master Planning and Regulation. 

The County wide Stormwater Master Plan prepared in 1988 was used to develop the Drainage SubElement of the County’s Growth Management Plan, which was prepared to meet the requirements of 

Chapter 163, Florida Statutes and Chapter 9J-5, Florida Administrative Code. The document proposes a 

plan, through goals, objectives, and policies, to implement the County wide Stormwater Management 

Plan that provides an acceptable level of service for stormwater controls and environmental management 

objectives. The Big Cypress Basin Watershed Plan, a master planning process initiated in 1996, is being 

developed in cooperation with the City of Naples and Collier County at a much greater level of detail by 

incorporating detailed surveying, field data measurements, and computer modeling for preparing detailed 

basin and sub-basin stormwater management/environmental resources studies. 

The latest 

amendment to the 

Drainage Sub-Element, 

included in Appendix 

A17, was May 9, 2000. 

The County further 

restricts the rate of 

discharge in some subbasins via Ordinance 

2001-27, which is 

included in Appendix 

A18. Areas of postdevelopment discharge 

regulation are seen in 

Figure 51. The 

Ordinance also has a 

provision to correct 

problematic surface 

water run-off from 

single family residential 

lots. 
February 2006 90 Naples Bay SWIM Reconnaissance 

Collier County Transfer of Development Right (TDR) Program 

The TDR program was adopted by ordinance February 2004. The intention is to direct development 

away from environmentally sensitive lands 

in the Rural Fringe Mixed Use (RFMU) 

District. The RFMU occurs in two places 

within the Study Area, both are East of 

County Road 951. Both sending and 

receiving areas are present. The two 

locations are 1) South and East of NaplesImmokalee Rd, and 2) the vicinity of Subbasin GGE #3, along the southern border of 

the Basin (Figure 52). Owners of sensitive 

“sending lands” can sell their residential 

development rights yet maintain limited 

permitted and conditional uses, as provided 

for in Collier County’s Land Development 

Code (LDC), Sub-Sections 2.03.08 and 

2.03.07. Credits from RFMU can be 

transferred into the less sensitive “receiving 

lands” (Urban Residential Fringe and 

RFMU District Receiving Lands) as 

provided in Section 2.6.39.4 and 2.6.39.5 of 

the LDC. TDR credits must be issued and 

recorded by Collier County in the public 

records. A registry for interested buyers and 

sellers has been created by the County. The 

program is more thoroughly explained at 

http://www.co.collier.fl.us/compplanning/td

r/TDRFAQs.htm. 

Southwest Florida Resource Conservation & Development Council (RD&CD), Inc. 

The non-profit organization established in 2002 consists of members from Charlotte, Collier, Glades, 

Hendry and Lee counties. The RC&DC was created to assist local communities in meeting their 

objectives of land conservation, water management, community development and land management. 

Their mission is to “preserve and enhance the natural resources of the area, promote economic stability 

and improve the quality of life for the residents of the area.” 

Figure 52. RFMU Sending and Receiving Lands. 
February 2006 91 Naples Bay SWIM Reconnaissance 

The Fiscal Year 2005 October 1, 2004 to September 30, 2005 – Annual Work Plan includes a planned 

project for Collier County Hard Clam Aquaculture. In anticipation of the Department of Agriculture and 

Consumer Services signing clam leases in approved areas of Collier County, assistance is planned for 

prospective clam growers. The work plan states that grants will be needed for surveying the leases and 

training individuals in clam aquaculture production and underwater diving 

(http://www.swfrpc.org/rcdc.htm). 

Rookery Bay National Estuarine Research Reserve (RBNERR) 

The RBNERR is a partnership program between NOAA and the FDEP. The Reserve is partially 

contained within the southern tip of the Naples Bay Study Area and is involved in research and 

monitoring, resource management, education and outreach, coastal training, and a volunteer program. 

“Collaborative research and monitoring efforts include analyzing the impacts of mosquito control aerial 

spraying, mangrove and oyster reef ecology, restoration ecology, estuarine fisheries, and nutrient cycling. 

Resource managers facilitate land acquisition, conduct habitat and hydrology restoration projects, 

eradicate and control invasive plants and animals, protect listed species, manage important habitats and 

wildlife and conduct prescribed fires to sustain native biodiversity.” Incorporation of adjacent stateowned lands within the RBNERR boundary has been proposed to NOAA (http://www.rookerybay.org/). 

Other resource management activities, including the routing of water through canals such that freshwater 

flows may be reduced to Naples Bay and increased to Rookery Bay are covered in several documents in 

the Modeling and Plans section of this report. 

Conservation Collier 

The Conservation Collier Land Acquisition program targets lands with high natural resource value 

throughout Collier County from willing sellers. Properties need to support at least two of the following 

criteria to qualify: rare habitat, aquifer recharge, flood control, water quality protection, and listed species 

habitat. A Land Acquisition Advisory Committee, appointed by the Collier County Board of County 

Commissioners, reviews and recommends selected properties for approval by the County Commission. 

As of June 2005, 12 properties/projects totaling approximately 835 acres, including 2 large multi-parcel 

projects, have been approved for purchase. 

Collier County Restoration Mapping 

The Collier County Restoration Mapping database is being developed to identify environmental 

restoration projects for water quality, hydrology, and/or biodiversity. Representatives from Federal, 

State, County and local governments as well as organizations and individuals outside of government are 

being coordinated to identify potential and existing restoration projects. Projects are identified, 

described, and costed using a database created in Microsoft Access and outlined on USGS topographic 
February 2006 92 Naples Bay SWIM Reconnaissance 

Figure 53. Current and recommended sampling stations 

(Taylor Engineering, Inc. 2005).

maps. The outlined polygons are then digitized into GIS coverages and spatially linked to the database. 

This effort will develop a product/tool that will be used in the alternative analysis and selection for the 

SWFFS. The database creation and GIS development follows similar restoration planning methodology 

used in Lee and Charlotte County that is currently being used for the SWFFS. 

RECOMMENDATIONS 

Naples Bay and its tributaries have been extensively monitored for water quality for the last 35 years. 

Its basins and drainage structures have been the basis for several intensive modeling efforts to determine 

the quantity and fate of storm water. Canal flow is well mapped and changes in volume monitored. 

Many concerns related to water quality and quantity improvement and management are identified in the 

items summarized in this report, as are data gaps and recommendations. However, several gaps exist in 

available data for the development of a SWIM plan. 

Evaluation of Naples Bay Water Quality and Hydrologic Data 

The SWFFS ACCESS database was recently evaluated for use in assessing current condition, trends, 

and water quality model setup and calibration for Naples Bay (Taylor Engineering, Inc. 2005). Taylor 

Engineering’s recommendations are provided verbatim here for convenience. 

Recommended Water Quality Data Collection

The insufficient water quality data from the 

present sampling program preclude calibration 

of the water quality model. Further, the data 

cannot support a process level water quality 

model that might simulate fluctuations in 

dissolved oxygen. However, the data should 

suffice for most of the necessary water quality 

model verification data for a two-dimensional 

model of the Bay. The data from present 

sampling programs would provide comparison 

information to evaluate errors in water quality 

model performance over the simulation period 

or periods. Additional water quality stations 

recommended for better water quality model 

(Figure 53) verification would include the 

following station locations: 
February 2006 93 Naples Bay SWIM Reconnaissance 

• Just inside Gordon Pass 

• Within the main passages from residential canal areas on the west side of the Bay 

• In the main body of the Bay south of Gordon Inlet 

• In the Intracoastal Water Way at the mouth of Lely Canal 

• At a constriction near the mouth of Henderson Creek 

Summary of Recommendations

Taylor Engineering envisions the use of a two-dimensional model to simulate long-term water 

circulation and water quality dynamics. This class of model would likely provide sufficient capability to 

simulate ambient water quality conditions for management of the Bay to achieve and maintain Class III 

water quality standards. However, calibrating the model would require additional sampling and data 

collection. Additional long-term sampling stations would likely increase the ability to verify model 

performance, develop management plans, and monitor changes in the system. 

Sufficient hydrologic data collected since 2000 from currently active hydrologic stations provide 

sufficient information for use in developing a limited calibrated water circulation model. Rainfall, flow at 

Golden Canal weir, and the Gordon River Extension weir, stage measurements from Haldeman Creek, 

Rock Creek, Lely Canal, Henderson Creek, and from gauges in the Gulf of Mexico would provide most 

of the data. Taylor Engineering recommends runoff modeling to provide stormwater flows from 

developed areas of the Basin, particularly the City of Naples. 

Given the absence of tide gauges in Naples Bay, published tidal ranges would substitute for direct 

measurement to provide a limited calibration of the hydraulic model. The addition of several tide gauges 

would greatly improve hydraulic model calibration and verification capabilities. 

Intensive 48-hour hydraulic and water quality parameter measurements during the dry and wet 

seasons would provide the ideal data sets for a detailed calibration of the hydraulic and water quality 

models. 

Data from monthly sampling efforts in the Bay, augmented by data from recommended additions to 

the current sampling network, would provide verification data for the hydraulic and water quality model. 

The recommended sampling stations would suffice for verification of the model calibration and 

simulation period performance testing. The new stations would extend the monitored area south to 

Henderson Creek, potentially affected by proposed changes in the Naples Bay Basin canal drainage 

system. 

Reconnaissance Observations 

The following are recommendations based on what was observed during the synthesis of information 

for this Reconnaissance Report. 
February 2006 94 Naples Bay SWIM Reconnaissance 

Additional data collection

While water quality and flow in general are being well sampled, a few basic pieces of information 

important for a complete understanding of surface water and its fate are missing in the Naples Bay area. 

Stream gauges are lacking in areas without control structures. More information on aquifers is needed in 

the study area rather than drawing inferences from the few cores completed in nearby areas, and in 

general a comprehensive summary of groundwater quality has not been completed. Testing for metals 

and pesticides has not been done consistently or in enough locations to draw sound conclusions. Further, 

distribution of residual organotin compounds should be conducted in areas of heavy boating 

activity/storage/repair activities. 

Monitoring Station Representation

Update or create GIS layers for monitoring locations. The current SFWMD GIS layer does not reflect 

current SFWMD or County sampling stations (i.e. records in GIS layer and DBHydro database do not 

match). This will allow display of monitoring station locations, as well as spatial analysis and display of 

data. This could prove to be very effective as a quantitative analysis and/or planning tool. Ideally, a GIS 

layer with a unique identification for each station could be joined to a comprehensive water quality water 

quantity database. It would be useful to differentiate stations that are currently monitored versus historic 

stations. Additionally, the many stations in the STORET database that have no data available should be 

eliminated from the GIS layer. A significant effort would be necessary to reconcile differences and 

overlap between data sets. 

Stormwater Treatment Systems Representation

Create GIS layer identifying stormwater treatment methods/systems. Various resources may be 

available with this information, though none are in GIS format. One resource is the regulatory related 

database which contains certified development information. Current ERP regulations call for stormwater 

BMPs. During permitting process, construction is certified to meet permit required standards. 

Certification information (project outfalls, CFS, pumps, etc) can be accessed through direct query, though 

information about location would have to be accessed indirectly using a permit number or other means 

(Steve Nagle, SFWMD, personal communication). Projects with regional significance have master 

drainage plans. Developments constructed prior to the ERP program are likely to have either inferior or 

absent stormwater treatment systems. Other, simpler means may prove to be effective as well, such as 

querying the property appraiser’s spatial database for construction dates. A map of stormwater 

management systems would allow for the potential to target areas with inferior stormwater treatment 

methods and improvement projects. 
February 2006 95 Naples Bay SWIM Reconnaissance 

Salinity modeling

The SFWMD is tentatively planning a salinity modeling project in partnership with the City of 

Naples. A recent nearby project that may be a useful resource is the USGS Estero Bay salinity patterns 

mapping (USGS, 2003). Fourteen salinity maps were created from monthly surface water and salinity 

data collected over an 18-month period. Surface water salinity maps were used to assess trends in 

freshwater inputs and saltwater movement within the estuary, and to evaluate water transport and 

residence time. Maps show seasonal variability, rivers of significance, and hydrologic barriers. 

Empirical salinity data collected within Naples Bay could be used to develop and/or verify planned 

salinity modeling efforts. 

Working Group Meetings 

Topics that were identified and discussed at the March working group meeting are characterized 

below: 

Watershed boundaries, natural and artificial, may be disputed, as they vary according to conditions 

and can be influenced by water management decisions. The boundaries used in the study, however, are 

suitable for the purposes of developing surface water improvement and management plans and projects. 

Current modeling techniques used by the BCB are regional, integrate surface and groundwater, and are 

not constrained by specific boundaries. 

The effects of altered hydrology on the structure and function of estuarine ecosystems in the region is 

well documented (Shirley et al. 2004; 2005). Performance measures to conserve natural biodiversity have 

been developed for other estuaries in the region (Popowski, 2003). It is recommended that the 

applicability of these performance measures and possibly other performance measures be developed early 

in the SWIM planning process to prioritize restoration activities and to assess the effectiveness of 

management actions. BCB management plans for water movement and storage should be formalized to 

include water levels maintained and quantities released such that the ecosystem needs are met. The term 

“Ecosystem Operating Plan” was suggested by workshop participants. It was suggested that 

consideration for the watershed management approach be given to the original water budget of the Basin, 

annualized water projections. It was stated that the effects of the inter-basin transfer of water should not 

be underestimated. 

Additional storage of water to reduce drainage effects in Northern Golden Gates Estates is desirable 

yet limited by presence of septic systems and flood control issues. Drainage issues are being addressed 

by the Restudy Demands Committee and GGE Homeowners Association. Much of this area was 

developed before current permitting requirements were in place and lack sufficient stormwater treatment. 

Increased population density in this area negatively affects water resources due to an increase in the 

number of septic systems and amount of impervious surfaces. 
February 2006 96 Naples Bay SWIM Reconnaissance 

Florida's Clean Marina and Florida Yards & Neighborhoods Program implementation should be 

strengthened within the Basin. The Clean Marina Program (CMP) educates, prevents degradation, and 

certifies businesses on a voluntary basis. CMP Clean Marina Designation indicates the business adheres 

to Marina Environmental Measures (MEMs). Florida Yards & Neighborhoods (FYN) educates and 

certifies home owners. Helpful concepts, tools and techniques for creating yards that use less irrigation, 

fertilizers, herbicides and pesticides resulting in improved stormwater runoff are provided. The FYN 

program also addresses shoreline management for waterfront homeowners. 

Other issues include: I-75 Canal connections with the aquifer allows for loss of surface water; human 

waste and gray-water from live-aboard marinas and unregulated mooring fields; availability of land for 

stormwater treatment systems; exotic plants and animals with the potential to clog drainage systems and 

those with the potential to improve water quality aspects respectively. 
February 2006 97 Naples Bay SWIM Reconnaissance 

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