Office of Water
Environmental Protection Office of Research and Development 2006
Agency Washington, DC 20460 http://www.epa.gov/nc:
National Estuary Program
Coastal Condition Report
llBTNEP
New Hampshire
4ft
ft
5ARASOTA BAY
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Front cover photo by Scott Taylor, Beaufort, NC
www.ScottTaylorPhoto.com
Inside cover photo by Paul Goetz
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ACKNOWLEDGMENTS
This National Estuary Program Coastal Condition Report
(NEP CCR) was prepared by the U.S. Environmental Protection Agency (EPA), Office of
Water (OW) and Office of Research and Development (ORD). The EPA Project Manager for
this document was Barry Burgan, who provided overall project coordination. The principal
authors for this document were Barry Burgan and Virginia Engle, Technical Director of
ORD's National Coastal Assessment (NCA) program within the Environmental Monitoring
and Assessment Program (EMAP). EPA was supported in the development of this document
by RTI International (RTI) and Johnson Controls World Services. The content of this report
was contributed by EPA and the U.S. Geological Survey (USGS), in cooperation with the
28 individual NEPs and many local, state, and federal agencies. Special appreciation is
extended to the following staff, who provided written materials, technical information,
reviews, and recommendations throughout the preparation of this document.
U.S. Environmental Protection Agency
Ed Ambrogio, Region 3
Richard Balla, Region 2
Darrell Brown, Office of Wetlands, Oceans, and Watersheds
Barry Burgan, Office of Wetlands, Oceans, and Watersheds
Mike Charpentier, Office of Research and Development
Robert Dietrich, Region 2
Virginia Engle, Office of Research and Development
Maryjo Feuerbach, Region 1
Austine Frawley, Region 1
Larry Gaugler, Region 2
Diane Myrick Gould, Region 1
Helen Grebe, Region 2
Linda Harwell, Office of Research and Development
James Harvey, Office of Research and Development
Amie Howell, Region 3
(amal Kadri, Office of Wetlands, Oceans, and Watersheds
Marilyn Katz, Office of Wetlands, Oceans and Watersheds
Andrew Kendall, Region 4
John Kiddon, Office of Research and Development
John Kushwara, Region 2
National Estuary Program Coastal Condition Report I
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U. S. Environmental Protection Agency
(cont.)
Janet Lambertson, Office of Research and
Development
Henry Lee, Office of Research and Development
John Macauley, Office of Research and Development
Fred McManus, Region 4
John McShane, Office of Wetlands, Oceans
and Watersheds
Walter Nelson, Office of Research and Development
Gerald Pesch, Office of Research and Development
Margherita Pryor, Region 1
Irene Purdy, Region 2
Suzanne Schwartz, Office of Wetlands, Oceans,
and Watersheds
Lisa Smith, Office of Research and Development
Kevin Summers, Office of Research and Development
Luisa Valiela, Region 9
Henry Walker, Office of Research and Development
U.S. Geological Survey
Peter Bourgeois
U.S. Fish and Wildlife Service
Jane E. MacLellan
NEP Estuary Programs
Albemarle-Pamlico National Estuary Program
(APNEP)
Bill Crowell, Director, APNEP, Raleigh, NC
Dean Carpenter, Science Coordinator,
North Carolina Department of Environment
and Natural Resources, Raleigh, NC
Barataria-Terrebonne National Estuary Program
(BTNEP)
Kerry St. Pe, Director, BTNEP, Thibodaux, LA
Richard DeMay, Senior Scientist, BTNEP,
Thibodaux, LA
Andrew Barron, Non-point Source Coordinator,
BTNEP, Thibodaux, LA
Joni Blanchard, Public Involvement Coordinator,
BTNEP, Thibodaux, LA
Deborah Schultz, Formal Education Coordinator,
BTNEP, Thibodaux, LA
Barnegat Bay National Estuary Program (BBNEP)
Bob Scro, Director, BBNEP, Toms River, NJ
Richard G. Lathrop, Director, Grant F. Walton
Center for Remote Sensing & Spatial Analysis,
Rutgers University, New Brunswick, NJ
Michael J. Kennish, Institute of Marine and
Coastal Sciences, Rutgers University,
New Brunswick, NJ
Mike DeLuca, Co-Chair, Science and Technical
Advisory Committee, BBNEP, Toms River, NJ
Jeanine Cava, BBNEP Project Associate,
Ocean County College, Toms River, NJ
Shannon Shinault, Public Outreach Coordinator,
BBNEP, Toms River, NJ
Buzzards Bay National Estuary Program (BB NEP)
Joe Costa, Director, BB NEP, East Wareham, MA
John Rockwell, Wetland Specialist, BB NEP,
East Wareham, MA
Tracy Warncke, Administrative Assistant, BB NEP,
East Wareham, MA
Casco Bay Estuary Partnership (CBEP)
Karen Hopkins Young, Director, CBEP, Portland, ME
Lee Doggett, Division of Environmental Assessment,
Maine Department of Environmental Protection,
Augusta, ME
Beverly Bayley-Smith, Assistant Director, CBEP,
Portland, ME
Michael Doan, Research Associate, Friends of Casco
Bay, South Portland, ME
Deborah Arbique, Administrative Assistant, CBEP,
Portland, ME
Center for the Inland Bays (GIB)
Edward A. Lewandowski, Executive Director, CIB,
Lewes, DE
Chris Bason, Science and Technical Coordinator,
CIB, Lewes, DE
Bennett Anderson, Delaware Department of Natural
Resources & Environmental Control, Dover, DE
Linda Popels, Science Coordinator, CIB, Lewes, DE
Sally Boswell, Education and Outreach Coordinator,
CIB, Lewes, DE
Loretta Smith, Administrative Assistant, CIB,
Lewes, DE
II National Estuary Program Coastal Condition Report
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Charlotte Harbor National Estuary Program
(CHNEP)
Lisa Beever, Director, CHNEP, Fort Myers, FL
Catherine A. Corbett, Senior Scientist, CHNEP,
Fort Myers, FL
Maran Brainard Hilgendorf, Communications
Manager, CHNEP, Fort Myers, FL
David A. Tomasko, Manager, Southwest Florida
Water Management District, Brooksville, FL
Coastal Bend Bays and Estuaries Program (CBBEP)
Ray Allen, Executive Director, CBBEP,
Corpus Christi, TX
Leo Trevino, Director of Project Implementation,
CBBEP, Corpus Christi, TX
James Bowman, Project Manager, CBBEP,
Corpus Christi, TX
Monika K. De La Garza, Public Relations &
Outreach Manager, CBBEP, Corpus Christi, TX
Galveston Bay Estuary Program (GBEP)
Helen E. Drummond, Program Director,
GBEP/Texas Commission on Environmental
Quality, Houston, TX
Steven R. Johnston, Monitoring and Research
Coordinator, GBEP/Texas Commission on
Environmental Quality, Houston, TX
Linda Broach, Aquatic Scientist, Texas Commission
on Environmental Quality, Houston, TX
Lisa Gonzalez, Research Scientist, Houston Advanced
Research Center, The Woodlands, TX
John Jacob, Environmental Quality Specialist, Texas
Cooperative Extension, Houston, TX
Indian River Lagoon National Estuary Program
(IRLNEP)
Troy Rice, Manager, St. Johns River Water
Management District, IRLNEP, Palm Bay, FL
Robert Day, St. Johns River Water Management
District, IRLNEP, Palm Bay, FL
Ed Garland, Regional Communications Coordinator,
St. Johns River Water Management District,
IRLNEP, Palm Bay, FL
Long Island Sound Study (LISS)
Mark Tedesco, Director, LISS, EPA Long Island
Sound Office, Stamford, CT
Paul Stacey, Connecticut Department of
Environmental Protection, Hartford, CT
Christine Olsen, Connecticut Department of
Environmental Protection, Hartford, CT
Robert Burg, Communication Coordinator, LISS,
EPA Long Island Sound Office, Stamford, CT
Lower Columbia River Estuary Partnership (LCREP)
Deborah Marriott, Executive Director, LCREP,
Portland, OR
Scott McEwen, Director of Technical Programs,
LCREP, Portland, OR
Jason Karnezis, Monitoring Coordinator, LCREP,
Portland, OR
Carolyn Myers Lindberg, Development &
Communications Director, LCREP,
Portland, OR
Matt Burlin, Habitat Restoration Coordinator,
LCREP, Portland, OR
Jill Leary, Water Quality Monitoring Coordinator,
LCREP, Portland, OR
Jennie Boyd, Stewardship Programs Manager,
LCREP, Portland, OR
Maryland Coastal Bays Program (MCBP)
Dave Blazer, Program Director, MCBP, Berlin, MD
Catherine Wazniak, Coastal Bays Monitoring
Coordinator, Maryland Department of Natural
Resources, Annapolis, MD
Roman Jesien, Science Coordinator, MCBP,
Berlin, MD
Carol J. Cain, Technical Coordinator, MCBP,
Berlin, MD
Dave Wilson, Jr., Public Outreach Coordinator,
MCBP, Berlin, MD
Matthew R. Hall, Biological Research Statistician,
Maryland Department of Natural Resources,
Annapolis, MD
Jane Thomas, Science Communicator,
University of Maryland, College Park, MD
National Estuary Program Coastal Condition Report III
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Massachusetts Bays Program (MBP)
Jan Smith, Executive Director, MBP, Boston, MA
Bruce Carlisle, Assistant Director, MBP, Boston, MA
Christian Krahforst, Marine Monitoring Scientist,
MBP, Boston, MA
Peter J. Hanlon, Outreach and Policy Coordinator,
MBP, Boston, MA
Mobile Bay National Estuary Program (Mobile Bay
NEP)
David W. Yeager, Director, Mobile Bay NEP,
Mobile, AL
Roberta Swarm, Deputy Director, Mobile Bay NEP,
Mobile, AL
J. Scott Brown, Alabama Department of
Environmental Management, Mobile, AL
Steven G. Summersell, Alabama Department of
Environmental Management, Mobile, AL
Mark E. Ornelas, Alabama Department of
Environmental Management, Mobile, AL
Lee Yokel, Outreach and Education Director,
Mobile Bay NEP, Mobile, AL
Morro Bay National Estuary Program (Morro Bay
NEP)
Dan Berman, Program Director, Morro Bay NEP,
Morro Bay, CA
Ann Kitajima, Program Manager for Volunteer
Monitoring Program, Morro Bay, CA
Cheryl Lesinski, Education and Outreach
Coordinator, Morro Bay NEP, Morro Bay, CA
Narragansett Bay Estuary Program (NBEP)
Richard Ribb, Program Director, NBEP,
Providence, RI
Chris Deacutis, Science Coordinator, NBEP,
Providence, RI
Thomas Ardito, Outreach and Policy Coordinator,
NBEP, Providence, RI
New Hampshire Estuaries Project (NHEP)
Jennifer Hunter, Director, NHEP, Durham, NH
Phil Trowbridge, Coastal Scientist, NHEP,
New Hampshire Department of Environmental
Services, Watershed Management Bureau,
Concord, NH
Dave Kellam, Project Coordinator, NHEP,
Durham, NH
Natalie Landry, Coastal Watershed Supervisor,
New Hampshire Department of Environmental
Services, Portsmouth, NH
New York/New Jersey Harbor Estuary Program
(NY/NJ HEP)
Robert M. Nyman, Director, NY/NJ HEP,
New York, NY
Cathy Yuhas, Technical Specialist, NY/NJ HEP,
New York, NY
Peter L. Sattler, Principal Environmental Planner,
Interstate Environmental Commission,
New York, NY
Michael P. Weinstein, President, New Jersey Marine
Sciences Consortium, Fort Hancock, NJ
Dennis J. Suszkowski, Science Director,
Hudson River Foundation, New York, NY
Jim Joseph, New Jersey Bureau of Shellfisheries,
New Jersey Department of Environmental
Protection, Trenton, NJ
Michael Celestino, New Jersey Bureau of
Shellfisheries, New Jersey Department of
Environmental Protection, Trenton, NJ
Carol Hoffman, New York State Department of
Environmental Conservation, Albany, NY
Ashley T. Pengitore, Passaic Valley Sewerage
Commissioners, Newark, NJ
Partnership for the Delaware Estuary (PDE)
Kathy Klein, Executive Director, PDE,
West Trenton, NJ
Martha Maxwell Doyle, Deputy Director, PDE,
West Trenton, NJ
Danielle Kreeger, Science Coordinator, PDE,
West Trenton, NJ
Carol R. Collier, Executive Director, Delaware
River Basin Commission, West Trenton, NJ
Bob Tudor, Deputy Executive Director, Delaware
River Basin Commission, West Trenton, NJ
Edward Santoro, Monitoring Coordinator, Delaware
River Basin Commission, West Trenton, NJ
Jessica Rittler Sanchez, River Basin Planner, Delaware
River Basin Commission, West Trenton, NJ
IV National Estuary Program Coastal Condition Report
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Partnership for the Delaware Estuary (PDE) (cont.)
Larry Niles, Chief, Endangered and Non-game
Species Program, New Jersey Division of
Fish and Wildlife, Trenton, NJ
Shaun Bailey, Marketing and Communications
Specialist, PDE, West Trenton, NJ
Deanne Ross, Program Specialist, PDE,
West Trenton, NJ
Sergio Huerta, Laboratory Administrator, Delaware
Division of Natural Resources, Dover, DE
Peconic Estuary Program (PEP)
Vito Minei, Program Director, PEP, Suffolk County
Department of Health Services, Office of
Ecology, Yaphank, NY
Bob Nuzzi, PEP, Suffolk County Department of
Health Services, Office of Ecology, Yaphank, NY
Robert Waters, PEP, Suffolk County Department of
Health Services, Office of Ecology, Yaphank, NY
Laura Bavaro, Senior Environmental Analyst/Suffolk
County Coordinator, PEP, Suffolk County
Department of Health Services, Office of
Ecology, Riverhead, NY
Martin Trent, PEP, Suffolk County Department of
Health Services, Office of Ecology, Yaphank, NY
Shana Miller, Technical Outreach Specialist,
New York Sea Grant, PEP, Suffolk County
Department of Health Services, Office of
Ecology, Yaphank, NY
Puget Sound Action Team (PSAT)
Brad Ack, Director, PSAT, Olympia, WA
Sarah Brace, Science Liaison, PSAT, Olympia, WA
Toni Weyman Droscher, Publications Editor &
Graphic Designer, PSAT, Olympia, WA
John Dohrmann, Director of Government Affairs,
PSAT, Olympia, WA
San Francisco Estuary Project (SFEP)
Marcia L. Brockbank, Program Manager, SFEP,
Oakland, CA
Mike Connor, Executive Director, San Francisco
Estuary Institute, Oakland, CA
Jennifer Hunt, Environmental Analyst, San Francisco
Estuary Institute, Oakland, CA
Chris Werme, San Francisco Estuary Institute,
Oakland, CA
Steve Weisberg, Executive Director, Southern
California Coastal Water Research Project,
Westminster, CA
Peggy Olofson, Director, San Francisco Estuary
Invasive Spartina Project, Berkeley, CA
Debbi Egter Van Wissekerke, Communications
Specialist, SFEP, Oakland, CA
San Juan Bay Estuary Partnership (SJBEP)
Jorge Bauza-Ortega, Director, SJBEP, San Juan, PR
Nyrma Nieves Brignoni, Outreach Coordinator,
SJBEP, San Juan, PR
Santa Monica Bay Restoration Commission (SMBRC)
Guang-yu Wang, Senior Scientist, SMBRC,
Los Angeles, CA
Joel Hanson, Program Coordinator, SMBRC,
Los Angeles, CA
Sarasota Bay Estuary Program (SBEP)
Mark Alderson, Executive Director, SBEP,
Sarasota, FL
Gary E. Raulerson, Senior Scientist, SBEP,
Sarasota, FL
Julia Burch, Public Outreach Coordinator, SBEP,
Sarasota, FL
Tampa Bay Estuary Program (TBEP)
Richard M. Eckenrod, Director, TBEP,
St. Petersburg, FL
Holly Greening, Senior Scientist, TBEP,
St. Petersburg, FL
Nanette Holland, Public Outreach Coordinator,
TBEP, St. Petersburg, FL
Tillamook Estuaries Partnership (TEP)
MarkTrenholm, Director, TEP, Garibaldi, OR
Bette Ross, Office Specialist, TEP, Garibaldi, OR
National Estuary Program Coastal Condition Report V
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VI National Estuary Program Coastal Condition Report
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COIMTB4TS
Executive Summary ES.2
Chapter 1
Introduction 2
Why Are Estuaries Important? 2
Population Pressures Affecting the NEPs 4
Why Be Concerned About the Health of Estuaries? 6
The National Estuary Program 6
Purpose and Format of This Report 8
Highlight: Why Isn't the Chesapeake Bay in the National Estuary Program? 9
Approaches Used to Measure Estuarine Condition 10
National Coastal Assessment (NCA) Program Monitoring Data 10
National Estuary Program (NEP) Monitoring Data 24
Chapter 2
U.S. National Estuary Program Coastal Condition—A National Snapshot 26
.27
NCA Indices of Estuarine Condition—U.S. NEP Estuaries
Population Pressures—A National Perspective 33
Correlation between NEP CCR Index Scores and Population Pressures 35
NEP Environmental Concerns 40
Chapter 3
Northeast Coast National Estuary Program Coastal Condition 44
Background 44
Population Pressures 45
NCA Indices of Estuarine Condition—Northeast Coast Region 45
NEP Estuaries and the Condition of the Northeast Coast Region 50
Casco Bay Estuary Partnership 54
Background 54
Environmental Concerns 55
Population Pressures 55
NCA Indices of Estuarine Condition—Casco Bay 55
Casco Bay Estuary Partnership Indicators of Estuarine Condition 58
Highlight: Trends in Toxic Chemicals in Casco Bay Sediments 60
Current Projects, Accomplishments, and Future Goals 63
Conclusion 63
National Estuary Program Coastal Condition Report VII
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New Hampshire Estuaries Project 64
Background 64
Environmental Concerns 65
Population Pressures 65
NCA Indices of Estuarine Condition—New Hampshire Estuaries 65
New Hampshire Estuaries Project Indicators of Estuarine Condition 69
Highlight: Mapping Impervious Surfaces in New Hampshire's
Coastal Watershed 70
Current Projects, Accomplishments, and Future Goals 73
Conclusion 74
Massachusetts Bays Program 75
Background 75
Environmental Concerns 76
Population Pressures 76
NCA Indices of Estuarine Condition—Massachusetts Bays .77
Massachusetts Bays Program Indicators of Estuarine Condition 80
Highlight: Monitoring and Ecological Assessment of the
Massachusetts Bays Ecosystem 82
Current Projects, Accomplishments, and Future Goals 85
Conclusion 85
Buzzards Bay Project National Estuary Program 86
Background 86
Environmental Concerns 87
Population Pressures 87
NCA Indices of Estuarine Condition—Buzzards Bay 87
Buzzards Bay National Estuary Program Indicators of Estuarine Condition 91
Highlight: Protecting the Endangered Roseate Tern 92
Current Projects, Accomplishments, and Future Goals 94
Conclusion 96
Narragansett Bay Estuary Program 97
Background 97
Environmental Concerns 98
Population Pressures 98
NCA Indices of Estuarine Condition—Narragansett Bay 99
Narragansett Bay Estuary Program Indicators of Estuarine Condition 103
Highlight: Fact-Based Findings in Narragansett Bay 104
Current Projects, Accomplishments, and Future Goals 107
Conclusion 107
Viii National Estuary Program Coastal Condition Report
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Long Island Sound Study 108
Background 108
Environmental Concerns 109
Population Pressures 109
NCA Indices of Estuarine Condition—Long Island Sound 110
Highlight: Tidal Marsh Loss in Long Island Sound 114
Long Island Sound Study Indicators of Estuarine Condition 116
Current Projects, Accomplishments, and Future Goals 118
Conclusion 119
Peconic Estuary Program 120
Background 120
Environmental Concerns 121
Population Pressures 121
NCA Indices of Estuarine Condition—Peconic Estuary 121
Peconic Estuary Program Indicators of Estuarine Condition 125
Highlight: Critical Lands Protection in the Peconic Estuary Watershed 128
Current Projects, Accomplishments, and Future Goals 130
Conclusion 130
New York/New Jersey Harbor Estuary Program 131
Background 131
Environmental Concerns 132
Population Pressures 132
NCA Indices of Estuarine Condition—New York/New Jersey Harbor 132
Highlight: New York/New Jersey Harbor—wide Water Quality Survey 136
New York/New Jersey Harbor Estuary Program Indicators of
Estuarine Condition 137
Current Projects, Accomplishments, and Future Goals 141
Conclusion 141
Barnegat Bay National Estuary Program 142
Background 142
Environmental Concerns 143
Population Pressures 143
NCA Indices of Estuarine Condition—Barnegat Bay 143
Barnegat Bay National Estuary Program Indicators of Estuarine Condition ... .147
Highlight: SAV Distribution, Abundance, and Health in Barnegat Bay 148
Current Projects, Accomplishments, and Future Goals 152
Conclusion 153
National Estuary Program Coastal Condition Report ix
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Partnership for the Delaware Estuary 154
Background 154
Environmental Concerns 155
Population Pressures 156
NCA Indices of Estuarine Condition—Delaware Estuary 156
Partnership for the Delaware Estuary Indicators of Estuarine Condition 160
Highlight: Horseshoe Crabs, Shorebirds, and People: The Many Facets of
Delaware Estuary's Population Ecology 164
Current Projects, Accomplishments, and Future Goals 166
Conclusion 166
Center for the Inland Bays 167
Background 167
Environmental Concerns 168
Population Pressures 168
NCA Indices of Estuarine Condition—Delaware Inland Bays .168
Highlight: Delaware Inland Bays Tributary Action Team 172
Center for the Inland Bays Indicators of Estuarine Condition 174
Current Projects, Accomplishments, and Future Goals .178
Conclusion .178
Maryland Coastal Bays Program 179
Background 179
Environmental Concerns 180
Population Pressures 180
NCA Indices of Estuarine Condition—Maryland Coastal Bays 181
Maryland Coastal Bays Program Indicators of Estuarine Condition 184
Highlight: Applied Monitoring: Incorporating Stable Isotope
Analysis into a Water Quality Index 186
Current Projects, Accomplishments, and Future Goals 192
Conclusion 192
Chapter 4
Southeast Coast National Estuary Program Coastal Condition 194
Background 194
Population Pressures 194
NCA Indices of Estuarine Condition—Southeast Coast Region 195
NEP Estuaries and the Condition of the Southeast Coast Region 199
X National Estuary Program Coastal Condition Report
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Albemarle-Pamlico National Estuary Program 202
Background 202
Environmental Concerns 203
Population Pressures 203
NCA Indices of Estuarine Condition—Albemarle-Pamlico
Estuarine Complex 204
Highlight: The FerryMon Project 208
Albemarle-Pamlico National Estuary Program Indicators of
Estuarine Condition 210
Current Projects, Accomplishments, and Future Goals 211
Conclusion 211
Indian River Lagoon National Estuary Program 212
Background 212
Environmental Concerns 213
Population Pressures 213
NCA Indices of Estuarine Condition—Indian River Lagoon 214
Highlight: Seagrass Monitoring in the Indian River Lagoon 218
Indian River Lagoon National Estuary Program Indicators of
Estuary Condition 220
Current Projects, Accomplishments, and Future Coals 222
Conclusion 222
Chapter 5
Gulf Coast National Estuary Program Coastal Condition 224
Background 224
Population Pressures 225
NCA Indices of Estuarine Condition—Gulf Coast Region 226
NEP Estuaries and the Condition of the Gulf Coast Region 231
Charlotte Harbor National Estuary Program 234
Background 234
Environmental Concerns 235
Population Pressures 235
NCA Indices of Estuarine Condition—Charlotte Harbor 236
Charlotte Harbor National Estuary Program Indicators of
F^stuarine Condition 238
Highlight: Hurricanes and Hypoxia in 2004 240
Current Projects, Accomplishments, and Future Goals 243
Conclusion 243
National Estuary Program Coastal Condition Report XI
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Sarasota Bay Estuary Program 244
Background 244
Environmental Concerns 245
Population Pressures 246
NCA Indices of Estuarine Condition—Sarasota Bay 246
Sarasota Bay Estuary Program Indicators of Estuarine Condition 249
Highlight: Improving Water Quality in the Sarasota Bay Watershed. 250
Current Projects, Accomplishments, and Future Goals 253
Conclusion 253
Tampa Bay Estuary Program 254
Background 254
Environmental Concerns 255
Population Pressures 255
NCA Indices of Estuarine Condition—Tampa Bay 256
Tampa Bay Estuary Program Indicators of Estuarine Condition 258
Highlight: Summary: Tampa Bay Habitat Restoration/Protection Master Plan . . . .262
Current Projects, Accomplishments, and Future Goals 265
Conclusion 265
Mobile Bay National Estuary Program 266
Background 266
Environmental Concerns 267
Population Pressures 268
NCA Indices of Estuarine Condition—Mobile Bay 268
Highlight: Invasive Species of Coastal Alabama and Mississippi 272
Mobile Bay National Estuary Program Indicators of Estuarine Condition .... .274
Current Projects, Accomplishments, and Future Goals 276
Conclusion 277
Barataria-Terrebonne National Estuary Program 278
Background 278
Environmental Concerns 279
Population Pressures 279
NCA Indices of Estuarine Condition—Barataria-Terrebonne
Estuarine Complex 280
Highlight: Maritime Forest Ridge and Marsh Restoration at
Port Fourchon, Louisiana 284
Barataria-Terrebonne National Estuary Program Indicators of
Estuarine Condition 286
Current Projects, Accomplishments, and Future Goals 288
Conclusion 288
XII National Estuary Program Coastal Condition Report
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Galveston Bay Estuary Program 289
Background 289
Environmental Concerns 290
Population Pressures 290
NCA Indices of Estuarine Condition—Galveston Bay 291
Galveston Bay Estuary Program Indicators of Estuarine Condition 294
Highlight: Case Study on Changes in Freshwater Wetland Habitat 296
Current Projects, Accomplishments, and Future Goals 301
Conclusion 301
Coastal Bend Bays and Estuaries Program 302
Background 302
Environmental Concerns 303
Population Pressures 303
NCA Indices of Estuarine Condition—Coastal Bend Bays 304
Coastal Bend Bays and Estuaries Program Indicators of
Estuarine Condition 307
Highlight: CBBEP Bacteria Source Tracking in Copano Bay 308
Current Projects, Accomplishments, and Future Goals 311
Conclusion 312
Chapter 6
West Coast National Estuary Program Coastal Condition 314
Background 314
Population Pressures 315
NCA Indices of Estuarine Condition—West Coast Region 315
NEP Estuaries and the Condition of the West Coast Region 319
Puget Sound Action Team 322
Background 322
Environmental Concerns 323
Population Pressures 323
NCA Indices of Estuarine Condition—Puget Sound 323
Highlight: Efforts to Address Low Dissolved Oxygen Levels in
Hood Canal, Washington 327
Puget Sound Action Team Indicators of Estuarine Condition 328
Current Projects, Accomplishments, and Future Goals 332
Conclusion 332
National Estuary Program Coastal Condition Report XIII
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Lower Columbia River Estuary Partnership 333
Background 333
Environmental Concerns 334
Population Pressures 334
NCA Indices of Estuarine Condition—Lower Columbia River Estuary 334
Highlight: Habitat Protection and Restoration in the Lower Columbia 338
Lower Columbia River Estuary Partnership Indicators of
Estuarine Condition 340
Current Projects, Accomplishments, and Future Goals 342
Conclusion 342
Tillamook Estuaries Partnership 343
Background 343
Environmental Concerns 344
Population Pressures 344
NCA Indices of Estuarine Condition—Tillamook Bay 345
Highlight: Addressing Bacterial Contamination in Tillamook Bay 348
Tillamook Estuaries Partnership Indices of Estuarine Condition 350
Current Projects, Accomplishments, and Future Goals 352
Conclusion 352
San Francisco Estuary Project .353
Background 353
Environmental Concerns 354
Population Pressures 354
NCA Indices of Estuarine Condition—San Francisco Estuary 354
Highlight: Ecosystem Indicators for the San Francisco Estuary 358
San Francisco Estuary Project Indicators of Estuarine Condition 360
Current Projects, Accomplishments, and Future Goals 364
Conclusion 365
Morro Bay National Estuary Program 366
Background 366
Environmental Concerns 367
Population Pressures 367
NCA Indices of Estuarine Condition—Morro Bay 368
Highlight: Kid's Beach Cleanup Event and Aerial Art a Success 371
Morro Bay National Estuary Program Indicators of Estuarine Condition 372
Current Projects, Accomplishments, and Future Goals 374
Conclusion 374
xiv National Estuary Program Coastal Condition Report
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Santa Monica Bay Restoration Commission 375
Background 375
Environmental Concerns 376
Population Pressures 376
NCA Indices of Estuarine Condition—Santa Monica Bay 376
Santa Monica Bay Restoration Commission Indicators of
Estuarine Condition 379
Highlight: Santa Monica Bay Stormwater Projects 380
Current Projects, Accomplishments, and Future Coals 384
Conclusion 384
Chapter 7
Puerto Rico National Estuary Program Coastal Condition 386
San Juan Bay Estuary Partnership 386
Background 386
Environmental Concerns 387
Population Pressures 387
NCA Indices of Estuarine Condition—San Juan Bay Estuary 388
Highlight: Getting the Message to the People—The San Juan Bay Estuary
Partnership Educational Outreach Efforts 392
San Juan Bay Estuary Partnership Indicators of Estuarine Condition 394
Current Projects, Accomplishments, and Future Goals 399
Conclusion 400
Appendix A
Procedures for Calculating Total Population, Population Growth Rate,
and Population Density for Various Geographic Areas 401
National Estuary Program Coastal Condition Report XV
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XVI National Estuary Program Coastal Condition Report
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Acronyms
ADEM
AET
ALAMAP
AMRAT
APNEP
BBNEP
BBNEP
BMP
BOD
BTNEP
BYPP
CAFOs
CBB
CBBEP
CBEP
CCMP
CCRWQCB
CDS
CHNEP
CIB
CISNet
CLPS
CPF
CPUE
CRSSA
CSO
CTDEP
CTR
CZM
ODD
DDE
DDT
DEP
DIN
DIP
DMF
DNA
Alabama Department of Environmental Management
Apparent Effects Threshold
Alabama Monitoring and Assessment Program
Alabama-Mississippi Rapid Assessment Team
Albemarle-Pamlico National Estuary Program
Buzzards Bay National Estuary Program
Barnegat Bay National Estuary Program
best management practice
biological oxygen demand
Barataria-Terrebonne National Estuary Program
Backyard Planting Program
confined animal feeding operations
Coalition for Buzzards Bay
Coastal Bend Bays and Estuaries Program
Casco Bay Estuary Partnership
Comprehensive Conservation and Management Plan
Central Coast Regional Water Quality Control Board
continuous deflective separation
Charlotte Harbor National Estuary Program
Center for the Inland Bays
Coastal Intensive Sites Network
Critical Lands Protection Strategy
Community Preservation Fund
catch per unit effort
Center for Remote Sensing and Spatial Analysis
combined sewer overflow
Connecticut Department of Environmental Protection
California Toxic Rule
Coastal Zone Management
p,p'-dichlorodiphenyldichloroethane
p,p'-dichlorodiphenyldichloroethylene
p,p'-dichlorodiphenyltrichloroethane
Department of Environmental Protection
dissolved inorganic nitrogen
dissolved inorganic phosphorus
Division of Marine Fisheries
deoxyribonucleic acid
National Estuary Program Coastal Condition Report XVII
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DNR
DNREC
DoD
DOI
DRBC
DSHS
DWQ
EMAP
EPA
EQB
ERDG
ERL
ERM
FDA
FDEP
FIPS
FWS
FYN
GAO
GBEP
GCRL
CIS
GLO
GPS
HAB
HCDOP
HEP
HRI
IEC
IEP
IRLNEP
kg/yr
LCREP
LDNR
LDWF
LIDAR
LISS
LTEIP
Department of Natural Resources
Department of Natural Resources and Environmental Control
U.S. Department of Defense
U.S. Department of the Interior
Delaware River Basin Commission
Department of State Health Services
Division of Water Quality
Environmental Monitoring and Assessment Program
U.S. Environmental Protection Agency
Environmental Quality Board
Ecological Research & Development Group
effects range low
effects range median
U.S. Food and Drug Administration
Florida Department of Environmental Protection
Federal Information Processing Standards
U.S. Fish and Wildlife Service
Florida Yards and Neighborhoods
U.S. Government Accountability Office
Galveston Bay Estuary Program
Gulf Coast Research Laboratory
geographic information systems
General Land Office
Global Positioning System
harmful algal bloom
Hood Canal Dissolved Oxygen Program
Harbor Estuary Program
Habitat Restoration Initiative
Interstate Environmental Commission
Interagency Ecological Project
Indian River Lagoon National Estuary Program
kilograms per year
Lower Columbia River Estuary Partnership
Louisiana Department of Natural Resources
Louisiana Department of Wildlife and Fisheries
Light Detection And Ranging
Long Island Sound Study
Long-Term Environmental Indicator Program
XVIII National Estuary Program Coastal Condition Report
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MAC
MAIA
MAR
Massachusetts CZM
MassWildlife
MBP
MCBP
MCL
MDE
MDPH
MFRMR
mg/kg
mg/L
mi
mL
Mobile Bay NEP
Morro Bay NEP
MWRA
NASA
NBEP
NCA
NCCRI
NCCR II
NCDENR
NCDOT
NEP
NEP CCR
NERR
NFWF
NHCP
NHEP
NJDEP
NJHDG
NMFS
NOAA
NPDES
NPS
NRCS
Manatee Awareness Coalition
Mid-Atlantic Integrated Assessment
multiple antibiotic resistance
Massachusetts Office of Coastal Zone Management
Massachusetts Division of Fisheries and Wildlife
Massachusetts Bays Program
Maryland Coastal Bays Program
maximum contaminant level
Maryland Department of the Environment
Massachusetts Department of Public Health
Maritime Forest Ridge and Marsh Restoration
milligram per kilogram
milligram per liter
square miles
milliliter
Mobile Bay National Estuary Program
Morro Bay National Estuary Program
Massachusetts Water Resources Authority
National Aeronautics and Space Administration
Narragansett Bay Estuary Program
National Coastal Assessment
National Coastal Condition Report
National Coastal Condition Report II
North Carolina Department of Environment and Natural Resources
North Carolina Department of Transportation
National Estuary Program
National Estuary Program Coastal Condition Report
National Estuarine Research Reserve
National Fish and Wildlife Foundation
New Hampshire Coastal Program
New Hampshire Estuaries Project
New Jersey Department of Environmental Protection
New Jersey Harbor Discharges Group
National Marine Fisheries Service
National Oceanic and Atmospheric Administration
National Pollution Discharge Elimination System
National Park Service
U.S. Natural Resource Conservation Service
National Estuary Program Coastal Condition Report XIX
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NRDA
NS&T
NWI
NYCDEP
NYC DOHMH
NYSDEC
ODEQ
OEHHA
ORD
OWOW
PAH
PCB
PDE
PEP
PIVOT
POTWs
ppm
ppt
PSAT
PVSC
RAM
RIDEM
RMP
SAV
SBEP
SCCWRP
SCDHS
SCWRRP
SET
SFEI
SEEP
SFRWQCB
SFWMD
SJBEP
SJRWMD
SMBRC
SMBRP
SPMD
Natural Resource Damage Assessment
National Status and Trends
National Wetland Inventory
New York City Department of Environmental Protection
New York City Department of Health and Mental Hygiene
New York State Department of Environmental Conservation
Oregon Department of Environmental Quality
California Office of Environmental Health Hazard Assessment
Office of Research and Development
Office of Wetlands, Oceans and Watersheds
polycyclic aromatic hydrocarbon
polychlorinated biphenyl
Partnership for the Delaware Estuary
Peconic Estuary Program
Performance Indicators Visualization and Outreach Tool
publicly owned treatment works
parts per million
parts per thousand
Puget Sound Action Team
Passaic Valley Sewerage Commissioners
Rapid Assessment Method
Rhode Island Department of Environmental Management
Regional Monitoring Program for Trace Substances
submerged aquatic vegetation
Sarasota Bay Estuary Program
Southern California Coastal Water Research Project
Suffolk County Department of Health Services
Southern California Water Resources Research Project
surface elevation table
San Francisco Estuary Institute
San Francisco Estuary Project
San Francisco Regional Water Quality Control Board
South Florida Water Management District
San Juan Bay Estuary Partnership
St. Johns River Water Management District
Santa Monica Bay Restoration Commission
Santa Monica Bay Restoration Project
semipermeable membrane device
XX National Estuary Program Coastal Condition Report
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STAC
STOP
STP
SWFWMD
SWIM
TAG
TAT
TBBI
TBEP
TBI
TBT
TCEQ
TEP
TMDL
TOG
TPWD
ug/kg
ug/L
uM
UNH
URI
USAGE
USDA
USGS
VIMS
VMP
voc
WCI
WDNR
WDOH
WHAT
WQI
WRP
WSDE
WWTP
Scientific and Technical Advisory Committee
Stop Throwing Out Pollutants Program
sewage treatment plant
Southwest Florida Water Management District
Surface Water Improvement and Management
Technical Advisory Committee
Tributary Action Team
Tampa Bay Benthic Index
Tampa Bay Estuary Program
The Bay Institute
tributyltin
Texas Commission on Environmental Quality
Tillamook Estuaries Partnership
Total Maximum Daily Load
total organic carbon
Texas Parks and Wildlife Department
microgram per kilogram
microgram per liter
micromolar
University of New Hampshire
University of Rhode Island
U.S. Army Corps of Engineers
U.S. Department of Agriculture
U.S. Geological Survey
Virginia Institute of Marine Studies
Volunteer Monitoring Program
volatile organic compound
Water Clarity Index
Washington Department of Natural Resources
Washington Department of Health
Wetland Health Assessment Toolbox
Water Quality Index
Wetlands Restoration Program
Washington State Department of Ecology
wastewater treatment plant
National Estuary Program Coastal Condition Report XXI
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EXECUTIVE SUMMARY
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EXECUTIVE SUMMARY
Estuaries are bodies of water that provide transition
zones between the fresh water from rivers and the saline
environment of the ocean. The various interactions that
occur between fresh water and salt water in estuaries
result from the specific physical and hydrological char-
acteristics of these waterbodies. These characteristics
produce unique environments that support wildlife and
fisheries and contribute substantially to the economy of
the United States.
The nation's estuaries are a subset of U.S. coastal
waters and encompass a wide variety of coastal habitats,
including wetlands, salt marshes, coral reefs, mangrove
and kelp forests, seagrass meadows, tidal mudflats, and
upwelling areas. These estuarine habitats provide
spawning grounds, nurseries, shelter, and food for fish,
shellfish, and other wildlife species, as well as nesting,
resting, feeding, and breeding habitat for 75% of water-
fowl and other migratory birds.
As part of the 1987 amendments to the Clean Water
Act, the Section 320 National Estuary Program (NEP)
promotes comprehensive planning efforts to help
protect nationally significant estuaries in the United
States that are deemed to be threatened by pollution,
development, or overuse. Since the inception of the
program, 28 estuaries have been nominated by their
respective state Governors and officially designated as
NEP estuaries, and in 2007, the NEP will celebrate
20 years of restoring and protecting these nationally
significant estuaries. As one of the U.S. Environmental
Protection Agency's (EPA's) most successful watershed
programs, the NEP demonstrates the effectiveness of a
stakeholder-driven, collaborative process to address
water quality problems and to target habitat restoration.
Individual NEPs are required to monitor the effec-
tiveness of their management activities to address
estuary-specific priority actions. The Clean Water Act
also requires that EPA report periodically on the condi-
tion of the nations estuarine waters. Coastal states
provide EPA with valuable information about the
condition of their estuarine resources; however, because
the individual states and the NEPs and their partners
use different approaches for data collection and the
evaluation of estuarine condition, it has been difficult
to compare this information among states, NEPs, or on
a regional or national basis.
To better address questions about the condition
of the nation's estuaries, EPA, the National Oceanic
and Atmospheric Administration (NOAA), the U.S.
Geological Survey (USGS), the U.S. Department of the
Interior (DOI), and the U.S. Department of Agriculture
(USDA) agreed to participate in a multi-agency effort to
assess the condition of all U.S. estuaries, including the
NEP estuaries. To minimize the problems created by
compiling data collected using different sampling
methods, the collaborating agencies chose to assess estu-
arine condition using nationally consistent monitoring
surveys, the results of which are compiled periodically
into a series of reports called the National Coastal
Condition Reports.
Published in 2001, the first National Coastal Condi-
tion Report (NCCR I) reported that the nation's collec-
tive estuarine resources were in fair condition. This
assessment was based on available data, collected from
1990 through 1996, that were used to characterize
about 70% of the nation's estuarine resources. Agencies
contributing data to the NCCR I included EPA,
NOAA, DOI, and USDA. The second National Coastal
Condition Report (NCCR II), published in 2004, was
based on available data from 1997 to 2000 that were
representative of 100% of the estuarine area of the
conterminous 48 states and Puerto Rico. These data
show that the nation's estuaries continue to be rated in
fair condition. Agencies contributing to the NCCR II
included EPA, NOAA, the U.S. Fish and Wildlife
Service (FWS), and USGS, as well as several state,
regional, and local organizations that provided informa-
tion on the current condition of the nation's coastal
waters.
IES.2 National Estuary Program Coastal Condition Report
-------
EXECUTIVE SUMMARY
The objective of this National Estuary Program
Coastal Condition Report (NEP CCR) is to report on
the condition of the nation's 28 NEP estuaries. The
NEP CCR presents two major types of monitoring
data for each NEP estuary: (1) data collected as part of
EPA's National Coastal Assessment (NCA) and (2) data
collected by the individual NEPs or by the NEPs in
partnership with interested stakeholders, including state
environmental agencies, universities, or volunteer moni-
toring groups. Together, these data paint a picture of the
overall condition of the coastal resources of the nations
NEP estuaries.
The ratings developed in this report are based solely
on NCA monitoring data and not the data collected by
the individual NEPs. The NCA data—the most
comprehensive and nationally consistent data available
related to estuarine condition—were collected from
1997 through 2003 for four primary indices of estu-
arine condition (water quality index, sediment quality
index, benthic index, and fish tissue contaminants
index). These indices were assigned a good, fair, or poor
rating for each NEP estuary according to the rating
criteria presented in Table ES-1. These ratings were then
used to create overall condition ratings for the collective
NEP estuaries of each coastal region (Northeast Coast,
Southeast Coast, Gulf Coast, West Coast, and Puerto
Rico) and the nation (Figure ES-1). The overall condi-
tion rating for the nation's collective NEP estuaries is
based on a weighted average of the regional index
scores. More detailed information on the component
indicators for water quality and sediment quality, when
available, is also presented throughout this report.
In addition to the NCA-based assessments, this
report provides individual profiles of the 28 NEP
estuaries that describe the indicators each NEP uses to
address specific environmental concerns, including
water and sediment quality, habitat quality, living
resources, and environmental stressors, as appropriate.
Each profile includes background information on the
NEP estuary discussed, maps of the NEP study area,
and data on the population pressures that affect the
study area, including the total population (2000), popu-
lation density (2000), and population growth rate
(1960-2000) in NOAA-designated coastal counties that
are within or transect the boundaries of the study area
(i.e., NEP-coincident coastal counties). A short discus-
sion of an individual NEP's current projects, accom-
plishments, and future goals is also provided in each
profile, as well as a Highlight article, developed by the
individual NEP, that describes a representative species,
program, or activity for the NER These profiles are not
meant to be exhaustive or comprehensive reports, but
are included to provide the reader with a perspective
about the variety of habitats and species that each NEP
estuary shelters, the salient or unique aspects about the
nature of the estuary, the problems of most concern to
local stakeholders, and the ongoing and planned initia-
tives to continue monitoring and managing the envi-
ronmental health of the estuary. The monitoring data
derived from the NEPs will be used to develop an effec-
tive management plan for protecting and improving the
condition of the nation's NEP resources.
war-
Estuanes are critical for the survival of a number of species,
including the Brown Pelican, which nests and breeds along the
nation's coasts (johnTheilgard).
National Estuary Program Coastal Condition Report ES.3
-------
Describing Estuarine Condition
This report presents two types of monitoring data
to provide a perspective on the condition of the nation's
NEP estuaries: data collected by the NCA and data
collected by the individual NEPs and their partners.
National Coastal Assessment
(NCA) Monitoring Data
The monitoring data derived from EPA's NCA are
used exclusively in this report to develop indices of
estuarine condition for the 28 NEP estuaries and to
calculate regional and national ratings of NEP estuarine
condition. The NCA survey was designed to assess the
percentage of the nation's estuaries and coastal waters
exhibiting poor, fair, or good condition using consistent
and comparable environmental indicators, and data from
this survey was used for the NCCR series, which includes
this NEP CCR. The probability survey design, indices,
and component indicators of the NCA survey are appro-
priate to assess estuarine condition at state, regional (e.g.,
Gulf Coast), or national scales. When probability survey
designs incorporate geographic areas smaller than a state,
as in the case of the NEPs, assessments can be made of the
condition of each strata, provided a sufficient number of
samples were taken to achieve the desired confidence level.
The NCA sampled a minimum of 20 (typically 35—50)
monitoring sites to assess the condition of each NEP
estuary. Twelve hundred and thirty-nine NCA sites were
sampled in the NEP estuarine areas. In addition, the NCA
was designed to assess condition during the summer season,
when estuaries are expected to be the most stressed (i.e.,
highest water temperature). These data are also used to
determine reference conditions to assess ecological
responses to stressors and to set state nutrient criteria.
Overall
Condition
Northeast Coast >
NEP Estuaries
OvsraJ]
Condition
West COBS-;
j \£P EziiK
Estuarine Health
Overall
Condition
Gulf Coast
NEP Estuaries
Water Quality Index
Sediment Quality Index
Benthic Index
Overall
Condition
Puerto Rico
NEP Estuaries
Fish Tissue
Contaminants Index
Figure ES-I. National and regional overall condition ratings for NEP estuaries based on NCA results (1997-2003).
ES.4 National Estuary Program Coastal Condition Report
-------
EXECUTIVE SUMMARY
Table ES-I. NCA Indices Used to Assess Estuarine Condition
Icon
Water
Quality
Index
Sediment
Quality
Index
Benthic
Index
Water Quality Index—This index is based on five water quality component indicators (dissolved inorganic nitrogen
[DIN], dissolved inorganic phosphorus [DIP], chlorophyll a, water clarity, and dissolved oxygen).
Ecological Condition by Site
Good: No component indicators are rated
poor, and a maximum of one component
indicator is rated fair.
Fair: One component indicator is rated
poor, or two or more component
indicators are rated fair.
Poor: Two or more component indicators
are rated poor.
Ranking by NEP Estuary or Region
Good: Less than 10% of the NEP estuarine area is in poor
condition, and more than 50% of the NEP estuarine area
is in good condition.
Fair: 10% to 20% of the NEP estuarine area is in poor condi-
tion, or more than 50% of the NEP estuarine area is in
combined poor and fair condition.
Poor: More than 20% of the NEP estuarine area is in poor
condition.
Sediment Quality Index—This index is based on three sediment quality component indicators (sediment toxicity,
sediment contaminants, and sediment total organic carbon [TOC]).
Ecological Condition by Site Ranking by NEP Estuary or Region
Good: Less than 5% of the NEP estuarine area is in poor
condition, and more than 50% of the NEP estuarine area
is in good condition.
Fair: 5% to 15% of the NEP estuarine area is in poor condi-
tion, or more than 50% of the NEP estuarine area is in
Good:
Fair:
Poor:
No component indicators are rated poor,
and the sediment contaminants indicator
is rated good.
No component indicators are rated poor,
and the sediment contaminants indicator
is rated fair.
One or more component indicators are
rated poor.
combined poor and fair condition.
Poor: More than 15% of the NEP estuarine area is in poor
condition.
Benthic Index (or a surrogate measure)—This index indicates the condition of the benthic community (organisms
living in estuarine sediments) and can include measures of benthic community diversity, the presence and abundance
of pollution-tolerant species, and the presence and abundance of pollution-sensitive species.
Ecological Condition by Site
Good, fair, and poor were
determined using regionally
dependent benthic index scores.
Ranking by NEP Estuary or Region
Good: Less than 10% of the NEP estuarine area has a poor
benthic index score, and more than 50% of the NEP estu-
arine area has a good benthic index score.
Fair: 10% to 20% of the NEP estuarine area has a poor benthic
index score, or more than 50% of the NEP estuarine area
has a combined poor and fair benthic index score.
Poor: More than 20% of the NEP estuarine area has a poor
benthic index score.
Fish Tissue Contaminants Index—This index indicates the level of chemical contamination in target
fish/shellfish species.
Fish
Tissue
Contaminants
Index
Ecological Condition by Site
Good: For all chemical contaminants listed
in Table 1-21 (Chapter I), composite
fish tissue contaminant concentra-
tions are below the EPA Advisory
Guidance* concentration range.
Fair: For at least one chemical contami-
nant listed in Table 1-21, composite
fish tissue contaminant concentra-
tions are within the EPA Advisory
Guidance concentration range.
Poor: For at least one chemical contami-
nant listed in Table 1-21, composite
fish tissue contaminant concentra-
tions are above the EPA Advisory
Guidance concentration range.
Ranking by NEP Estuary or Region
Good: Less than 10% of the fish samples analyzed (Northeast
Coast region) or the monitoring stations where fish were
caught (all other regions) are in poor condition, and more
than 50% of the fish samples analyzed (Northeast Coast
region) or the monitoring stations where fish were caught
(all other regions) are in good condition.
Fair: 10% to 20% of the fish samples analyzed (Northeast Coast
region) or the monitoring stations where fish were caught
(all other regions) are in poor condition, or more than
50% of the fish samples analyzed (Northeast Coast region)
or the monitoring stations where fish were caught (all
other regions) are in combined poor and fair condition.
Poor: More than 20% of the fish samples analyzed (Northeast
Coast region) or the monitoring stations where fish were
caught (all other regions) are in poor condition.
*The EPA Advisory Guidance concentration is based on the non-cancer ranges for all contaminants except PAH (benzo(a)pyrene), which are
based on a cancer range because a non-cancer range for PAHs does not exist (seeTable I-21,Chapter I).
National Estuary Program Coastal Condition Report ES.5
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Given the parameters of the NCA methodology, the
NEP CCR is not designed to assess the temporal vari-
ability or extent (i.e., how often within a summer these
conditions exist or the area affected) of highly variable
water quality parameters (e.g., nutrient, chlorophyll a,
or dissolved oxygen concentrations). In addition, the
report does not provide the specific location of poor,
fair, or good conditions, but rather the proportion of a
larger area that exhibits such conditions, nor does it
answer local estuary-specific management questions
regarding the location, temporal extent, or frequency of
degraded conditions for rapidly changing parameters.
This report is appropriate for defining the percentage
of the nation's NEP waters (nationally, regionally, and
on an individual estuary basis) that exhibit poor, fair, or
good conditions for fairly stable summer characteristics,
such as sediment contaminant levels and benthic condi-
tion, which often reflect conditions integrated over
months or even years. However, to maintain NCA
monitoring at a reasonable cost, measurements were
taken one time per sampling site during the summer
over a modest number of sites; therefore, the resulting
NCA survey data provide a less accurate view of the
ephemeral conditions associated with an estuary's water
column, where water quality conditions may change
weekly, daily, or even hourly during a summer sampling
period.
National Estuary Program
(NEP) Monitoring Data
To assess the overall condition of each NEP estuary,
the NCA data should be evaluated in addition to data
collected locally by the NEPs over a longer time period
and at more sampling locations. For example, degraded
benthic condition may not necessarily be caused solely
by the high sediment contaminant levels measured by
the NCA, but may also be caused by short-term stresses,
such as sporadic hypoxia or algal blooms. The NCA
"snapshot" approach may not capture these stresses
because they occur outside the summer diurnal
sampling period; therefore, an assessment of NEP-
specific data is necessary.
The NEP monitoring data are derived from the
individual NEPs and are discussed in this report to
provide information on NEP monitoring methods and
indicators developed to address site-specific estuarine
concerns. Because these data are collected using
methods unique to each individual NEP, they generally
cannot be used to make comparisons among estuaries at
the regional or national level. A summary of the data is
provided in the individual NEP profiles in the hope
that information about the types of indicators that have
been developed, implemented, and found to be effective
in assessing spatial and temporal trends for one NEP
estuary will also prove useful to other NEPs.
Boating, fishing, swimming, and bird watching are just a few of the numerous recreational activities that people enjoy in estuaries
(Toni Droscher, PSAT).
ES.6 National Estuary Program Coastal Condition Report
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To find out if there is an NEP in your coastal area
and to obtain detailed environmental monitoring data
for the 28 NEP estuaries, please visit www.epa.gov/
owow/estuaries, www.nationalestuaries.org, or
www.epa.gov/emap.
Summary of Findings
With this NEP CCR, the collaborating agencies and
the individual NEPs strive to provide a benchmark of
estuarine condition that paints a comprehensive picture
of the nation's NEP estuaries. The report indices are
based on the large amount of NCA monitoring data
collected from 1997 through 2003 on the condition of
the nation's NEP estuaries. NCA rating scores for estu-
arine condition are based on a 5-point system, where a
score of less than 2.0 is rated poor; 2.0 to less than 2.3
is rated fair to poor; 2.3 to 3.7 is rated fair; greater than
3.7 to 4.0 is rated good to fair; and greater than 4.0 is
rated good.
The major findings of this report are as follows:
• An assessment of the ecological monitoring data
shows that the overall condition of the nation's
NEP estuaries is generally fair (2.7), but that
regionally, the Puerto Rico (1.5) and Northeast
Coast (1.5) regions are rated poor, the Gulf Coast
(2.75) and West Coast (2.5) regions are rated fair,
and the Southeast Coast region is rated good to
fair (4.0) for overall condition (Table ES-2). The
EXECUTIVE SUMMARY
overall condition ratings for the nation's NEP
estuaries are based on four primary indices of
estuarine condition—a water quality index, sedi-
ment quality index, benthic index, and fish tissue
contaminants index.
The water quality index for the nation's collective
NEP estuaries is rated fair (3.6), with the North-
east Coast (3.0), Gulf Coast (3.0), West Coast
(3.0), and Puerto Rico (3.0) regions rated fair and
the Southeast Coast region (5.0) rated good for
this index. Water quality data, including data on
the five component indicators (DIN, DIP, chloro-
phyll a, water clarity, and dissolved oxygen), were
available for all NEP estuaries of the United
States.
The sediment quality index for the nation's
collective NEP estuaries is rated fair to poor (2.1),
with the Northeast Coast (1.0), West Coast (1.0),
and Puerto Rico (1.0) regions rated poor; the
Gulf Coast region (2.0) rated fair to poor; and the
Southeast Coast region (4.0) rated good to fair for
this index. Sediment quality index ratings were
based on three component indicators: sediment
toxicity, sediment contaminants, and sediment
TOC. For some NEPs, two of the three compo-
nent indicators for assessing sediment quality were
not monitored, and the sediment quality index
was based solely on the measurement of one
component indicator. Typically, sediment TOC
Table ES-2. Regional and National Rating Scores3 for Indices of Estuarine Condition and Overall Condition
for the Nation's NEP Estuaries
Index
Water Quality Index
Sediment Quality
Index
Benthic Index
Fish Tissue
Contaminants Index
Overall Condition
Northeast
Coast
3
1
1
1
1.5
Southeast
Coast
5
4
3
4
4.0
Gulf
Coastb
3
2
2
4
2.75
West
Coast
3
1
5
1
2.5
Puerto United
Ricoc States'1
3 3.6
1 2.1
1 2.7
1 2.6
1.5 2.7
a Rating scores are based on a 5-point system, where a score of less than 2.0 is rated poor; 2.0 to less than 2.3 is rated fair to poor; 2.3 to 3.7 is
rated fair; greater than 3.7 to 4.0 is rated good to fair; and greater than 4.0 is rated good.
bThis rating score does not include the impact of the hypoxic zone in offshore Gulf Coast waters.
cThis rating score includes only San Juan Bay Estuary, Puerto Rico.
d The U.S. score is based on an areally weighted mean of the regional index scores.
National Estuary Program Coastal Condition Report ES.7
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was more consistently monitored among sites than
sediment toxicity or sediment contaminant
concentrations. The NCA did not evaluate the
Peconic Estuary for sediment quality, and only
sediment TOC data were available for the four
NEP estuaries located in Florida (Indian River
Lagoon, Charlotte Harbor, Sarasota Bay, and
Tampa Bay).
The benthic index for the nation's collective NEP
estuaries is rated fair (2.7), with the Northeast
Coast (1.0) and Puerto Rico (1.0) regions rated
poor, the Gulf Coast region (2.0) rated fair to
poor, the Southeast Coast region (3.0) rated fair,
and the West Coast region (5.0) rated good for
this index. Benthic indices were developed for the
NEP estuaries of the Northeast Coast, Southeast
Coast, and Gulf Coast regions, and benthic
community diversity was used as a surrogate indi-
cator of biological condition for the West Coast
and Puerto Rico regions. No assessment was
possible using the benthic community diversity
indicator for three West Coast estuaries (Lower
Columbia River Estuary, Morro Bay, and Santa
Monica Bay).
The fish tissue contaminants index for the
nation's collective NEP estuaries is rated fair (2.6),
with the Northeast Coast (1.0), West Coast (1.0),
and Puerto Rico (1.0) regions rated poor, and the
Southeast Coast (4.0) and Gulf Coast (4.0)
regions rated good to fair for this index. NCA
data for the fish tissue contaminants index were
not available for several of the NEP estuaries,
including Casco Bay, the Indian River Lagoon,
Charlotte Harbor, Sarasota Bay, and Tampa Bay.
Nationally, 37% of the NEP estuaries are in poor
overall condition (Table ES-3, Figure ES-2).
Regionally, roughly 100% of Puerto Rico's NEP
estuary (San Juan Bay Estuary) is in poor overall
condition, and 46% of the Northeast Coast, 46%
of the Gulf Coast, 36% of the West Coast, and
23% of the Southeast Coast NEP estuaries are in
poor overall condition.
Missing
2%
Good
32%
Poor
37%
Figure ES-2. Overall
condition data for U.S.
NEP estuaries (U.S.
EPA/NCA).
Comparison of NEP Estuaries
with All U.S. Estuaries
A primary goal of the NCCR series is to provide a
benchmark of estuarine condition to measure the
success of estuarine programs over time. To achieve this
goal, the conditions reported in the NCCR series and
the NEP CCR need to be comparable. Comparing data
between the NCCR II (inclusive of both NEP and
non-NEP estuaries) and the NEP CCR i.s complicated
because, in some cases, common indicators were not
available for both reports. For example, the NCCR II
used five environmental indices to determine coastal
condition—water quality, sediment quality, benthic
Table ES-3. Percent of NEP Estuarine Area in Poor Condition by Index and Region
Index
Water Quality Index
Sediment Quality
Index
Benthic Index
Fish Tissue
Contaminants Index
Overall Condition
Northeast
Coast
9
21
26
38
46
Southeast
Coast
4
6
15
10
23
Gulf
Coast
13
15
20
12
46
West
Coast
4
17
4
32
36
Puerto
Rico
8
33
65
40
100
United
States
8
15
17
23
37
ES.8 National Estuary Program Coastal Condition Report
-------
EXECUTIVE SUMtt
condition, fish tissue contaminant concentrations, and
coastal habitat condition; however, information on
coastal habitat condition was not available for the
current NEP CCR. To facilitate a comparison between
the two reports, the rating scores for the NCA indices
reported in the NCCR II were recalculated, to the
extent possible, using the methods followed in the NEP
CCR. The coastal habitat index and its effect on
regional and national ratings were excluded from the
NCCR II scores presented in this report. Table ES-4
summarizes the rating scores by index and region,
comparing the NCCR II and the NEP CCR results.
Table ES-4 shows that the overall condition score for
the nation's collective NEP estuaries is 2.7 (rated fair);
this score is comparable to the overall condition score of
2.6 (rated fair) for all U.S. estuaries (both NEP and
non-NEP estuaries). On a national basis, it appears that
the collective NEP estuaries score slightly higher for two
of the four indices (water quality index and benthic
index) than the scores for all U.S. estuaries, comparably
for the fish tissue contaminants index, and slightly
lower for the sediment quality index.
Regionally, the rating results are somewhat mixed
when comparing NEP estuaries to all U.S. estuaries,
although the regional overall condition scores are not
appreciably different between the two groups (within
0.25 points or less of the corresponding score). For
example, the regional overall condition scores for the
NEP estuaries are higher for the Northeast CoaM and
West Coast regions, comparable for the Southeast Co HI
and Gulf Coast regions, and lower for Puerto RJCO th in
the regional overall condition scores for all estuaries
(both NEP and non-NEP).
It is noteworthy that the most complete data
set collected in the NCA was for the water quality
index, whereas data for the sediment quality index
(predominately for the sediment toxiciry and sediment
contaminants component indicators), benthic index,
and fish tissue contaminants index were missing for
some NEPs.
EPA's Clean Water State Revolving Fund Programs
2005 Annual Report noted that significant improve-
ments in wastewater treatment plants (WWTPs) since
1987 have resulted in expanded capacity for secondary
and tertiary treatment of wastewater to remove nutri-
ents, heavy metals, and organic contaminants. These
strides, coupled with more stringent water quality
standards for industrial dischargers, have resulted in
water quality improvements in many areas; however, the
legacy of contamination remains in the sediments of
many estuaries as byproducts of the Industrial Revolu-
tion and years of discharging without the protective
mandates of the Clean Water Act. This residual
contamination may result in reduced benthic commu-
nity health and in the bioaccumulation of chemical
contaminants in fish and shellfish tissues.
Table ES-4. Regional and National Rating Scores'" by Index for All U.S. Estuaries (NCCR) and for NEP Estuaries
Index
Water Quality
Index
Sediment
Quality Index
Benthic Index
Fish Tissue
Contaminants
Index
Overall
Condition
Northeast
Coast
NCCR
2
1
1
1
1.25
NEP
3
1
1
1
I.SO
Southeast
Coast
NCCR
4
4
3
5
4.0
NEP
5
4
3
4
4.0
Gulf
Coast
NCCR
3
3
2
3
2.75
NEP
3
2
2
4
2.75
West
Coast
NCCR
3
2
3
1
2.25
NEP
3
1
5
1
2.50
Puerto
Rico
NCCR
3
1
1
NA
1.67
NEP
3
1
1
1
1.50
United
States
NCCR
3.0
2.6
2.2
2.6
2.6
NEP
3.6
2.1
2.7
2.6
2.7
* Rating scores are based on a 5-point system, where a score of less than 2.0 is rated poor; 2.0 to less than 2.3 is rated fair to poor; 2.3 to 3.7 is
rated fair; greater than 3.7 to 4.0 is rated good to fair; and greater than 4.0 is rated good.
National Estuary Program Coastal Condition Report ES.9
-------
Population Pressures Affecting
the NEPs
Population pressures on coastal counties coincident
with the individual NEP study areas or collectively on
NEP-coincident coastal counties within a specific region
were evaluated with respect to both temporal and spatial
perspectives using total population (2000), population
density (2000), and percent population growth rate
(1960-2000). Total population provides a perspective oi
the total number of individuals using the various
resources within the NEP-coincident coastal counties at
any point in time, and population density provides a
measure of how saturated the associated NEP-coinci-
dent coastal counties are with respect to human devel-
opment. The population growth rate over a specific
time interval provides an indication of how quickly
human development in an area occurs and the coin-
ciding infrastructure development that would be needed
to provide for the associated residential and commercial
development and services. When assessed collectively,
these population measures provide information about
the pressures exerted by society on the NEP coastal
ecosystems.
Regionally, the NEP-coincident coastal counties of
the Northeast Coast region contained the highest total
population in 2000 (38 million), followed by the West
Coast (30 million), Gulf Coast (11 million), and
Southeast Coast (3 million) regions. Population density
values also showed that the NEP-coincident coastal
counties of the Northeast Coast region have the highest
regional density (1,055 persons/mi2), followed by the
West Coast (421 persons/mi2), Gulf Coast (287
persons/mi ), and Southeast Coast (168 persons/mi2)
regions. By comparison, Puerto Rico had the highest
population density in 2000 of any NEP region (5,055
persons/mi2). In contrast, population growth rates for
these same regional areas show a different pattern, with
the Gulf Coast region having the highest growth rate
(133%), closely followed by the Southeast Coast (131%)
and West Coast (100%) regions, and lastly by the
Northeast Coast (24%) region.
Estuarine waters serve as habitat and breeding areas for hundred of species of birds and other wildlife (John Theilgard).
ES.1 0 National Estuary Program Coastal Condition Report
-------
EXECUTIVE SUMMARY
Correlation Between NEP CCR
Index Scores and Population
Pressures
Population data reveal some patterns for both total
population and population density with respect to
population pressures within the NEP-coincident coastal
counties. As shown in Table ES-5, when the population
in the coastal counties is greater than 2 million people,
as it is for 11 NEPs, the overall condition scores for
these NEPs range from 1.0 (rated poor) to 3.0 (rated
fair), with a mean score of 2.26 (rated fair to poor). For
the 8 NEPs with populations between 1 to 2 million
people, the overall condition scores range from 1.5
(rated poor) to 5.0 (rated good), with a mean score of
3.30 (rated fair). For the 9 NEPs with populations less
than 1 million people, the overall condition scores range
from 1.75 (rated poor) to 5.0 (rated good), with a mean
score of 3.45 (rated fair). Although it is clear that the
NEPs with the highest populations (> 2 million) showed
the lowest overall condition scores, as well as scores with
the smallest range of values, the overall condition scores
for the other two population groups varied widely;
however, the mean overall condition scores tended to
be slightly higher in the NEPs with the lowest total
population.
The population density results (Table ES-6) are
very similar to the total population results. For the
5 NEPs with population densities greater than 1,000
persons/mi2 in NEP-coincident coastal counties, the
overall condition scores range from 1.0 (rated poor) to
4.33 (rated good), with a mean score of 2.16 (rated fair
to poor). For the 8 NEPs with population densities
ranging from 500 to 1,000 persons/mi2, the overall
condition scores range from 1.75 (rated poor) to 3.5
(rated fair), with a mean score of 2.58 (rated fair).
Finally, for the 15 NEPs with the lowest population
densities (less than 500 persons/mi ), the overall condi-
tion scores range from 1.75 (rated poor) to 5.0 (rated
good), with a mean score of 3.39 (rated fair).
A slight difference among the three population density
groups shows an increase in the mean overall condition
scores as the population density decreases.
Although the mean overall condition scores based on
total population and population density within the
NEP-coincident coastal counties appear to exhibit some
patterns, it should be noted that within any of the total
population groups (Table ES-5) or population density
groups (Table ES-6), there is a high degree of variability
in the overall condition scores for the individual NEPs
that can be inconsistent with the patterns exhibited in
the mean overall condition scores.
Table ES-5. Comparison of Total Population of NEP-Coincident Coastal Counties with the NCA Mean Overall
Condition Scores for the NEP Estuaries
Total Population of
NEP-Coincident
Coastal Counties
Range in NCA
Overall Condition
Scores Observed
NCA Mean
Overall
Condition Score
Number of
NEP
Estuaries
> 2 million
1.0-3.0
2.26
II
1-2 million
1.5-5.0
3.30
< I million
1.75-5.0
3.45
Table ES-6. Comparison of Population Density of NEP-Coincident Coastal Counties with the NCA Mean Overall
Condition Scores for the NEP Estuaries
Population Density of
NEP-Coincident
Coastal Counties
Range in NCA
Overall Condition
Scores Observed
NCA Mean
Overall
Condition Score
Number of
NEP
Estuaries
> 1,000 persons/mi2
1.0-4.33
2.16
500-1,000 persons/mi2
1.75-3.5
2.58
500 persons/mi2
1.75-5.0
3.39
IS
National Estuary Program Coastal Condition Report ES.11
-------
NEP Environmental Concerns
The NEP estuaries have been affected by a wide
variety of environmental concerns, several of which have
been adopted by the NEPs as priority management
activities for their respective estuaries. For this report,
more that two dozen major environmental concerns
were identified by the NEPs, including the following:
• Habitat loss/alteration
• Declines in fish and wildlife populations
• Excessive nutrients
• Toxic chemical contaminants
• Pathogens
• Alteration of freshwater flows
• Introduction of invasive species.
Some environmental concerns have commonality
in many NEPs, whereas others are more NEP-specific
because they relate to the unique climactic, hydrologic,
geologic, or geomorphologic conditions associated with
an individual estuary. Figure ES-3 shows a variety of
environmental concerns identified by the 28 NEPs.
Shortcomings of Available Data
This NEP CCR provides estimates of estuarine
condition on a national, regional, and individual scale
for the 28 NEP estuaries. These estimates are based on
nationally consistent and comparable NCA data on four
primary indices of estuarine condition. For about one-
third of the NEP estuaries, however, complete data on
all four NCA indices were not available. As a result, an
NEP estuary and its respective region rnay have received
either a higher or a lower overall condition score and
rating than would have been achieved if the missing
data were available for use in the analysis of estuarine
condition. This report makes the best use of the avail-
able NCA data to characterize and assess the condition
of the nation's NEP estuaries; however, it cannot repre-
sent all individual NEP estuarine systems at all of the
appropriate temporal and spatial scales necessary to
assess the overall condition of the these estuaries.
In addition to the NCA data presented in this report,
the individual NEPs have also been mandated the
responsibility of monitoring environmental conditions
in their individual estuaries to assess whether the
U.S. coastal areas are home to roughly 40% of the U.S. population (JohnTheilgard).
ES.1 2 National Estuary Program Coastal Condition Report
-------
Habitat Loss/Alteration
Species Loss/Decline
Nutrients
Toxics
Pathogens
Freshwater Inflow
Introduced/Pest Species
Sedimentation
Contaminated Seafood
Human Population Growth
Conventional Pollutants
Land Use
Dredging/Disposal
Floatable Debris
HABs and/or Red/Brown Tides
Non-point Source Pollution
Hypoxia (Low Oxygen)
Stormwater
Drinking Water Problems
Hydrologic Alteration
Oil Spills
Swimming Area Closings
Wastewater
Flooding
National Estuary Program Environmental Concerns
J28
J25
J2I
]20
Jio
Us
Zl"
o
10 IS 20
Number of Estuary Programs
25
30
Figure ES-3. List of environmental concerns of the nation's 28 individual NEPs.
environmental health of the estuary is degrading and, if
possible, to help restore ecological condition. Because
each NEP estuary's suite of environmental concerns are
site-specific, each state, NEP, and its stakeholders have
often developed monitoring and assessment methods
that are unique to their estuary. Individual NEP moni-
toring may not be randomized spatially (as was done for
the NCA) because NEP monitoring may target specific
areas to ascertain specific sources of contamination or to
obtain more detailed information about a particular
environmental concern relevant to the NEP estuary.
It is important that the users of this report realize the
shortcomings and limitations of the data presented,
both from the NCA and from the individual NEPs.
Both of these data sources taken together can often
show very different results for the same estuarine index
or component indicator. For example, although the
NCA survey data may indicate that dissolved oxygen
concentrations in the water column are in good condi-
tion, this assessment is based on monitoring conducted
in an estuary during daylight hours only for a one-day
period in the summer season during a given year. In
contrast, the individual NEP monitoring data may indi-
cate that dissolved oxygen levels at the same site are
poor based on hourly monitoring conducted over a
24-hour monitoring cycle, including hours after dark
when oxygen concentrations often drop due to plant
respiration. Both of these data collection methods are
correct within the limitations of the conditions under
which the monitoring was conducted and the analysis
used to evaluate the data.
National Estuary Program Coastal Condition Report ES.13
-------
Conclusion
There was no consistent and comparable NCA estu-
arine survey at the inception of the NEP. However,
based on the probabilistic sampling results collected by
the NCA from 1997 through 2003, the NEP estuaries
scored equal to or higher than all U.S. estuaries
combined.
During the past 20 years, population pressures along
the coasts have increased. By 2000, more than two-
thirds of the coastal population lived in NEP-coincident
counties, which comprise less than 6% of the coastal
land area. Since 1987, as NEPs have attempted to
address their individual environmental concerns, they
have made many improvements to areas that are
assessed by NCA. For example, work by the individual
NEPs and their partners to make improvements in
WWTPs, assist with the implementation of stormwater
management plans, or identify primary sources of non-
point source pollution may result in better ratings for
water quality parameters in the NEP estuaries. The
NEPs have also directed resources towards addressing
some environmental concerns that are not directly
assessed by the NCA. For example, habitat loss and
alteration is listed as an environmental concern for all
28 NEP estuaries, and the individual NEPs have
worked hard to monitor, conserve, protect, and restore
important habitats (e.g., SAV, wetlands) in their study
areas, including restoring and/or protecting more than
one million acres of habitat between 2000 and 2006.
Tourism, fisheries, and other commercial activities thrive on the wealth of natural resources supplied by estuaries (John Theilgard).
ES.14 National Estuary Program Coastal Condition Report
-------
CHAPTER I INTRODUCTION
l«£]
-------
CHAPTER I
INTRODUCTION
The National Estuary Program Coastal Condition
Report (NEP CCR), a comprehensive report on the
condition of the nation's National Estuary Program
(NEP) waters, is a collaborative effort among the indi-
vidual NEPs and the U.S. Environmental Protection
Agency's (EPA's) National Coastal Assessment (NCA),
Office of Wetlands, Oceans and Watersheds (OWOW),
and Office of Research and Development (ORD).
The first National Coastal Condition Report (NCCR
I) (U.S. EPA, 2001) assessed the condition of the
nation's coasts using data from 1990—1996 that were
provided by several existing coastal programs, including
EPA's Environmental Monitoring and Assessment
Program (EMAP), the U.S. Fish and Wildlife Service's
(FWS's) National Wetland Inventory (NWI), and the
National Oceanic and Atmospheric Administration's
(NOAA's) National Status and Trends (NS&T)
Program. The second in this series of reports, the
National Coastal Condition Report II (NCCR II) (U.S.
EPA, 2004a), assessed coastal condition using data from
1997-2000 that were provided by the NCA and the
NWI. The NEP CCR is similar to the NCCR series
in structure, but instead of assessing national coastal
condition, it focuses specifically on the condition of
the 28 NEP estuaries using NCA data collected from
1997 through 2003. The NEP CCR also presents
recent monitoring data collected and analyzed by the
individual NEPs for a variety of estuarine indicators.
Figure 1-1 shows the study areas assessed for all 28 NEP
estuaries of the conterminous 48 states and Puerto Rico.
Why Are Estuaries Important?
Estuaries Are Valuable and Productive
Natural Ecosystems
Estuaries are bodies of water that receive both fresh
water and sediment influx from rivers and tidal influx
from the ocean, thus providing transition zones between
the fresh water of rivers and the saline environment of
the sea. This interaction produces a unique environ-
ment that supports diverse habitats for a wide variety of
living resources, such as fish and wildlife, and
contributes substantially to the economy of coastal
areas.
Estuaries are critical for the survival of a number of
species. Many fish and shellfish species, including most
commercially and recreationally important species, rely
on the sheltered waters of estuaries as protected places
to spawn and for their offspring to grow and develop
(giving estuaries the nickname "nurseries of the sea").
Estuarine waters also serve as habitat and breeding areas
for hundreds of species of birds and other wildlife,
including marine mammals such as manatees, seals, sea
lions, otters, porpoises, and whales.
In addition to serving as important wildlife habitat, estuaries
perform valuable services that benefit human communities
(JohnTheilgard).
2 National Estuary Program Coastal Condition Report
-------
CHAPTER I INTRODUCTION
27
Northeast Coast
I. Casco Bay
2. New Hampshire Estuaries
3. Massachusetts Bays
4. Buzzards Bay
5. Narragansett Bay
6. Long Island Sound
7. Peconic Estuary
8. New York/New Jersey Harbor
9. Barnegat Bay
10. Delaware Estuary
11. Delaware Inland Bays
12. Maryland Coastal Bays
Southeast Coast
13. Albemarle-Pamlico
Estuarine Complex
14. Indian River Lagoon
Gulf Coast
15. Charlotte Harbor
16. Sarasota Bay
17. Tampa Bay
18. Mobile Bay
19. Barataria-Terrebonne
Estuarine Complex
20. Galveston Bay
21. Coastal Bend Bays
West Coast
22. Puget Sound
23. Lower Columbia River Estuary
24. Tillamook Bay
25. San Francisco Estuary
26. Morro Bay
27. Santa Monica Bay
Puerto Rico
28. San Juan Bay Estuary
i—^^
Figure I -1. A map of the study areas for each of the 28 NEP estuaries.
Estuaries Have Many Human Uses
In addition to serving as important habitat for
wildlife, estuaries perform valuable services that benefit
human communities. Tourism, fisheries, and other
commercial activities thrive on the wealth of natural
resources supplied by estuaries. The many commercially
important fish and shellfish that depend on estuaries
include striped bass, shad, salmon, sturgeon, shrimp,
crabs, lobster, clams, oysters, mussels, and bay scallops.
Estuaries also supply water for industrial uses; lose water
to freshwater diversions for drinking and irrigation uses;
serve as the critical terminals for the nation's marine
transportation system and the U.S. Navy; provide a
point of discharge for municipalities and industries; and
are the downstream end of non-point source runoff,
serving as filters for pollutants and sediments carried in
water flowing from upstream. Wetland plants along the
edge of estuaries act as a natural buffer between the land
and the ocean, absorbing flood waters, dissipating storm
surges, and helping to prevent erosion by stabilizing the
shoreline.
Estuaries also provide community benefits, such as
recreation, scientific knowledge, education, and
aesthetic values. They are often the cultural centers of
coastal communities, serving as the focal point for local
commerce, recreation, celebrations, customs, and tradi-
tions. Boating, fishing, swimming, surfing, and bird
watching ate just a few of the numerous recreational
activities that people enjoy in estuaries.
National Estuary Program Coastal Condition Report 3
-------
CHAPTER I
INTRODUCTION
Population Pressures Affecting
the NEPs
The coastal areas surrounding estuaries are among
the most populated areas in the nation. Although the
nations narrow fringe of coastal land represents only
13% of the total contiguous land area of the United
States, it is home to roughly 43% of the U.S. population
(Figure 1-2).
A comparison of U.S. population data (1960—2000)
for the nation and various geographic areas (e.g., all
non-coastal counties, all coastal counties, and all NEP-
coincident coastal counties) reveals that the largest
percentage of the U.S. population (57%) lived in non-
coastal counties in 2000 (Figure 1-3). Of the 43% of
the U.S. population living in NOAA-designated coastal
counties in 2000, almost 69% lived in NEP-coincident
coastal counties, which represent less than 6% of the
coastal land area of the contiguous United States
(Cuilliton et al., 1990; U.S. Census Bureau, 1991;
Certain aspects of the nation's economic activity
depend on estuaries and other coastal waters:
• Estuaries provide habitat for more than 75% of U.S.
commercial fish catch and for 80% to 90% of the recre-
ational fish catch. Estuarine-dependent fisheries are
among the most valuable within regions and across the
nation.
• Commercial and recreational fishing, boating, tourism,
and other coastal industries provide more than 28
million jobs nationwide and generate $54 billion in goods
and services each year.
• There are 25,500 recreational facilities along the U.S.
coasts and almost 44,000 mi2 of outdoor public recre-
ation areas.The average American spends 10 recreational
days on the coast each year. More than 180 million
Americans—nearly 70% of the U.S. population—visit
ocean and bay beaches annually, and coastal recreation
and tourism generate $8 to $ 12 billion in annual revenue.
Sources: NOAA, 1990; NRC, 2000.
Figure 1-2. Population distribution in the United States in 2000 (U.S. Census Bureau, 2001).
4 National Estuary Program Coastal Condition Report
-------
CHAPTER I INTRODUCTION
2001). It should be noted that these calculations
include only marine NOAA-designated coastal counties
for the lower 48 states. For the purposes of this report,
the populations of the counties bordering the Great
Lakes were processed as non-coastal counties. This
topic, along with a discussion of NEP-coincident
counties, can be found in Appendix A of this report.
Figure 1-4 shows the population densities for these
same geographic areas during this same time period
(1960-2000). Although the rate of increase in popu-
lation density is relatively constant, there is clearly great
variability (a 10-fold difference) between the population
density of non-coastal counties versus NEP-coincident
coastal counties. For example, the population density in
the NEP-coincident coastal counties in 2000 was
highest at almost 500 persons/mi2, whereas the popula-
tion density in the conterminous 48 states was about
100 persons/mi and in non-coastal counties was a mere
60 persons/mi2. The population density in all U.S.
coastal counties in 2000 was about 300 persons/mi2. As
shown in Table 1 -1, the population growth rate for all
U.S. coastal counties from 1960 to 2000 was 70%,
compared to 48% for non-coastal counties and 57% for
the nation. The population growth rate for this same
period within NEP-coincident coastal counties was
59%, slightly more than the national population growth
rate (U.S. Census Bureau, 1991; 2001).
300
250
200
ISO
I 100
I
50
I960
D U.S. D Coastal
NEP Coastal
Non-coastal
D U.S. D Coastal
NEP Coastal
Non-coastal
Figure 1-3. Total population data for the United States from
1960 to 2000 (U.S. Census Bureau, 199 I; 2001).
Figure 1-4. Population density data for the United States from
960 to 2000 (U.S. Census Bureau, 199 I; 2001).
1
Table l-l. Comparison of U.S. Total Population, Population Density, and Population Growth Rate for the Nation,
Coastal Counties, NEP-coincident Coastal Counties, and Non-coastal Counties* (U.S. Census Bureau, 1991;
2001)
United States
Coastal counties
NEP-coincident coastal counties
Non-coastal counties
*Excludes population and land area from Alaska,
Total
population,
2000
(millions)
280
119
82
Population
density,
2000
(persons/mi2)
94
308
498
160 62
Hawaii, and U.S.Territories.
Percent
population
growth rate,
1960-2000
57
70
59
48
Land area
(mi2)
2,959,060
387,470
164,380
2,571,590
National Estuary Program Coastal Condition Report 5
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CHAPTER I
INTRODUCTION
Why Be Concerned About
the Health of Estuaries?
The economy of many coastal areas is based
primarily on the natural beauty and bounty of estuaries,
and the livelihoods of the people who live and work in
these areas are affected when these estuaries are imper-
iled. Because a disproportionate percentage of the
nation's population lives in coastal communities, the
increased activities of municipalities, commerce,
industry, and tourism in these areas have created envi-
ronmental pressures that threaten coastal resources.
These pressures include increased solid waste produc-
tion; higher volumes of urban non-point source runoff;
loss of green space and wildlife habitat; declines in
ambient water and sediment quality; and increased
demands for wastewater treatment, irrigation and
potable water, and energy supplies. In addition, residen-
tial and commercial development continue to destroy
estuarine wetlands and alter the quantity and timing of
freshwater flow, which is critical to river and estuarine
function. In effect, the same human uses that are
desired of coastal waters also have the potential to lessen
their value. This report not only discusses indices of
estuarine condition that gauge the extent to which NEP
habitats and resources have been altered, but it also
addresses connections between estuarine condition and
the ability of estuaries to meet human expectations for
their use.
The National Estuary F'rogram
As the U.S. population grows and the demands
imposed on our nation's natural resources increase, so
too does the importance of protecting these resources
for their natural, economic, and aesthetic values. It is
the mission of EPA's NEP to restore and protect
Americas nationally significant estuaries. Through its
approach of inclusive, community-based planning and
action on the watershed level, the NEP is an important
initiative in conserving U.S. estuarine resources and an
effective model for the protection and management of
other coastal areas.
Established as part of the 1987 amendments to
Section 320 of the Clean Water Act, the NEP promotes
comprehensive planning efforts to help protect nation-
ally significant estuaries judged to be threatened by
pollution, development, or overuse. Section 320
requires the development of a Comprehensive
Conservation and Management Plan (CCMP) for
attaining or maintaining water quality in each NEP
estuary. Aspects of water quality addressed by the
CCMPs include the protection of public water supplies;
the protection and propagation of a balanced, indige-
nous population of shellfish, fish, and wildlife; and the
maintenance of recreational opportunities, both in and
on the water. The objective of each individual NEP is to
create and implement a CCMP that addresses the entire
range of environmental problems facing an NEP
The NEP promotes comprehensive planning efforts to help protect nationally significant estuaries judged to be threatened by pollution,
development, or overuse (JohnTheilgard),
6 National Estuary Program Coastal Condition Report
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CHAPTER I INTRODUCTION
estuary, as well as to maintain the estuary's economic
and social value; therefore, NEPs are required to
monitor the effectiveness of their CCMPs to achieve
measurable results. By providing grants and technical
assistance, EPA helps state and local governments
achieve these goals and share "lessons learned" among
the individual NEPs and with other coastal communi-
ties.
Although EPA administers the national-level NEP,
program decisions and activities for the 28 individual
NEPs are carried out by committees of local govern-
ment officials, private citizens, and representatives from
other federal agencies, academic institutions, industry,
and estuary user-groups. Estuaries are selected for inclu-
sion in the NEP through a nomination process, with
nominations submitted to EPA during designated
nomination periods by the Governor of the state where
the estuary is located. Table 1-2 provides a current list
of the nation's NEP estuaries, as well as the year these
estuaries received NEP designation.
Once selected for inclusion in the national program,
each individual NEP must create decision-making
committees comprised of relevant stakeholders to iden-
tify and prioritize the problems in their estuary. Most
NEPs choose a management framework that includes a
Management Committee to oversee the routine opera-
tion of the program; a Policy Committee comprised of
high-level representatives from federal, state, and local
government agencies; a Technical Advisory Committee
to guide technical decisions; and a Citizens' Advisory
Committee to represent the interests of estuary user-
groups and the public. Together, these committees
develop the CCMP to protect the NEP estuary and its
resources.
The flexible and collaborative nature of the NEP
has allowed the 28 individual NEPs to develop many
innovative approaches to address local problems;
approaches uniquely tailored to local environmental
conditions and to the needs of local communities and
stakeholders. At the same time, the national structure
Table 1-2. U.S. Estuaries in the National Estuary Program (U.S. EPA, 2006d)
Northeast Coast
Year of
Entry
Puerto Rico
Year of
Entry
CascoBay.ME 1990
New Hampshire Estuaries, NH 1995
Massachusetts Bays, MA 1990
Buzzards Bay, MA 1987
Narragansett Bay, Rl and MA 1987
Long Island Sound, CT and NY 1987
Peconic Estuary, NY 1992
New York/New Jersey Harbor, NY and NJ 1988
Barnegat Bay, NJ 1995
Delaware Estuary, NJ, PA, and DE 1988
Delaware Inland Bays, DE 1988
Maryland Coastal Bays, MD 1995
Southeast Coast
Albemarle-Pamlico Estuarine Complex, NC
andVA 1987
Indian River Lagoon, FL 1990
San Juan Bay Estuary, PR
Gulf Coast
1992
Charlotte Harbor, FL 1995
Sarasota Bay, FL 1988
Tampa Bay, FL 1990
Mobile Bay, AL 1995
Barataria-Terrebonne Estuarine Complex, LA 1991
Galveston Bay.TX 1988
Coastal Bend Bays.TX 1992
West Coast
Puget Sound, WA 1987
Lower Columbia River Estuary, WA and OR 1995
Tillamook Bay, OR 1994
San Francisco Estuary, CA 1987
MorroBay.CA 1995
Santa Monica Bay, CA 1988
National Estuary Program Coastal Condition Report 7
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CHAPTER I INTRODUCTION
facilitates the sharing of successful management
approaches, technologies, and ideas. Effective projects
and innovative programs carried out by an individual
NEP often serve as models for similar initiatives for
other NEPs and coastal areas.
Although environmental results are often slow to be
realized, positive signs of improving environmental
conditions are already emerging from the activities of
the individual NEPs. The NEPs have worked hard to
monitor, conserve, protect, and restore important habi-
tats (e.g., submerged aquatic vegetation [SAV], wet-
lands) in their study areas, including restoring and/or
protecting more than one million acres of habitat since
2000 (U.S. EPA, 2006b). They are also demonstrating
success in finding effective institutional arrangements
from which to manage their estuaries, including secur-
ing and leveraging funds and improving public educa-
tion and citizen participation through outreach efforts.
Purpose and Format of This
Report
The purpose of this NEP CCR is to present a broad
baseline picture of the condition of the nation's NEP
estuaries from 1997 through 2003, as well as additional
information about the specific conditions and chal-
lenges of each NEP estuary. This report uses currently
available data to compare the condition of the nation's
NEP estuaries to each other, as well as regionally and
nationally; however, it is not intended to be a compre-
hensive literature review of estuarine information.
Instead, this report uses NCA data on four primary
indices of estuarine condition and data collected by
individual NEPs on a variety of site-specific indicators
to provide insight into current estuarine condition. This
report also presents data gaps and other issues that envi-
ronmental managers focus on to make more reliable
assessments as to how the condition of the nation's NEP
estuaries may be changing with time. This NEP CCR
will serve as a continuing benchmark for analyzing the
progress of the NEPs and is expected to be followed in
subsequent years by reports on more specialized estu-
arine issues.
Chapter 2 of this report presents available NCA data
on a national scale for the 28 NEP estuaries in the
conterminous 48 states and Puerto Rico. These data arc-
then broken down and analyzed for the NEP estuaries
of five geographic regions: Northeast Coast (Chapter 3),
Southeast Coast (Chapter 4), Gulf Coast (Chapter 5),
West Coast (Chapter 6), and Puerto Rico (Chapter 7).
These chapters include a regional overview of NEP
estuarine condition and profiles of the individual NEPs
in that region. Each NEP profile presents information
on the specific indicators used by an NEP to evaluate
water and sediment quality, habitat quality, living
resources, and other environmental stressors in their
estuary, as well as an overview of the current projects,
accomplishments, and future goals of the individual
program. The NEPs were also asked to provide a short
Highlight article for each profile describing either a
specific aspect of their estuary or an exemplary program
developed at the local estuary level to address site-
specific environmental concerns. These articles are
intended to illustrate the unique living resources of the
estuary, as well as innovative monitoring methods,
successful restoration/remediation efforts, or novel deci-
sion-making and management efforts undertaken at the
local level. The diversity of the subjects described in the
Highlight articles speaks to the wide spectrum of
programs and monitoring approaches that exist among
the 28 NEP estuaries.
8 National Estuary Program Coastal Condition Report
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CHAPTER I INTRODUCTION
Chesapeake Bay Program
Why Isn't the Chesapeake Bay in the National Estuary Program?
The largest estuary in the United States, the
Chesapeake Bay, is protected under its own federally
mandated program that is separate from, but related
to, the NEE In fact, the approach and methods of the
NEP were developed from the foundation laid by
earlier efforts to protect Chesapeake Bay. Chesapeake
Bay was the first estuary in the United States to be
targeted for restoration and protection. In 1983, the
Governors of Maryland, Virginia, and Pennsylvania;
the Mayor of the District of Columbia; and the EPA
Administrator signed the Chesapeake Bay Agreement,
committing their states, the District of Columbia, and
EPA to prepare plans for protecting and improving
water quality and living resources in Chesapeake Bay.
The Chesapeake Bay Program evolved as an institu-
tional mechanism to restore the Bay and to meet the
goals of the Chesapeake Bay Agreement. This program
guides and coordinates multi-state and multi-agency
activities.
The Chesapeake Bay Program raised awareness of
the need to establish federal-state partnerships to
protect estuaries threatened by pollution, develop-
ment, and overuse. The NEP was established in
response to the recognition of a need to protect not
only the Chesapeake Bay but also the many other
nationally significant estuaries throughout the country.
Atlantic
Ocean
National Estuary Program Coastal Condition Report 9
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CHAPTER I INTRODUCTION
Approaches Used to Measure
Estuarine Condition
There are two major approaches presented in each
chapter of this report for evaluating estuarine condition.
The first approach uses unbiased, quality-assured moni-
toring data collected nationally by the EPA NCA to
make consistent comparison ratings of four primary
indices of estuarine condition (water quality index,
sediment quality index, benthic index, and fish tissue
contaminants index) among the NEP estuaries. The
resulting ratings for each index are then used to calcu-
late an individual NEP rating, a regional NEP rating,
and a national rating of NEP estuarine condition. Using
the NCA approach, estuarine condition for the indi-
vidual NEP estuaries and regions can be expressed in
terms of the percent of estuarine area in good, fair, or
poor condition and can be compared nationally. The
overall condition and index ratings for the nation's
collective NEP estuaries are based on an areally
weighted mean of the regional overall condition and
index scores. NCA sampling for each estuary is typically
conducted at sites during a one-day period over the
summer months for one to two years; therefore, the
NCA data present only a "snapshot" of what is occur-
ring in the estuary at that time.
The second approach presented in this report uses
estuary-specific monitoring data collected by the indi-
vidual NEPs and their partners in support of local
problem-solving efforts. For some NEP estuaries,
monitoring data have been collected continuously for
more than a decade, and some estuarine indicators may
be monitored on an hourly, daily, weekly, monthly,
quarterly, or yearly basis. These monitoring data can
provide a more detailed view of the various cyclic
changes that may occur daily or seasonally in an estuary
to evaluate long-term changes in an indicator; however,
because the individual NEPs use a variety of approaches
and methods for data collection and evaluation, it is
often difficult to compare this information among estu-
aries or on a national basis. Table 1-3 compares some of
the differences in temporal and spatial monitoring
between the two monitoring approaches presented in
this report.
Each of the two approaches has strengths and weak-
ness, but the resulting information taken together paints
a more precise picture of the overall condition of the
resources of the NEP estuaries than can be gleaned from
either program approach individually. The two moni-
toring approaches are described in the following
sections.
National Coastal Assessment
(NCA) Monitoring Data
EPA's NCA provides representative data on four
indices of estuarine condition (water quality index, sedi-
ment quality index, benthic index, and fish tissue conta-
minants index) for the 28 NEP estuaries. These four
primary indices were selected because of the availability
Table 1-3. Monitoring Approaches of the NCA and NEP
Parameter
NCA Approach
Individual NEP Approach
Indicators
monitored
Water quality index
Sediment quality index
Benthic index
Fish tissue contaminants index
Highly variable, but may include some or all of
the four NCA indices, as well as a variety of
other site-specific indicators
Selection of
sampling sites
Randomized spatially throughout
the estuary
Randomized spatially and/or targeted to monitor
a specific area of the estuary that is known to be
contaminated or degraded
Sampling
frequency
One day during the summer sampling
period (July-August), which is considered
to be the most stressful period of the
year; therefore, monitoring is able to
capture evidence of degradation
Variable, but may be hourly, daily, weekly,
monthly, quarterly, or annually, depending on
the indicator being monitored
Sampling period
1997-2003 (The years of sampling
differ slightly, depending on the
specific NEP estuary, but fall within
this time interval)
Historic data may be available for 20 years
or more
10 National Estuary Program Coastal Condition Report
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CHAPTER I INTRODUCTION
of relatively consistent data for these indices for most of
the nation's estuaries. The indices do not address all
characteristics of estuaries that are valued by society, but
they do provide information on both the ecological
condition and the effects of human use on estuaries.
Characterizing the NEP estuaries using each of the
four indices involves two steps. The first step is to assess
condition at individual monitoring sites within an NEP
estuarine area for each index and component indicator.
The site-condition rating criteria for each index and
component indicator are determined based on existing
criteria, guidelines, or interpretation of scientific
literature. For example, dissolved oxygen conditions
(a component indicator of the water quality index) are
considered poor if dissolved oxygen concentrations are
less than 2 mg/L. This value is widely accepted as
representative of hypoxic conditions; therefore, this
benchmark for poor condition is strongly supported by
scientific evidence (Diaz and Rosenberg, 1995; U.S.
EPA, 2000a).
The second step is to assign index ratings for each
NEP estuary and region based on the condition of the
monitoring sites within an NEP estuary or region. For
example, for an estuary or region to be rated poor with
regard to dissolved oxygen concentrations, more than
15% of the NEP estuarine area must have concentra-
tions measured at less than 2 mg/L. The criteria bound-
aries for the NEP estuary and the regional ratings (i.e.,
percentages used to rate each index of estuarine condi-
tion) were determined as a median of the responses
provided through a survey of environmental managers,
resource experts, and the knowledgeable public. The
following sections provide detailed descriptions of each
index and component indicator, as well as the criteria
for determining the ratings for the four primary indices
by site, NEP estuary, and region as good, fair, or poor.
Water Quality
Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll o
Water Clarity
Dissolved Oxygen
Figure 1-5. Component
ndicators of the water
quality index.
Water Quality Index
The water quality index is made up of five compo-
nent indicators: dissolved inorganic nitrogen (DIN),
dissolved inorganic phosphorus (DIP), chlorophyll a,
water clarity, and dissolved oxygen (Figure 1-5). Some
nutrient inputs to estuaries (such as DIN and DIP) are
necessary for a healthy, functioning estuarine ecosystem;
however, when nutrients from various sources, such as
sewage and fertilizers, are introduced into an estuary,
the concentration of available nutrients can increase
beyond natural background levels. This increase in the
rate of supply of organic matter is called eutrophication
and may result in a host of undesirable water quality
conditions (Figure 1 -6). Excess nutrients can lead to
excess plant production (phytoplankton or algae) and to
increased chlorophyll a concentrations that can decrease
water clarity and lower concentrations of dissolved
oxygen.
Sewage effluent
»»f Phytoplankton Bloom
- * thrives on nutrients
Dissolved Oxygen
trapped in
lighter layer
Dissolved Oxygen
from wave action
and photosynthesis
Less dense
freshwater
Decomposition
I
. Dissolved Oxygen used up
* by microorganism respiration
" v » —
Nutrients
released by bottom sediments
Dissolved Oxygen consumed
More dense
seawater
Fish will avoid
hypoxia if possible
Shellfish
and other
benthic
organisms
unable
to escape
hypoxia
Decomposition of organic
matter in sediments
Figure 1-6. Eutrophication can occur when the concentration
of available nutrients increases beyond normal levels.
National Estuary Program Coastal Condition Report 11
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CHAPTER I INTRODUCTION
The water quality index used in this report is
intended to characterize acutely degraded water quality
conditions and does not consistently identify sites expe-
riencing occasional or infrequent hypoxia, nutrient
enrichment, or decreased water clarity. As a result, a
rating of poor for the water quality index means that
the site is likely to have consistently poor condition
during the monitoring period. If a site is designated as
fair or good, the site did not experience poor condition
on the date sampled, but could be characterized by poor
condition for short time periods. In order to assess the
level of variability in the index at a specific site over
time, increased or supplemental sampling is needed.
Dissolved Nitrogen and Phosphorus I DIN
and DIP are necessary and natural nutrients required
for the growth of phytoplankton, the primary producers
that form the base of an estuary's food chain; however,
excessive DIN and DIP can result in large, undesirable
phytoplankton blooms. For this report, DIN and DIP
were determined chemically through the collection of
filtered surface water at each site. NCA surveys were
conducted in late summer—not the most likely period
for maximal nutrient values in East Coast and Gulf
Coast estuaries, but the period of expected peak concen-
trations for West Coast estuaries.
NCA monitoring sites were rated good, fair, or poor
for DIN and DIP using the criteria shown in Tables 1 -4
and 1-5- These ratings were then used to calculate DIN
and DIP ratings for each NEP estuary and region.
Chlorophyll a I For this report, the surface concen-
trations of chlorophyll a were determined from a
filtered portion of water collected at each site. Surface
chlorophyll a concentrations at a site were rated good,
fair, or poor using the criteria shown in Table 1-6.
These ratings were then used to calculate chlorophyll a
ratings for each NEP estuary and region.
Water Clarity \ Clear waters are valued by society
and contribute to the maintenance of healthy and
productive ecosystems. Light penetration into estuarine
waters is important: for the healthy growth of SAV,
which serves as food and habitat for the resident biota.
The NCA estimates water clarity using specialized
equipment that compares the amount and type of light
reaching the water surface to the light at a depth of
1 meter, as well as by using a Secchi disk. Water clarity
varies naturally among different parts of the nation;
therefore, the water clarity index (WCI) is based on a
ratio of observed clarity to regional reference conditions:
WCI = (observed clarity at 1 meter/regional reference
clarity at 1 meter). The reference conditions for the
NEP estuaries and regions were determined by exam-
ining available data for each of the regions. Conditions
Table 1-4. Criteria for Assessing Dissolved Inorganic
Nitrogen (DIN)
East/Gulf < O.I mg/L 0.1-0.5 mg/L > 0.5 mg/L
Coast sites
West Coast < 0.5 mg/L 0.5-1.0 mg/L > I mg/L
sites
Puerto Rico < 0.05 mg/L 0.05-0.1 mg/L > 0.1 mg/L
sites
NEP
Estuary
or
Region
Less than
10% of the
NEP estuarine
area is in poor
condition, and
more than
50% of the
NEP estuarine
area is in good
condition.
10% to 25%
of the NEP
estuarine area
is in poor
condition, or
more than
50% of the
NEP estuarine
area is in
combined poor
and fair
condition.
More than
25% of the
NEP estuarine
area is in poor
condition.
Table 1-5. Criteria for Assessing Dissolved Inorganic
Phosphorus(DIP)
East/Gulf < 0.01 mg/L 0.01-0.05 mg/L > 0.05 mg/L
Coast sites
West Coast < 0.01 mg/L 0.01-O.I mg/L > O.I mg/L
sites
Puerto Rico < 0.005 mg/L 0.005-0.01 mg/L > 0.01 mg/L
sites
NEP
Estuary
or
Region
Less than
10% of the
NEP estuarine
area is in poor
condition, and
more than
50% of the
NEP estuarine
area is in good
condition.
10% to 25%
of the NEP
estuarine area
is in poor
condition, or
more than
50% of the
NEP estuarine
area is in
combined poor
and fair
condition.
More than
25% of the
NEP estuarine
area is in poor
condition.
1 2 National Estuary Program Coastal Condition Report
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CHAPTER I INTRODUCTION
Table 1-6. Criteria for Assessing Chlorophyll a
East/Gulf/ < 5 Mg/L 5-20 Mg/L > 20 Mg/L
West Coast
sites
Puerto Rico < 0.5 Mg/L 0.5-1 Mg/L > I Mg/L
sites
NEP
Estuary
or
Region
Less than
10% of the
NEP estuarine
area is in poor
condition, and
more than
50% of the
NEP estuarine
area is in good
condition.
10% to 20%
of the NEP
estuarine area
is in poor
condition, or
more than
50% of the
NEP estuarine
area is in
combined poor
and fair
condition.
More than
20% of the
NEP estuarine
area is in poor
condition.
were set at 10% of incident light available at a depth of
1 meter for areas with normal turbidity (most of the
United States), 5% for areas with naturally high
turbidity (Alabama, Georgia, Louisiana, South Carolina,
and parts of Delaware), and 20% for areas with signifi-
cant SAV beds or active programs for SAV restoration
(southern Laguna Madre, the Big Bend region of
Florida, the region from Tampa Bay to Florida Bay, the
Indian River Lagoon, and portions of the Chesapeake
Bay). Table 1-7 summarizes the rating criteria for water
clarity for each monitoring site and for the NEP estu-
aries and regions.
Table I -7. Criteria for Assessing Water Clarity
Individual
sampling
sites
NEP
Estuary
or
Region
WCI ratio is
greater than
2.
Less than
10% of the
NEP estuarine
area is in poor
condition, and
more than
50% of the
NEP estuarine
area is in good
condition.
WCI ratio is
between
I and 2.
WCI ratio is
less than I.
10% to 20%
of the NEP
estuarine area
is in poor
condition, or
more than
50% of the
NEP estuarine
area is in
combined poor
and fair
condition.
More than
25% of the
NEP estuarine
area is in poor
condition.
Dissolved Oxygen \ Dissolved oxygen is necessary
for all estuarine life. Many states use a dissolved oxygen
threshold average concentration of 4 to 5 mg/L to set
their water quality standards, and concentrations below
approximately 2 mg/L are thought to be stressful to
many estuarine organisms (Diaz and Rosenberg, 1995;
U.S. EPA, 2000a). Low oxygen levels (hypoxia) or a
lack of oxygen (anoxia) most often occur in bottom
waters and affect the organisms that live in the sedi-
ments. These conditions often accompany the onset of
severe bacterial degradation, sometimes resulting in the
presence of algal scums and noxious odors; however, in
some estuaries, low oxygen levels occur periodically or
may be a part of an estuary's natural ecology. Therefore,
although it is easy to show a snapshot of the conditions
of the nation's estuaries concerning oxygen concentra-
tions, it is difficult to interpret whether this snapshot is
representative of all summertime periods (such as repre-
sentative of the variable daily conditions in Narragansett
Bay) or the result of natural physical processes.
Unless otherwise noted, the dissolved oxygen data
presented in this report were collected as part of the
NCA survey. Table 1 -8 summarizes the dissolved
oxygen rating criteria for the individual monitoring sites
and for the NEP estuaries and regions.
Table 1-8. Criteria for Assessing Dissolved Oxygen
Individual
sampling
sites
NEP
Estuary
or
Region
5 mg/L
Less than
5% of the
NEP estuarine
10% to 20%
of the NEP
estuarine area
2 mg/L
More than
15% of the
NEP estuarine
area is in poor is in poor area is in poor
condition, and
more than
50% of the
NEP estuarine
area is in good
condition.
condition, or
more than
50% of the
NEP estuarine
area is in
combined poor
and fair
condition.
condition.
National Estuary Program Coastal Condition Report 1 3
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CHAPTER I INTRODUCTION
Calculating the Water Quality Index
Once DIN, DIP, chlorophyll a, water clarity, and
dissolved oxygen were assessed for a given site, a water
quality index rating was calculated for the site based on
these five component indicators. Table 1-9 summarizes
the rating criteria for developing a water quality index
for an individual sampling site. The water quality index
was then calculated for each NEP estuary and region
using the criteria in Table 1-10.
Table 1-9. Criteria for Determining the Water Quality
Index Rating by Site
Rating
Good
Fair
Poor
I
Missing
Criteria
A maximum of one component indicator is
rated fair, and no component indicators are
rated poor.
One of the component indicators is rated
poor, or two or more component indicators
are rated fair.
Two or more of the five component indicators
are rated poor.
Two component indicators are missing,
and the available component indicators do
not suggest a poor or fair rating.
Table 1-10. Criteria for Determining the Water Quality
Index Rating by NEP Estuary or Region
Rating
Criteria
Good
Fair
Poor
I
Less than 10% of the NEP estuarine area is in
poor condition, and more than 50% of the NEP
estuarine area is in good condition.
10% to 20% of the NEP estuarine area is in
poor condition, or more than 50% of the NEP
estuarine area is in combined poor and fair
condition.
More than 20% of the NEP estuarine area is
in poor condition.
they can disrupt the benthic community of inverte-
brates, shellfish, and crustaceans that live in or on the
sediments. To the extent that the contaminants become
concentrated in the organisms, they pose a risk to orga-
nisms throughout the food web—including humans.
Several factors influence the extent and severity of
sediment contamination. Fine-grained, organic-rich
sediments are efficient at scavenging pollutants and are
likely to become resuspended and be transported to
distant locations. Thus, silty sediments high in total
organic carbon (TOG) are potential sources of contami-
nation. Conversely, organic-rich particles bind some
toxicants so strongly that the threat to organisms can be
greatly reduced.
Physical and chemical characteristics of surface sedi-
ments are the result of interacting forces controlling
chemical input and particle dynamics at any particular
site. When assessing estuarine condition, researchers
measure the potential for sediments to affect bottom-
dwelling organisms. The sediment quality index is based
on three component indicators of sediment condition:
direct measures of sediment toxicity, sediment contami-
nant concentrations, and the sediment TOC concentra-
tion (Figure 1-7).
The NCA survey measured the concentrations of
91 chemical constituents in sediments to determine the
sediment contaminants component of the index.
Sediment toxicity was evaluated by measuring the
survival of the marine amphipod Ampelisca abdita
following 10-day exposure to the sediments under labo-
ratory conditions. The sediment TOC concentration
was measured on a dry-weight basis. The results of these
evaluations may be used to identify the most polluted
areas and may provide clues regarding the sources of
contamination.
Sediment Quality Index
Another issue of major environmental concern in
estuaries is the contamination of sediments with toxic
chemicals. A wide variety of metals and organic
substances, such as polycyclic aromatic hydrocarbons
(PAHs), polychlorinated biphenyls (PCBs), and
pesticides, are discharged into estuaries from urban,
agricultural, and industrial sources in a watershed.
These contaminants adsorb onto suspended particles
and eventually accumulate in depositional basins, where
Sediment Quality
Index
Sediment Toxicity
Sediment
Contaminants
Total Organic
Carbon (TOC)
Figure 1-7.
Component indicators of
the sediment quality
index.
14 National Estuary Program Coastal Condition Report
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CHAPTER I INTRODUCTION
Sediment Contaminant Criteria (Long et al., 1995)
ERM (Effects Range Median)—Determined for each
chemical as the SOth percentile (median) in a database of
ascending concentrations associated with adverse biological
effects.
ERL (Effects Range Low)—Determined for each
chemical as the I Oth percentile in a database of ascending
concentrations associated with adverse biological effects.
Some researchers and managers would prefer that the
sediment triad (sediment contaminants, sediment toxi-
city, and benthic communities) be used to assess sedi-
ment condition (poor condition would require all three
elements to be poor), or that poor sediment condition
be determined at least based on the joint occurrence of
elevated sediment contaminant concentrations and high
sediment toxicity (see text box—Alternative Views for a
Sediment Quality Index). However, benthic community
attributes are included in this assessment of estuarine
condition as an independent variable (see the Benthic
Index section in this chapter), rather than as a compo-
nent of sediment quality.
In this report, the focus of the sediment quality
index is on sediment condition, not just sediment toxi-
city. Attributes of sediments other than toxicity can
result in unacceptable changes in biotic communities.
For example, organic enrichment through wastewater
disposal can have an undesired effect on biota, and
elevated contaminant levels can have undesirable
ecological effects (e.g., changes in benthic community
structure) that are not directly related to acute toxicity
(as measured by the Ampelisca test). For these reasons,
the sediment quality index used in this report combines
sediment toxicity, sediment contaminants, and TOG to
assess sediment condition. The condition of estuarine
sediment is assessed as poor (high potential for exposure
effects on biota) if any one of the component elements
is rated poor; assessed as fair if the sediment contami-
nants indicator is rated fair; and assessed as good if all
three component indicators are at levels that would be
unlikely to result in adverse biological effects due to
sediment quality.
Alternative Views for a Sediment Quality Index
Some resource managers object to using ERM and ERL
values to calculate the sediment quality index because
the index is also based on actual measurements of toxi-
city. Because ERMs are acknowledged to be no greater
than 50% predictive of toxicity, these managers believe
that the same weight should not be given to a nontoxic
sample with an ERM exceedance as is given to a sample
that is actually toxic. O'Connor et al. (1998), using a
1,508-sample EPA and NOAA database, found that 38%
of ERM exceedances coincided with amphipod toxicity
(i.e., were toxic); 13% of the ERL exceedances (no ERM
exceedance) were toxic; and only 5% of the samples
that did not exceed ERL values were toxic. O'Connor
and Paul (2000) expanded the 1,508-sample data set to
2,475 samples, and the results remained relatively
unchanged (41 % of the ERM exceedances were toxic,
and only 5% of the nonexceedances were toxic). As a
result, these researchers and managers believe that the
sediment quality index used in this report should not
result in a poor rating if sediment contaminant criteria
are exceeded, but the sediment is not toxic.
When assessing estuarine condition, researchers measure the
potential for sediments to affect bottom-dwelling organisms
(Morro Bay NEP).
National Estuary Program Coastal Condition Report 1 5
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CHAPTER I INTRODUCTION
Sediment Toxicity I Researchers applied a srandard
direct test of toxicity at thousands of sites to measure
the survival of amphipods (commonly found, shrimp-
like benthic crustaceans) exposed to sediments for 10
days under laboratory conditions. As in all tests of toxi-
city, survival was measured relative to that of amphipods
exposed to uncontaminated reference sediment. The
criteria for rating sediment toxicity based on amphipod
survival for each sampling site are shown in Table 1-11,
and Table 1-12 shows how these site data were used to
evaluate sediment toxicity by NEP estuary or region. It
should be noted that for this component indicator,
unlike the others, only a good or poor rating is
possible—there is no fair rating.
Table l-ll. Criteria for Assessing Sediment Toxicity
by Site
Rating Criteria
Good
Poor
I
The amphipod survival rate is greater than
or equal to 80%.
The amphipod survival rate is less than 80%.
Table 1-12. Criteria for Assessing Sediment Toxicity
by NEP Estuary or Region
Rating
Criteria
Good
Poor
Less than 5% of the NEP estuarine area is in
poor condition.
5% or more of the NEP estuarine area is in
poor condition.
Contaminants that absorb onto suspended particles can disrupt
the benthic community of invertebrates, shellfish, and crustaceans
that live in or on the sediments (Morro Bay NEP),
Sediment Contaminants I There are no absolute
chemical concentrations that correspond to sediment
toxicity, but ERL and ERM values are used as guide-
lines in assessing sediment contamination (Table 1-13).
ERM is the median concentration (50th percentile) of a
contaminant observed to have adverse biological effects
in the literature studies examined. A more protective
indicator of contaminant concentrations is the ERL
Table 1-13. ERM and ERL Guidance Values in
Sediments (Long et al., 1995)
Metala
Arsenic
Cadmium
Chromium
Copper
Lead
Mercury
Nickel
Silver
Zinc
Analyteb
Acenaphthene
Acenaphthylene
Anthracene
Fluorene
2-Methyl naphthalene
Naphthalene
Phenanthrene
Benz(a)anthracene
Benzo(a)pyrene
Chrysene
Dibenzo(a,h)anthracene
Fluoranthene
Pyrene
Low molecular-weight PAH
High molecular-weight PAH
Total PAHs
4,4'-DDE
Total DDT
Total PCBs
ERL
8.2
1.2
81
34
46.7
0.15
20.9
1
ISO
ERL
16
44
85.3
19
70
160
240
261
430
384
63.4
600
665
552
1,700
4,020
2.2
1.6
22.7
ERM
70
9.6
370
270
218
0.71
51.6
3.7
410
ERM
500
640
1,100
540
670
2,100
1,500
1,600
1,600
2,800
260
5,100
2,600
3,160
9,600
44,800
27
46.1
180
a units are ug/g dry sediment, equivalent to ppm
b units are ng/g dry sediment, equivalent to ppb
1 6 National Estuary Program Coastal Condition Report
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CHAPTER I INTRODUCTION
criterion, which is the 10th percentile concentration of
a contaminant represented by studies demonstrating
adverse biological effects in the literature. Ecological
effects are not likely to occur at contaminant concentra-
tions below the ERL criterion. The criteria for rating
sediment contaminants at individual sampling sites are
shown in Table 1-14, and Table 1-1 5 shows how these
data were used to create ratings for the NEP estuaries
and regions.
Table 1-14. Criteria for Assessing Sediment
Contaminants by Site
Rating
Good
Fair
Poor
1
1
Criteria
No ERM values are exceeded, and less
five ERL values are exceeded.
Five or more ERL values are exceeded
An ERM value is exceeded for one or
contaminants.
than
more
Table 1-15. Criteria for Assessing Sediment
Contaminants by NEP Estuary or Region
Rating
Criteria
Good
Fair
Poor
I
I
Less than 5% of the NEP estuarine area is in
poor condition.
5% to 15% of the NEP estuarine area is in
poor condition.
More than 15% of the NEP estuarine area is in
poor condition.
Total Organic Carbon Sediment contaminant
availability or organic enrichment can be altered in areas
where there is considerable deposition of organic matter.
Sediment toxicity from organic matter is assessed by
measuring the sediment TOG. The criteria for rating
TOG concentrations at individual sampling sites arc-
shown in Table 1-16, and Table 1-17 shows how these
data were used to create ratings for the NEP estuaries
and regions.
Table 1-16. Criteria for Assessing TOC by Site (concen-
trations on a dry-weight basis)
Rating Criteria
Good • The TOC concentration is less than 2%.
Fair The TOC concentration is between 2% and 5%.
Poor I The TOC concentration is greater than 5%.
Table 1-17. Criteria for Assessing TOC by NEP Estuary
or Region
Rating
Criteria
Good
Fair
Poor
1
I
Less than 20% of the NEP estuarine area is in
poor condition.
20% to 30% of the NEP estuarine area is in
poor condition.
More than 30% of the NEP estuarine area is in
poor condition.
Calculating the Sediment Quality Index
Once all three sediment quality component indica-
tors (sediment toxicity, sediment contaminants, and
sediment TOG) were assessed for a given site, a sedi-
ment quality index rating was calculated for the site.
The sediment quality index was rated good, fair, or
poor for each site using the criteria shown inTable 1-18.
The sediment quality index was then calculated for each
NEP estuary and region using the criteria shown in
Table 1-19.
Table 1-18. Criteria for Determining the Sediment
Quality Index by Site
Rating Criteria
Good
Fair
Poor
1
I
None of the component indicators are rated
poor, and the sediment contaminants indicator
is rated good.
None of the component indicators are rated
poor, and the sediment contaminants indicator
is rated fair.
One or more of the component indicators
are rated poor.
Table 1-19. Criteria for Determining the Sediment
Quality Index by NEP Estuary or Region
Rating
Criteria
Good
Fair
Poor
1
I
Less than 5% of the NEP estuarine area is in
poor condition, and more than 50% of the NEP
estuarine area is in good condition.
5% to 15% of the NEP estuarine area is in
poor condition, and more than 50% of the NEP
estuarine area is in combined poor and fair
condition.
More than 15% of the NEP estuarine area is in
poor condition.
National Estuary Program Coastal Condition Report 1 7
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CHAPTER I INTRODUCTION
Benthic Index
The worms, clams, and crustaceans that inhabit the
bottom substrates of estuaries are collectively called
benthic macroinvertebrates, or benthos. These organ-
isms play a vital role in maintaining sediment and water
quality and are an important food source for bottom-
feeding fish, shrimp, ducks, and marsh birds. Benthos
are often used as indicators of disturbances in estuarine
environments because they are not very mobile; thus,
they cannot avoid environmental problems. Benthic
population and community characteristics are sensitive
indicators of chemical contaminant and dissolved-
oxygen stress, salinity fluctuations, and sediment distur-
bance and serve as reliable indicators of estuarine envi-
ronmental quality. To distinguish degraded benthic
habitats from undegraded benthic habitats, EMAP and
NCA have developed regional (Northeast, Southeast,
and Gulf coasts) benthic indices of environmental
condition for estuaries that reflect changes in the diver-
sity and population size of indicator species (Engle et
al., 1994; Weisberg et al., 1997; Engle and Summers,
1999; Van Dolah et al., 1999; Paul et at., 2001). These
indices reflect changes in benthic community diversity
and the abundance of pollution-tolerant and pollution-
sensitive species. A high benthic index rating means that
samples taken from an estuary's sediments contain a
wide variety of species, a low proportion of pollution-
tolerant species, and a high proportion of pollution-
sensitive species. A low benthic index rating indicates
that the benthic communities are less diverse than
expected, are populated by more pollution-tolerant
species than expected, and contain fewer pollution-
sensitive species than expected. The benthic condition
data presented throughout this report were collected by
the NCA unless otherwise noted. Indices vary among
the regions because species assemblages depend on
prevailing temperatures, salinities, and the silt-clay
content of sediments. A benthic index was rated poor
when the index values for the Northeast, Southeast, and
Gulf coasts' diversity or species richness, abundance of
pollution-sensitive species, and abundance of pollution-
tolerant species fell below a certain threshold. It should
be noted that the benthic indices used in the Northeast
are designed to discriminate between good and poor
categories; a fair category does not exist.
Not all regions included in this report have devel-
oped benthic indices. Indices for the New England
Coast north of Cape Cod (Acadian Province), the West
Coast, and Puerto Rico are being developed and are not
available for reporting at this time. The benthic index
used in the Northeast region south of Cape Cod
(Virginian Province) was developed by EMAP and
NCA; however, EPA used the Shannon-Weiner
Diversity Index to evaluate the benthic community for
the NEP estuaries of the Acadian Province because the
index used for the Virginian Province did not produce
good results for these estuaries. In the West Coast and
Puerto Rico regions, benthic community diversity was
determined for each site as a surrogate for the benthic
index. Values for benthic community diversity were
examined regionally to determine if diversity varied
directly with either salinity or sediment silt-clay content
(the two natural variables most likely to influence
The abundant population growth in U.S. coastal areas increases the demands imposed on the natural, economic, and aesthetic value of
estuaries (JohnTheilgard).
1 8 National Estuary Program Coastal Condition Report
-------
estuarine benthic diversity). If there was no significant
relationship between diversity and these natural gradi-
ents in a region (as in Puerto Rico), then a surrogate
benthic index was used based on the lower 95% confi-
dence limit for the mean benthic diversity measures. If
there was a significant relationship between diversity
and either of these natural gradients in a region (as in
the West Coast NEP estuaries), then a surrogate benthic
index was used based on the ratio of observed to
expected diversity. Expected diversity was determined
based on the statistical relationship of site diversity to
site salinity (or silt-clay content). Poor condition was
defined as less than 75% of the expected benthic diver-
sity at a particular salinity (expected diversity was deter-
mined by a regression between diversity and salinity).
Table 1-20 shows the good, fair, and poor rating criteria
for sites in the different regions of the country, which
were used to calculate an overall rating for each NEP
estuary and region.
CHAPTER I INTRODUCTION
The relationship between poor benthic condition
(poor benthic index values) and environmental stressors
(e.g., water quality and sediment quality indices and
their component indicators) is examined using the co-
occurrence of these factors in each region. In all regions,
some sites with poor benthic community condition did
not co-occur with high levels of environmental stressors
measured by the NCA. The sites that do not co-occur
with the poor water quality and sediment quality
indices may be the result of physical habitat degradation
(a parameter not measured by the NCA).
Fish Tissue Contaminants Index
Chemical contaminants may enter a marine
organism in several ways: direct uptake from contami-
nated water, consumption of contaminated sediment, or
consumption of previously contaminated organisms.
Once these contaminants enter an organism, they tend
Table 1-20. Regional Criteria for Assessing Benthic Condition
Region
Fair
Northeast Coast sites
Acadian Province
Virginian Province
Shannon-Weiner Diversity
Index is greater than 0.63
Benthic index score is
greater than 0.0
NA*
NA*
Shannon-Weiner Diversity
Index is less than
or equal to 0.63
Benthic index score is
less than 0.0
Southeast Coast sites
Benthic index score is
greater than 2.5
Benthic index score is
between 2.0 and 2.5
Benthic index score is
less than 2.0
Gulf Coast sites
Benthic index score is
greater than 5.0
Benthic index score is
between 3.0 and 5.0
Benthic index score is
less than 3.0
West Coast sites
(compared to expected
diversity)
Benthic index score is more
than 90% of the lower limit
(lower 95% confidence
interval) of expected mean
diversity for a specific salinity
Benthic index score is
between 75% and 90%
of the lower limit of
expected mean diversity
for a specific salinity
Less than 75% of
observations had
expected diversity
Puerto Rico sites
(compared to upper 95%
confidence interval for mean
regional benthic diversity)
Benthic index score is more
than 90% of the lower limit
(lower 95% confidence
interval) of mean diversity
in unstressed habitats
in Puerto Rico
Benthic index score is
between 75% and 90%
of the lower limit of mean
diversity in unstressed
habitats in Puerto Rico
Benthic index score is
less than 75% of the
lower limit of mean
diversity for unstressed
habitats in Puerto Rico
NEP Estuary or Region
Less than 10% of the NEP
estuarine area has a poor
benthic index score,
and more than 50% of
the NEP estuarine area
has a good index score
10% to 20% of the NEP
estuarine area has a poor
benthic index score, or
more than 50% of
the NEP estuarine area has
a combined fair and poor
benthic index score
More than 20% of the NEP
estuarine area has a poor
benthic index score
! By design, these indices discriminate between good and poor conditions only.
National Estuary Program Coastal Condition Report 1 9
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CHAPTER I
INTRODUCTION
to remain in the animal's tissues and may build up with
subsequent feedings. When fish consume contaminated
organisms, they may "inherit" the levels of contami-
nants in the organisms they consume. This same inheri-
tance of contaminants occurs when humans consume
fish with contaminated tissues. Contaminant residues
can be examined in the fillets, whole-body portions, or
specific organs of target fish and shellfish species and are
compared with risk-based EPA Advisory Guidance
criteria for fish contaminants (U.S. EPA, 2000b).
For the NCA surveys, target fish were collected
from all stations where fish were available, and whole-
body contaminant burdens were determined. No EPA
Advisory Guidance criteria exist to assess the ecological
risk of whole-body contaminants for fish, but EPA
Advisory Guidance (U.S. EPA, 200b) can be used as a
basis for estimating advisory determinations, even if the
data are based on whole-fish or organ-specific body
burdens (Table 1-21). The whole-fish contaminant
information collected by the NCA for U.S. NEP estu-
aries was compared with risk-based thresholds based on
Table 1-21. Risk-based EPA Advisory Guidelines for
Recreational Fishers (U.S. EPA, 2000b)
Contaminant
Arsenic (inorganic)b
Cadmium
Mercury
Selenium
Chlordane
DDT (total)
Dieldrin
Endosulfan
Endrin
Heptachlor epoxide
Hexachlorobenzene
Lindane
Mi rex
Toxaphene
PAH (Benzo[a]pyrene)
PCB (total)
Concentration
Range3 (mg/L)
3.5-7.0
0.35-0.70
0.12-0.23
5.9-12.0
0.59-1.2
0.059-0.12
0.059-0.12
7.0-14.0
0.35-0.70
0.015-0.031
0.94-1.9
0.35-0.70
0.23-0.47
0.29-0.59
0.0016-0.0032
0.023-0.047
Health
Endpoint
non-cancer
non-cancer
non-cancer
non-cancer
non-cancer
non-cancer
non-cancer
non-cancer
non-cancer
non-cancer
non-cancer
non-cancer
non-cancer
non-cancer
cancerc
non-cancer
a Range of concentrations associated with non-cancer and cancer health
endpoint risk for consumption of four 8-ounce meals per month
b Inorganic arsenic estimated as 2% of total arsenic
c A non-cancer concentration range for PAHs does not exist
the consumption of four 8-ounce meals per month for
selected contaminants (approach used by many state
advisory programs) and assessed for non-cancer and
cancer health endpoints (U.S. EPA, 2000b). Table 1-22
shows the rating criteria for the fish tissue contaminants
index for each site, and Table 1-23 shows how these
data were used to create ratings for the NEP estuaries
and the regions.
Table 1-22. Criteria for Determining the Fish Tissue
Contaminants Index by Monitoring Station
Rating Criteria
Good | For all chemical contaminants listed in
Table 1-21, the measured concentrations fall
below the range of the EPA Advisory Guidance*
criteria for risk-based consumption associated
with four 8-ounce meals per month.
Fair For at least one chemical contaminant listed
in Table I-21, the measured concentration falls
within the range of the EPA Advisory Guidance
criteria for risk-based consumption associated
with four 8-ounce meals per month.
Poor I For at least one chemical contaminant listed
in Table 1-21, the measured concentration
exceeds the maximum value in the range of
the EPA Advisory Guidance criteria for
risk-based consumption associated with four
8-ounce meals per month.
The EPA Advisory Guidance concentration is based on the non-cancer
ranges for all contaminants except PAH (benzo(a)pyrene), which are
based on a cancer range because a non-cancer range for PAHs does
not exist (see Table 1-21).
Table 1-23. Criteria for Determining the Fish Tissue
Contaminants Index by NEP Estuary or Region
Rating
Criteria
Good
Fair
Poor
I
Less than 10% of the fish samples analyzed
(Northeast Coast region) or the monitoring
stations where fish were caught (all other
regions) are in poor condition, and more than
50% of the fish samples analyzed (Northeast
Coast region) or the monitoring stations where
fish were caught (all other regions) are in good
condition.
10% to 20% of the fish samples analyzed
(Northeast Coast region) or monitoring
stations where fish were caught (all other
regions) are in poor condition, or more than
50% of the fish samples analyzed (Northeast
Coast region) or the monitoring stations
where fish were caught (all other regions) are
in combined poor and fair condition.
More than 20% of the fish samples analyzed
(Northeast Coast region) or the monitoring
stations where fish were caught (all other
regions) are in poor condition.
20 National Estuary Program Coastal Condition Report
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CHAPTER I
INTRODUCTION
Summary of NCA Rating Criteria
The rating criteria for the NCA survey data used in this report are summarized in Table 1-24 (primary indices)
and Tables 1-25 and 1-26 (component indicators).
Table 1-24. NCA Indices Used to Assess Estuarine Condition
Icon Water Quality Index—This index is based on
water clarity, and dissolved oxygen).
Ecological Condition by Site
Good: No component indicators are rated
poor, and a maximum of one component
Water indicator is rated fair.
Quality Fair: One component indicator is rated
Index poor, or two or more component
indicators are rated fair.
Poor: Two or more component indicators
are rated poor.
Sediment
Quality
Index
Benthic
Index
five water quality component indicators (DIN, DIP, chlorophyll a,
Ranking by NEP Estuary or Region
Good: Less than 10% of the NEP estuarine area is in poor
condition, and more than 50% of the NEP estuarine area
is in good condition.
Fair: 10% to 20% of the NEP estuarine area is in poor condi-
tion, or more than 50% of the NEP estuarine area is in
combined poor and fair condition.
Poor: More than 20% of the NEP estuarine area is in poor
condition.
Sediment Quality Index—This index is based on three sediment quality component indicators (sediment toxicity,
sediment contaminants, and sediment TOC).
Ecological Condition by Site
Good: No component indicators are rated poor,
and the sediment contaminants indicator
is rated good.
Fair: No component indicators are rated poor,
and the sediment contaminants indicator
is rated fair.
Poor: One or more component indicators are
rated poor.
Ranking by NEP Estuary or Region
Good: Less than 5% of the NEP estuarine area is in poor
condition, and more than 50% of the NEP estuarine area
is in good condition.
Fair: 5% to 15% of the NEP estuarine area is in poor condi-
tion, or more than 50% of the NEP estuarine area is in
combined poor and fair condition.
Poor: More than 15% of the NEP estuarine area is in poor
condition.
Benthic Index (or a surrogate measure)—This index indicates the condition of the benthic community (organisms
living in estuarine sediments) and can include measures of benthic community diversity, the presence and abundance
of pollution-tolerant species, and the presence and abundance of pollution-sensitive species.
Ecological Condition by Site Ranking by NEP Estuary or Region
Good, fair, and poor were Good: Less than 10% of the NEP estuarine area has a poor
determined using regionally
dependent benthic index scores.
benthic index score, and more than 50% of the NEP estu-
arine area has a good benthic index score.
Fair: 10% to 20% of the NEP estuarine area has a poor benthic
index score, or more than 50% of the NEP estuarine area
has a combined poor and fair benthic index score.
Poor: More than 20% of the NEP estuarine area has a poor
benthic index score.
Fish
Tissue
Contaminants
Index
Fish Tissue Contaminants Index-
fish/shellfish species.
Ecological Condition by Site
Good: For all chemical contaminants listed
in Table 1-21, composite fish tissue
contaminant concentrations are
below the EPA Advisory Guidance*
concentration range.
Fair: For at least one chemical contami-
nant listed in Table 1-21, composite
fish tissue contaminant concentra-
tions are within the EPA Advisory
Guidance concentration range.
Poor: For at least one chemical contami-
nant listed in Table 1-21, composite
fish tissue contaminant concentra-
tions are above the EPA Advisory
Guidance concentration range.
-This index indicates the level of chemical contamination in target
Ranking by NEP Estuary or Region
Good: Less than 10% of the fish samples analyzed (Northeast
Coast region) or the monitoring stations where fish were
caught (all other regions) are in poor condition, and more
than 50% of the fish samples analyzed (Northeast Coast
region) or the monitoring stations where fish were caught
(all other regions) are in good condition.
Fair: 10% to 20% of the fish samples analyzed (Northeast Coast
region) or the monitoring stations where fish were caught
(all other regions) are in poor condition, or more than
50% of the fish samples analyzed (Northeast Coast region)
or the monitoring stations where fish were caught (all
other regions) are in combined poor and fair condition.
Poor: More than 20% of the fish samples analyzed (Northeast
Coast region) or the monitoring stations where fish were
caught (all other regions) are in poor condition.
*The EPA Advisory Guidance concentration is based on the non-cancer ranges for all contaminants except PAH (benzo(a)pyrene), which are
based on a cancer range because a non-cancer range for PAHs does not exist (see Table 1-21).
National Estuary Program Coastal Condition Report 21
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CHAPTER I
INTRODUCTION
Table 1-25. NCA Criteria for the Five Component Indicators Used in the Water Quality Index to Assess NEP
Estuarine Condition
Dissolved Inorganic Nitrogen (DIN)
Ecological Condition by Site
Ranking by NEP Estuary or Region
Good: Surface concentrations are less than 0.1 mg/L
(NE, SE, Gulf), 0.5 mg/L (West), or 0.05 mg/L (tropical)*.
Good: Less than 10% of the NEP estuarine area is in poor
condition, and more than 50% of the NEP estuarine area is
in good condition.
Fair: Surface concentrations are 0.1-0.5 mg/L (NE, SE,
Gulf), 0.5-1.0 mg/L (West), or 0.05-0.1 mg/L (tropical).
Fair: 10% to 25% of the NEP estuarine area is in poor
condition, or more than 50% of the NEP estuarine area
is in combined poor and fair condition.
Poor: Surface concentrations are greater than 0.5 mg/L
(NE, SE, Gulf), 1.0 mg/L (West), or 0.1 mg/L (tropical).
Poor: More than 25% of the NEP estuarine area is in poor
condition.
Dissolved Inorganic Phosphorus (DIP)
Ecological Condition by Site
Ranking by NEP Estuary or Region
Good: Surface concentrations are less than 0.01 mg/L
(NE, SE, Gulf), 0.01 mg/L (West), or 0.005 mg/L (tropical).
Good: Less than 10% of the NEP estuarine area is in poor
condition, and more than 50% of the NEP estuarine area is
in good condition.
Fair: Surface concentrations are 0.01-0.05 mg/L (NE, SE,
Gulf), 0.01-O.I mg/L (West), or 0.005-0.01 mg/L (tropical).
Fair: 10% to 25% of the NEP estuarine area is in poor
condition, or more than 50% of the NEP estuarine area
is in combined poor and fair condition.
Poor: Surface concentrations are greater than 0.05 mg/L
(NE, SE, Gulf), 0.1 mg/L (West), or 0.01 mg/L (tropical).
Poor: More than 25% of the NEP estuarine area is in poor
condition.
Chlorophyll a
Ecological Condition by Site
Ranking by NEP Estuary or Region
Good: Surface concentrations are less than 5 ug/L
(less than 0.5 ug/L for tropical ecosystems).
Good: Less than 10% of the NEP estuarine area is in poor
condition, and more than 50% of the NEP estuarine area is in
good condition.
Fair: Surface concentrations are between 5 ug/L and
20 ug/L (between 0.5 ug/L and I ug/L for tropical
ecosystems).
Fair: 10% to 20% of the NEP estuarine area is in poor
condition, or more than 50% of the NEP estuarine area is in
combined poor and fair condition.
Poor: Surface concentrations are greater than 20 ug/L
(greater than I ug/L for tropical ecosystems).
Poor: More than 20% of the NEP estuarine area is in poor
condition.
Water Clarity
Note:A water clarity index (WO) is calculated by dividing observed clarity at I meter by a regional reference clarity at I meter.
This regional reference is 10% for most of the United Stotes, 5% for areas with naturally high turbidity, and 20% for areas with
significant SAV beds or active SAV restoration programs.
Ecological Condition by Site
Ranking by NEP Estuary or Region
Good: WCI ratio is greater than 2.
Good: Less than 10% of the NEP estuarine area is in poor
condition, and more than 50% of the NEP estuarine area is in
good condition.
Fair: WCI ratio is between I and 2.
Fair: 10% to 25% of the NEP estuarine area is in poor
condition, or more than 50% of the NEP estuarine area is in
combined poor and fair condition.
Poor: WCI ratio is less than I.
Poor: More than 25% of the NEP estuarine area is in poor
condition.
*Tropical ecosystems in this NEP CCR. include San Juan Bay Estuary, Puerto Rico.
22 National Estuary Program Coastal Condition Report
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CHAPTER I I INTRODUCTION
Table 1-25. NCA Criteria for the Five Component Indicators Used in the Water Quality Index to Assess NEP
Estuarine Condition (continued)
Dissolved Oxygen
Ecological Condition by Site
Ranking by NEP Estuary or Region
Good: Concentrations are greater than 5 mg/L.
Good: Less than 5% of the NEP estuarine area is in poor
condition, and more than 50% of the NEP estuarine area is in
good condition.
Fair: Concentrations are between 2 mg/L and 5 mg/L.
Fair: 5% to 15% of the NEP estuarine area is in poor
condition, or more than 50% of the NEP estuarine area
is in combined poor and fair condition.
Poor: Concentrations are less than 2 mg/L.
Poor: More than 15% of the NEP estuarine area is in poor
condition.
Table 1-26. NCA Criteria for Measurements for the Three Component Indicators Used in the Sediment Quality
Index to Assess NEP Estuarine Condition
Sediment Toxicity is evaluated as part of the sediment quality index using a 10-day static toxicity test with the amphipod
Ampelisca abdita.
Ecological Condition by Site
Ranking by NEP Estuary or Region
Good: Mortality* is less than or equal to 20%.
Good: Less than 5% of the NEP estuarine area is in poor
condition.
Poor: Mortality is greater than 20%.
Poor: 5% or more of the NEP estuarine area is in poor
condition.
Sediment Contamination is evaluated as part of the sediment quality index using ERM and ERL guidelines.
Ecological Condition by Site
Ranking by NEP Estuary or Region
Good: No ERM values are exceeded, and fewer than five ERL Good: Less than 5% of the NEP estuarine area is in poor
values are exceeded. condition.
Fair: No ERM values are exceeded, and five or more ERL
values are exceeded.
Fair: 5% to 15% of the NEP estuarine area is in poor
condition.
Poor: One or more ERM values are exceeded.
Poor: More than 15% of the NEP estuarine area is in poor
condition.
Sediment Total Organic Carbon (TOC) is measured as part of the sediment quality index.
Ecological Condition by Site
Ranking by NEP Estuary or Region
Good: The TOC concentration is less than 2%.
Good: Less than 20% of the NEP estuarine area is in poor
condition.
Fair: The TOC concentration is between 2% and 5%.
Fair: 20% to 30% of the NEP estuarine area is in poor
condition.
Poor: The TOC concentration is greater than 5%.
Poor: More than 30% of the NEP estuarine area is in poor
condition.
*Test mortality is adjusted for control mortality.
National Estuary Program Coastal Condition Report 23
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CHAPTER I INTRODUCTION
How the NCA Indices Are Summarized
Overall condition for each region was calculated by
summing the scores for the available regional indices
and dividing by the number of available indices (i.e.,
equally weighted), where good = 5; fair = 4, 3, or 2
(based on position in percent range); and poor = 1.
The Southeast Coast, for example, received the
following scores:
Index
Water Quality Index
Sediment Quality Index
Benthic Index
Fish Tissue Contaminants Index
Total Score
Overall Condition
Score
5
4
3
4
16
16/4 = 4
.0
The national index scores and the overall condition
score are calculated based on a weighted average of the
regional scores for each index. The national ratings are
assigned to each index score and overall condition score
based on these regional scores, rather than on the
percentage of area in good, fair, or poor condition. The
indices were weighted based on the NEP estuarine area
contributed by each geographic area, not the total
estuarine area contributed by each region. For example,
the weighted average for the water quality index was
calculated by summing the products of the regional
water quality index scores and the area contributed by
the NEPs in each region (Figure 1-8). These weighting
factors were used for all indices. The national overall
condition score was then calculated by summing each
national index score and dividing by four.
Puerto Rico
Gulf of
Mexico
24%
Northeast
26%
Southeast
28%
The NCA and the individual NEPs have the same goal of
measuring estuarine condition, but these programs often
use different monitoring methods and analysis procedures.
Even when the indices used by these two programs seem
to measure the same parameter, they may not be directly
comparable because of differences in the methodology,
time and spatial scales, and seasonality of the monitoring
design. For instance, although the NCA may monitor
chlorophyll a in an estuary over the course of a single
week during the summer at randomly selected sites, an
individual NEP may collect chlorophyll a samples every day,
all year, but target the sampling to sites where nutrient
inputs are anticipated to be high. Both types of information
are important for learning about estuarine condition,
but the information cannot be directly compared due to
differences in methodology, time and spatial scales, and
seasonality.
National Estuary Program
(NEP) Monitoring Data
To measure the effectiveness of their CCMPs, each of
the 28 individual NEPs develops a strategy for
collecting and analyzing environmental monitoring
data. Each program is also expected to develop indica-
tors for measuring the change in estuarine conditions
over time. In this report, indicator data have been
collected from the individual NEPs to provide a specific
picture of the conditions in each NEP estuary. Some of
the more commonly assessed water quality indicators
among the NEPs are nitrogen, chlorophyll a, and
dissolved oxygen concentrations. Many NEPs are also
concerned about habitat loss and have used a variety of
methods, such as satellite imagety, geographic informa-
tion systems (GIS) mapping, and aerial surveys, to track
the changes in habitat coverage over time. Because the
NEPs are able to choose the types of monitoring data
and analytical methods that best fit their estuary's
particular environmental conditions and concerns, the
resulting data includes a variety of different measure-
ments that are not readily comparable among the
estuaries. This report takes advantage of region- and
site-specific information from the individual NEPs to
present a description of the condition of each NEP
estuary, which is supplemented by the nationally
consistent data provided by the NCA.
Figure 1-8. Percentage of NEP estuarine area contributed by
each geographic region assessed in this report.
24 National Estuary Program Coastal Condition Report
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CHAPTER 2
U.S. NATIONAL ESTUARY PROGRAM COASTAL
CONDITION—A NATIONAL SNAPSHOT
'••V
-------
CHAPTER 2
U.S. NATIONAL ESTUARY PROGRAM COASTAL
CONDITION—A NATIONAL SNAPSHOT
EPA summarizes environmental conditions in the
28 NEP estuaries to allow for statistical comparisons
of coastal conditions nationwide. As discussed in
Chapter 1, assessments of estuarine condition were
developed for each individual NEP estuary and for the
collective NEP estuaries on a regional and national
basis. This chapter presents the national estuarine
condition ratings for the collective NEP estuaries, as
well as information on the regional estuarine condition
ratings for the five U.S. regions discussed in this report.
More in-depth information on the estuarine condition
of these regions and the 28 individual NEP estuaries is
provided in the regional summary sections and NEP
profiles presented in Chapters 3 through 7.
The overall condition of the NEP estuaries of the
United States is rated fair, with the water quality index,
benthic index, and fish tissue contaminants index each
rated fair and the sediment quality index rated fair to
poor at the national level. Figure 2-1 shows the overall
condition and estuarine index ratings for the nation and
for the five regions discussed in this report. These
ratings are based on monitoring data collected as part of
the NCA, which sampled 1,239 sites within U.S. NEP
estuaries from 1997 through 2003, with the majority of
Overall Condition
U.S. NEP
Estuaries
Overall
Condition
J Jor'chaast Coess
Estuarine Health
Water Quality Index
Sediment Quality Index
Benthic Index
_^ 1 Fish Tissue
I 1 Contaminants Index
Overall
Condition
Gulf Coast
NEP Estuaries
Overall
Condition
Puerto Kieo
NEP Estuaries
Figure 2-1. National and regional overall condition ratings for the nation's NEP estuaries (U.S. EPA/NCA).
26 National Estuary Program Coastal Condition Report
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CHAPTER 2 U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
the samples (95%) collected between 1999 and 2001.
Of the four NCA indices rated for NEP estuaries
nationwide, only the water quality index for the
Southeast Coast region and the benthic index for the
West Coast region were rated good.
The ratings for the individual NEP estuaries and the
five geographic regions were based on the criteria
outlined in Tables 1-24, 1-25, and 1-26 of this report,
and overall condition ratings for each region were devel-
oped by averaging the four regional estuarine index
ratings. Based on these calculations, the Northeast
Coast region is rated fair for the water quality index;
poor for the sediment quality, benthic, and fish tissue
contaminants indices; and poor for overall condition.
The Southeast Coast region is rated good for the water
quality index; good to fair for the sediment quality
index; fair for the benthic index; good to fair for the
fish tissue contaminants index; and good to fair for
overall condition. The Culf Coast region is rated fair for
the water quality index; fair to poor for the sediment
quality and benthic indices; good to fair for the fish
tissue contaminants index; and fair for overall condi-
tion. The West Coast region is rated fair for the water
quality index; poor for the sediment quality index; good
for the benthic index; poor for the fish tissue contami-
nants index; and fair for overall condition. Finally, the
sole NEP estuary (San Juan Bay Estuary) in Puerto Rico
is rated fair for the water quality index; poor for the
sediment quality, benthic, and fish tissue contaminants
indices; and poor for overall condition.
NCA Indices of Estuarine
Condition—U.S. NEP Estuaries
This section presents EPAs NCA monitoring data,
which were used to rate the four primary indices of
estuarine condition discussed in this report. Based on
NCA data, the overall condition of the nation's NEP
estuaries is rated fair, with 37% of the nation's collective
NEP estuarine area rated poor (Figure 2-2). The overall
condition score was calculated by averaging the rating
scores for the individual indices (water quality, sediment
quality, benthic, and fish tissue contaminants). Figure
2-3 shows the percent of the nation's NEP estuarine
area rated good, fair, poor, or missing for each of the
parameters considered. Each NCA survey site was
visited only once during the summer season; therefore,
the results emerging from the NCA study form a
"snapshot" of estuarine condition at a site, rather than a
description of long-term conditions. This approach
provides an accurate assessment of conditions in the rela-
tively stable media of sediment and the associated benthic
community, as well as of fish tissue contamination condi-
tions that change relatively slowly over time; however, it
provides a less accurate view of the ephemeral conditions
associated with the water column, where water quality
conditions may change weekly or even daily during a
summer sampling period.
Overall Condition
U.S. NEP Estuaries (2.7)
Water Quality Index (3.6)
Sediment Quality Index (2.1)
Benthic Index (2.7)
Fish Tissue Contaminants
Index (2.6)
Figure 2-2. The
overall condition of
the nation's NEP
estuarine area is fair
(U.S. EPA/NCA).
Overall Condition
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Estuarine Area
Missing
Figure 2-3. Percentage of estuarine area achieving each rating for all
indices and component indicators - U.S. NEP estuaries (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 27
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CHAPTER 2
U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
Water Quality Index
Based on NCA data (representing five component
indicators—DIN, DIP, chlorophyll a, water clarity, and
dissolved oxygen), the water quality index for the
nation's collective NEP estuaries is rated fair. The index
shows that 8% of the nation's NEP estuarine area is
rated poor for water quality, and 54% of the area is
rated fair (Figure 2-4). These categories combine to
show that 62% ± 3% of the nation's NEP estuaries are
experiencing a moderate to high degree of eutrophica-
tion. Poor water quality condition is generally character-
ized by degradation in the water quality variable (i.e.,
increased chlorophyll a concentrations and decreased
dissolved oxygen concentrations). Moderate eutrophi-
cation shows some minor degradation in response
variables, but poor water quality condition is more
likely to be characterized by degradation due to
environmental stressors, such as increased nutrient
concentrations and reduced water clarity.
The Gulf Coast region shows the highest propor-
tional area of NEP estuaries in poor condition (13%)
for water quality, although the water quality index for
this region is rated fair. NEP estuaries along the
Northeast Coast, West Coast, and Puerto Rico also had
water quality indices rated fair, with 9%, 4%, and 8%
of NEP estuarine waters in these regions rated poor for
water quality, respectively. The water quality index for
the Southeast Coast region is rated good, with only 4%
of this region's NEP estuarine area rated poor for water
quality.
Missing
4%
Figure 2-4. Water
quality index data for
U.S. NEP estuaries
(U.S. EPA/NCA).
The sampling conducted by EPA's NCA is designed to
estimate the percent of NEP estuarine area (nationally or
regionally) in varying conditions; these estimates are
displayed as pie diagrams. Many of the figures in this report
illustrate environmental measurements made at specific
locations (colored dots on maps); however, these dots
(color) represent the value of the index specifically at the
time of sampling. Additional sampling may be required to
define variability and to confirm impairment or the lack of
impairment at specific locations.
Dissolved Nitrogen and Phosphorus I Nutrient
concentrations for summertime conditions in the
nation's NEP estuaries are rated good for DIN concen-
trations and fair for DIP concentrations. Nutrient
concentrations in summer are expected to be generally
lower than at other times of year, except on the West
Coast, where Pacific upwelling events often produce
higher nutrient concentrations in the summer. Because
of the expectation for lower nutrient concentrations,
reference conditions were modified (reduced by 50%)
for NEP estuaries of the Northeast Coast, Southeast
Coast, and Gulf Coast regions.
DIN concentrations were uniformly low throughout
the nation's NEP estuaries, with only 3% of the nation's
NEP estuarine area characterized by poor conditions.
Most DIN concentrations that exceeded reference
conditions were in the NEP waters of the Northeast
Coast (10%) and Puerto Rico (23%) regions. DIP
concentrations exceeded the regional reference condi-
tions in 12% of the nation's NEP estuarine area.
Elevated summer DIP concentrations were observed in
10% to 20% of the area of most NEP regions (except
for NEP estuaries of the Southeast Coast region, where
only 6% exceeded these values). In addition, elevated
DIN and DIP concentrations in the NEP estuaries of
the Northeast Coast, Gulf Coast, and Puerto Rico
regions correspond to elevated chlorophyll a concentra-
tions in these estuaries.
28 National Estuary Program Coastal Condition Report
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CHAPTER 2 U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
Chlorophyll a I High concentrations of chlorophyll
am a waterbody indicate the potential for problems
related to the overproduction of algae and increased
eutrophic conditions. The collective NEP estuaries of
the United States are rated fair for chlorophyll a
concentrations, with 52% of the nation's NEP estuarine
area rated fair and 4% of the area rated poor. The Gulf
Coast, Southeast Coast, and Puerto Rico regions were
also rated fair for this component indicator, whereas
chlorophyll a conditions in the Northeast Coast and
West Coast regions were rated good.
Water Clarity I Water clarity for the nation's NEP
estuaries is rated fair. Three different regional reference
conditions were established for measuring water clarity
conditions (Table 2-1).
The NCA estimates that 18% of the nation's NEP
estuaries do not meet regional reference conditions for
good water clarity. NEP estuaries with poor water
clarity are distributed throughout the country, but the
West Coast (35%), Gulf Coast (31%), and Puerto Rico
(17%) regions have the greatest proportion of NEP
waters not meeting the conditions for good water
clarity.
Table 2-1. Reference Conditions for Water Clarity
in the Nation's NEP Estuaries
Reference Condition
(ambient surface
light that reaches a
depth of I meter)
Area Type
5%
20%
10%
Areas having high natural levels
of suspended solids in the water
(e.g., Delaware Estuary, Barataria-
Terrebone Estuarine Complex,
Mobile Bay) or extensive
wetlands
Areas having extensive SAV beds
(e.g., Indian River Lagoon,
southern Laguna Madre of the
Coastal Bend Bays) or desiring
to re-establish SAV (e.g., Tampa
Bay)
The remainder of the country
Interpretation of Instantaneous Dissolved
Oxygen Information
Although NCA results do not suggest that low dissolved
oxygen concentrations are a pervasive problem, the
instantaneous measurements on which these results are
based may have underestimated the magnitude and
duration of low dissolved oxygen events at any given site.
Long-term observations by other investigators have
revealed increasing trends in the frequency and area! extent
of hypoxic events in some coastal areas. For example,
extensive year-round or seasonal monitoring data over
multiple years in such places as Narragansett Bay in Rhode
Island have shown a much higher incidence of hypoxia than
is depicted in the present NCA data, indicating that
although hypoxic conditions do not exist continuously,
they can occur occasionally to frequently for generally
short durations of time (hours).
Dissolved Oxygen \ Dissolved oxygen condition
for the nation's NEP estuaries is rated good; however,
the majority of NEP estuaries are not located in areas
where severe hypoxic and anoxic water conditions have
occurred historically, such as the waters found offshore
of the Mississippi Delta region in the Gulf of Mexico.
In addition, NCA estimates do not reflect the
dystrophic nature of some estuarine systems, where
dissolved oxygen levels are acceptable during daylight
hours but decrease to low levels during the night. Many
of these systems and their associated biota are adapted
to this cycle, which is common in wetland, swamp, and
blackwater ecosystems; however, because all NCA
survey measurements were taken during daylight hours,
these dystrophic events would not be detected by the
NCA surveys.
The reference value used in the NCA analysis for
poor dissolved oxygen is less than 2 rng/L in bottom
waters. This guideline was chosen because this concen-
tration is clearly indicative of potential harm to estu-
arine organisms. Approximately 3% of the NEP estu-
arine area experienced dissolved oxygen concentrations
less than 2 mg/L in bottom waters. Although most
regions of the country were rated good for dissolved
oxygen concentrations, the Southeast Coast and Puerto
Rico regions were rated fair.
National Estuary Program Coastal Condition Report 29
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CHAPTER 2 ' U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION- -A NATIONAL SNAPSHOT
Sediment Quality Index
The sediment quality index for the nations collective
NEP estuaries is rated fair to poor. This index is based
on an assessment of sediment toxicity, sediment
contaminant concentrations, and the percentage of
sediment TOC, and about 15% of the nation's NEP
estuarine area displayed a poor rating for one of these
component indicators (Figure 2-5). The largest propor-
tion of NEP estuarine area in poor condition was found
in the Puerto Rico (33%), Northeast Coast (21%), and
West Coast (17%) regions. Poor sediment quality
condition in these regions is primarily the result of high
TOC and sediment toxicity levels (Puerto Rico),
elevated contaminant concentrations (Northeast Coast),
and a high percentage of toxic sediments (West Coast).
The Gulf Coast region received a fair to poor rating for
sediment quality because 15% of this region's NEP
estuarine area was rated poor for sediment contaminant
concentrations. The Southeast Coast region received a
good to fair regional rating for this index, with only 6%
of the NEP estuarine area found to be in poor condi-
tion.
Sediment Toxicity I The NCA determined sedi-
ment toxicity by exposing test organisms to sediments
from each sampling site and evaluating the effects of
these sediments on the survival of the exposed organ-
isms. Sediment toxicity tests using the benthic organism
Ampelisca abdita showed significant mortalities associ-
ated with sediments in 7% of the nation's NEP estu-
arine area; therefore, sediment toxicity for the nation's
collective NEP estuaries is rated poor. Regionally, sedi-
ment toxicity was observed most often in the NEP estu-
aries of the Puerto Rico (29%), West Coast (18%), and
Northeast Coast (9%) regions.
Missing
2% Poor
Figure 2-5. Sediment
quality index data for
U.S. NEP estuaries
(U.S. EPA/NCA).
Sediment Contaminant Criteria (Long et al., 1995)
ERM (Effects Range Median)—Determined for each
chemical as the 50th percentile (median) in a database of
ascending concentrations associated with adverse biological
effects.
ERL (Effects Range Low)—Determined for each
chemical as the I Oth percentile in a database of ascending
concentrations associated with adverse biological effects.
Sediment Contaminants I The NCA analyzed
collected sediments for nearly 100 chemical contami-
nants at each sampling site, including 25 PAHs,
22 PCBs, 25 pesticides, and 15 metals. ERM and ERL
values were used as guidelines to ascertain sediment
condition, and poor condition was determined as an
exceedance of one or more ERMs. Sediment contami-
nation for the nation's NEP estuaries is rated fair, with
ERM values exceeded in sediments from 8% of the
nation's NEP estuarine area. The highest proportion of
sediments exceeding these guidelines occurred in the
NEP estuaries of the Northeast Coast (15%) and Gulf
Coast (11%) regions, which were both rated fair for
sediment contaminants. The West Coast and Puerto
Rico were also rated fair for this component indicator,
with 5% of each region's NEP estuarine area rated poor.
Only the Southeast Coast region was rated good for
sediment contaminant concentrations, with none of its
estuarine area rated poor.
Total Organic Carbon I TOC in estuarine sedi-
ments is often a source of food for benthic organisms;
however, high levels of sediment TOC can result in
significant changes in an estuary's benthic community
structure and the predominance of pollution-tolerant
species. The nation's collective NEP estuaries were rated
good for sediment TOC, with only 2% of the U.S.
NEP estuarine area rated poor for this component
indicator. In addition, all five NEP regions outlined in
this report received good regional ratings for sediment
TOC.
30 National Estuary Program Coastal Condition Report
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CHAPTER 2
U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
Benthic Index
As shown in Table 2-2, the criteria used to assess
benthic condition differed for the various geographic
regions of the United States. The benthic index for the
nation's NEP estuaries is rated fair, with the index
showing that 17% of the nation's NEP estuarine area
supports benthic communities in poor condition
(Figure 2-6). Benthic communities that are rated poor
are characterized by lower-than-expected diversity and a
high population of pollution-tolerant species, or they
contain fewer-than-expected pollution-sensitive species,
as measured by multimetric benthic indices. The
Northeast Coast and Puerto Rico regions are both rated
poor for the benthic index, with 26% and 65% of NEP
estuarine area in those regions rated poor, respectively.
The Gulf Coast region is rated fair to poor for this
index, with 20% of the NEP estuarine area rated poor
Table 2-2. Regional Criteria for Assessing Benthic Condition
Missing
Figure 2-6.
Benthic index
data for U.S. NEP
estuaries
(U.S. EPA/NCA).
and an additional 27% rated fair for benthic communi-
ties. The Southeast Coast region is rated fair for benthic
condition, with 15% of its NEP estuarine area rated as
having poorer-than-expected benthic communities.
Finally, the West Coast region is rated good for this
index, with only 4% of the region's NEP estuarine area
characterized as poor.
Region
Fair
Northeast Coast sites
Acadian Province
Virginian Province
Shannon-Weiner Diversity
Index score is
greater than 0.63
Benthic index score is
greater than 0.0
NA*
NA*
Shannon-Weiner Diversity
Index score is less than
or equal to 0.63
Benthic index score is
less than 0.0
Southeast Coast sites
Benthic index score is
greater than 2.5
Benthic index score is
between 2.0 and 2.5
Benthic index score is
less than 2.0
Gulf Coast sites
Benthic index score is
greater than 5.0
Benthic index score is
between 3.0 and 5.0
Benthic index score is
less than 3.0
West Coast sites
(compared to expected
diversity)
Benthic index score is more
than 90% of the lower limit
(lower 95% confidence
interval) of expected mean
diversity for a specific salinity
Benthic index score is
between 75% and 90%
of the lower limit of
expected mean diversity
for a specific salinity
Less than 75% of
observations had
expected diversity
Puerto Rico sites
(compared to upper 95%
confidence interval for mean
regional benthic diversity)
Benthic index score is more
than 90% of the lower limit
(lower 95% confidence
interval) of mean diversity
for unstressed habitats
in Puerto Rico
Benthic index score is
between 75% and 90%
of the lower limit of mean
diversity for unstressed
habitats in Puerto Rico
Benthic index score is
less than 75% of the
lower limit of mean
diversity for unstressed
habitats in Puerto Rico
NEP Estuary or Region
Less than 10% of the NEP
estuarine area has a poor
benthic index score,
and more than 50% of
the NEP estuarine area has
a good benthic index score
10% to 20% of the NEP
estuarine area has a poor
benthic index score, or
more than 50% of
the NEP estuarine area has
a combined poor and fair
benthic index score
More than 20% of the NEP
estuarine area has a poor
benthic index score
: By design, these indices discriminate between good and poor conditions only.
National Estuary Program Coastal Condition Report 31
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CHAPTER 2
U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
Fish Tissue Contaminants Index
Based on a weighted average of the regional scores,
the fish tissue contaminants index for the nation's NEP
estuaries is rated fair. Nationally, the index shows
elevated levels of chemical contaminants in fish/shellfish
tissues from 23% of the stations where fish were caught
(Figure 2-7). The NCA collected fish for analysis of
whole-body burdens of chemical contaminants (i.e.,
contaminants from the entire fish—fillets, head, skin,
and organs), with the exception of a few stations that
examined both edible fillets and whole-body burdens.
The NCA examined samples (5—10 fish of a target
species per station) from 330 stations throughout the
nation's NEP estuarine waters and performed chemical
analysis for about 90 specific contaminants.
The percentage of stations where fish were caught
with elevated contaminant concentrations may have
been increased in part due to the use of juvenile fish
rather than fish of commercial size. The use of juvenile-
sized fish could increase the likelihood of obtaining
higher whole-body concentrations of contaminants,
especially for those contaminants not found in muscle
tissue. EPA Advisory Guidance describing risk-based
concentrations of contaminants of concern for recre-
ational and subsistence fishers (few contaminant guide-
lines exist for wildlife protection) applies to fillet,
whole-body, and organ-specific concentrations (U.S.
EPA, 2000b). Whole-body concentrations for many
chemical contaminants (e.g., dioxins, PCBs,
organochlorine pesticides) are higher than the concen-
trations found in muscle tissue (fillets); however,
mercury concentrations can be severely underestimated
using whole-body concentration data because mercury
is concentrated primarily in the muscle tissue. Although
Figure 2-7. Fish
tissue contaminants
index data for U.S.
NEP estuaries (U.S.
EPA/NCA).
In the bioaccumulation process, chemical contaminants
bioaccumulate in the tissues of aquatic organisms to
concentrations many times higher than those found in
seawater. In addition, these tissue concentrations in fish
and other aquatic organisms may be increased at each
successive level of the food web (Figure 2-8). As a result,
top predators in a food web may have concentrations of
chemical contaminants in their tissues at levels a million
times higher than the concentrations found in seawater.
A direct comparison of fish advisory contaminants and
sediment contaminants is not possible because states
often issue advisories for groups of chemicals; however,
five of the top six contaminants most often associated
with fish advisories (e.g., PCBs, DDT, dieldrin, chlordane,
and dioxins) are among the contaminants most often
responsible for a Tier I National Sediment Inventory
classification (i.e., associated adverse effects to aquatic life
or human health are probable) of waterbodies based on
potential human health effects (U.S. EPA, 1997).
Humans
Bald Eagle
Cormorant
Lake Trout^,
Chinook Salmon
Sculpin
Bottom Feeders
Coho
Salmon
Plankton
Bacteria and Fungi
Dead Plants
and Animals
Figure 2-8. Bioaccumulation process (U.S. EPA/NCA).
32 National Estuary Program Coastal Condition Report
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CHAPTER 2 U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
mercury concentrations can be three to five times more
concentrated in muscle tissue than in whole-body
samples, about one-third of the coastal states often use
whole-body concentrations to set fish advisories for
waters where consumer groups eat whole fish.
The West Coast and Puerto Rico regions are rated
poor for fish tissue contaminants in their NEP estuaries,
with 32% and 40% of stations sampled, respectively,
showing above-Guidance concentrations for at least one
chemical contaminant. The Northeast Coast region is
also rated poor, with 38% of the samples analyzed rated
poor. Chemical contaminants detected in fish tissues
generally included total PCBs, DDT and its metabo-
lites, total PAHs, and mercury. Twelve percent of
stations sampled in Gulf Coast NEP estuaries and 10%
of stations sampled in Southeast Coast NEP estuaries
showed elevated tissue concentrations, and both regions
are rated good to fair for this index.
Population Pressures—
A National Perspective
Population pressures on the coastal counties coinci-
dent to an individual NEP study area, or collectively on
coastal counties coincident to all NEP study areas in a
specific region, must be evaluated not only as total
population, but also with thought to population density
and population growth rate; therefore, total population
values need to be assessed from both a temporal and
spatial perspective. Population density provides a
measure of how saturated the associated NEP-coinci-
dent coastal counties are with respect to human devel-
opment. In contrast, the population growth rate over a
specific time interval provides an indication of how
quickly human development in an area occurs, as well
as the coinciding infrastructure development that would
be necessary to provide such essentials as residential
housing and commercial development, highways and
other transportation facilities, safe drinking water, and
municipal and industrial treatment of wastes. Explosive
population growth may not provide adequate time for
state, county, or local government planning to meet
increased infrastructure needs; to adequately monitor
environmental indicators to assess trends affecting water,
sediment, and habitat quality and the health of living
resources; or to take action to reduce ecosystem degra-
dation when it is identified. When assessed collectively,
these measures provide information about the pressures
society is exerting on the NEP coastal ecosystems.
For example, the NEP-coincident counties of the
Northeast Coast region contained the highest total
population in 2000 (38 million), followed by the West
Coast (30 million), Gulf Coast (11 million), and
Southeast Coast (3 million) regions (Table 2-3).
Population density values also show that the NEP-
coincident counties of the Northeast Coast had the
highest regional density (1,055 persons/mi2) in 2000,
followed by the West Coast (421 persons/mi2), Gulf
Coast (287 persons/mi2), and the Southeast Coast
(168 persons/mi2) regions; however, the NEP study area
of San Juan Bay Estuary (Puerto Rico) had the highest
population density in 2000 of any of the five regions
(5,055 persons/mi2). In contrast to total population
and population density, population growth rates
(1960—2000) for these same regions show a different
pattern, with the Gulf Coast having the highest growth
rate (133%), closely followed by both the Southeast
Coast (131%) and the West Coast (100%), and lastly
by the Northeast Coast (24%) region (Culliton et al.,
1990; U.S. Census Bureau, 1991; 2001).
With respect to individual NEP study areas, there is
a wide difference in total population, population
density, and population growth rate, as well as in the
size of the land area of NEP-coincident coastal counties.
Researchers assess population pressures to determine how
increased population affects estuarine condition (JohnTheilgard).
National Estuary Program Coastal Condition Report 33
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CHAPTER 2 U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
Table 2-3. Total Population, Population Density, and Population Growth Rate for NEP-coincident Coastal Counties
(U.S. Census Bureau, 1991; 2001)
NEP Estuarine Area
Northeast Coast
Casco Bay
New Hampshire Estuaries
Massachusetts Bays
Buzzards Bay
Narragansett Bay
Long Island Sound
Peconic Estuary
New York/New Jersey Harbor
Barnegat Bay
Delaware Estuary
Delaware Inland Bays
Maryland Coastal Bays
Southeast Coast
Albemarle-Pamlico Estuarine Complex
Indian River Lagoon
Gulf Coast
Charlotte Harbor
Sarasota Bay
Tampa Bay
Mobile Bay
Barataria-Terrebonne Estuarine Complex
Galveston Bay
Coastal Bend Bays
West Coast
Puget Sound
Lower Columbia River Estuary
Tillamook Bay
San Francisco Estuary
Morro Bay
Santa Monica Bay
Puerto Rico
San Juan Bay Estuary
Land Area
(mi2)
35,894
4,671
2,002
2,829
1,714
5,001
6,750
911
5,470
1,921
12,138
942
475
1 8,963
14,452
4,511
39,482
9,719
1,320
5,214
2,827
8,824
6,720
10,374
70,043
20,118
11,875
1,101
10,357
3,308
26,794
233
233
Population for
NEP-coincident
Counties, 2000
(millions)
37.876
0.646
0.433
4.224
1.245
4.922
14.647
1.419
16.943
1.550
9.376
0.157
0.047
3.192
1.804
1.388
11.334
2.976
0.590
3.339
0.540
1.627
4.376
0.548
29.504
4.114
1.644
0.024
8.740
0.247
14.828
1.177
1.177
Population
Density, 2000
(persons/mi2 )
1,055
138
216
1,493
726
984
2,170
1,558
3,097
807
772
166
98
168
125
308
287
306
447
640
191
184
651
53
421
205
138
22
844
75
553
5,055
5,055
Percent
Population
Growth Rate,
1960-2000
24
48
148
23
72
28
14
113
13
132
35
114
96
131
71
327
133
251
304
190
49
28
182
36
100
121
78
28
96
204
99
NA
NA
NA = not available
34 National Estuary Program Coastal Condition Report
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CHAPTER 2 ! U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
For example, the total population in 2000 for coastal
counties coincident to NEP study areas ranged from
24,000 (Tillamook Bay) to 16,943,000 (New York/New
Jersey Harbor)—almost a 1,000-fold difference.
Population density also varied in the NEP-coincident
coastal counties, ranging from 22 persons/mi2
(Tillamook Bay) to 5,055 persons/mi2 (San Juan Bay
Estuary)—a more than a 200-fold difference. Finally,
population growth rates from 1960 to 2000 varied
widely and ranged from a low of 13% (New York/New
Jersey Harbor) to a high of 304% (Sarasota Bay). In
addition, the land areas of NEP-coincident coastal
counties range in size from 233 mi2 (San Juan Bay
Estuary) to 26,794 mi2 (Santa Monica Bay). The evalu-
ation of these parameters is important in assessing
population pressures on an individual estuary or coastal
region.
Correlation between NEP CCR
Index Scores and Population
Pressures
The NCA data reveal some patterns with respect to
an individual NEP study area's total population and
population density and its overall condition score and
rating. Mean overall condition improves with decreasing
population, although the ranges vary widely. As shown
in Table 2-4, for the 11 NEPs with populations greater
than 2 million people, the overall condition scores range
from 1.0 (rated poor) to 3.0 (rated fair), with a mean
overall condition score of 2.26 (rated fair to poor). For
the 8 NEPs with populations between 1 to 2 million
people, the overall condition scores range from 1.5
(rated poor) to 5.0 (rated good), with a mean score of
3.30 (rated fair). For the 9 NEPs with populations less
than 1 million people, the overall condition scores range
from 1.75 (rated poor) to 5.0 (rated good), with a mean
score of 3.45 (rated fair). Although it is clear that the
NEPs with the greatest populations (> 2 million) show
the lowest overall condition scores, as well as scores
within the smallest range of values, the overall condition
scores for the other two population ranges (1—2 million,
< 1 million) vary widely. In addition, the mean overall
condition score for the group of NEPs with the lowest
overall population (< 1 million) is only slightly higher as
compared to the score for the intermediate population
group (1—2 million).
As shown in Table 2-5, the overall condition scores
with respect to population density are very similar to
those found with respect to total population. For the
5 NEP study areas with population densities greater
than 2,000 persons/mi2, the overall condition scores
Environmental degradation has led to major declines in
native fish that depend upon estuaries for their existence
(Jim Ramaglia).
Table 2-4. Comparison of Total Population of NEP-Coincident Coastal Counties with NCA Mean Overall
Condition Scores
Total Population of
NEP-Coincident
Coastal Counties
> 2 million
1—2 million
< 1 million
Range in NCA
Overall Condition
Scores Observed
1.0-3.0
1 .5-5.0
1.75-5.0
NCA Mean
Overall
Condition Score
2.26
3.30
3.45
Number of
NEP
Estuaries
II
8
9
National Estuary Program Coastal Condition Report 35
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CHAPTER 2
U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
range from 1.0 (rated poor) to 4.3 (rated good), with a
mean overall condition score of 2.16 (rated fair to
poor). These estuaries include San Juan Bay Estuary
(5,055 persons/mi2), New York/New Jersey Harbor
(3,097 persons/mi2), Long Island Sound (2,170
persons/mi2), Peconic Estuary (1,558 persons/mi2), and
the Massachusetts Bays (1,493 persons/mi2). It should
be noted that although the Peconic Estuary had the
highest overall condition score (4.33), no data were
collected for a sediment quality index for this estuary;
therefore, this score does not reflect an assessment of
sediment toxicity, sediment contaminant concentra-
tions, or sediment TOC. If the Peconic Estuary is not
used in the population density analysis, then the overall
condition scores oi: the other 4 NEPs range from 1.0
(rated poor) to 2.5 (rated fair), and the mean overall
condition score drops from 2.16 (rated fair to poor) to
1.63 (rated poor). For the 8 NEPs with population
densities ranging from 500 to 1,000 persons/mi2, the
overall condition scores range from 1.75 (rated poor) to
3.5 (rated fair), with a mean score of 2.58 (rated fair).
Finally, for the 15 NEPs with the lowest population
densities (less than 500 persons/mi2), the overall condi-
tion scores range from 1.75 (rated poor) to 5.0 (rated
good), with a mean score of 3.39 (rated fair). As shown
for total population, there is a slight increase in the
mean overall condition scores for these groups as the
population density decreases.
Although the mean overall condition scores based on
total population and population density for the NEP-
coincident coastal counties appear to exhibit some
patterns, it should be noted that within any of the total
population groups (Table 2-4) or population density
groups (Table 2-5), there is a high degree of variability
in the range of overall condition scores for the indi-
vidual NEPs because unmeasured indices or component
indicators may exert effects on an estuary's overall
condition score.
For example, one confounding issue is that for 9 of
the 28 NEP estuaries (almost a third), component indi-
cator data were not collected for one or more of the
primary indices of estuarine condition. In the Northeast
Coast region, NCA data for the fish tissue contaminants
index and the sediment quality index were unavailable
for Casco Bay and the Peconic Estuary, respectively. In
the Southeast Coast region, NCA data for the fish tissue
contaminants index and two components of the sedi-
ment quality index (sediment toxicity and sediment
contaminant concentrations) were not available for the
Indian River Lagoon. In the Gulf Coast region, data
from the three Florida NEP estuaries were missing for
evaluating the fish tissue contaminants index and two
components of the sediment quality index (sediment
toxicity and sediment contaminant concentrations).
Finally, a benthic index could not be calculated for three
of the West Coast region's seven estuaries (the Lower
Columbia River Estuary, Morro Bay, and Santa Monica
Bay). If data had been collected and/or applicable for
these indices and component indicators, the overall
condition scores for the individual NEP estuaries may
have been considerably different from those developed
using less than a full suite of data.
Table 2-5. Comparison of Population Density of NEP-Coincident Coastal Counties with NCA Mean Overall
Condition Scores
Population Density of
NEP-Coincident
Coastal Counties
> 1 ,000 persons/mi2
500-1,000 persons/mi2
< 500 persons/mi2
Range in NCA
Overall Condition
Scores Observed
1.0-4.33
1.75-3.5
1.75-5.0
NCA Mean
Overall
Condition Score
2.16
2.58
3.39
Number of
NEP
Estuaries
5
8
15
36 National Estuary Program Coastal Condition Report
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CHAPTER 2
U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
The previous sections of this chapter have discussed
the national and regional ratings for the NEP estuaries,
which are based on NCA scores for four primary
indices of estuarine condition (water quality index, sedi-
ment quality index, benthic index, fish tissues contami-
nants index). The NCA results for the nation's 28 indi-
vidual NEP estuaries for these four indices, as well as
for the component indicators for the water and sedi-
ment quality indices, are shown in Figures 2-9 through
2-12. These figures provide an easy way to compare the
various ratings and scores for each index and compo-
nent indicator among the individual NEP estuaries, as
well as regionally and nationally. The figures also show
where data were unavailable to assess an index or
component indicator for an individual estuary. The
index ratings for the five NEP regions outlined in this
report will be discussed further in the regional summary
sections of Chapters 3 through 7.
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue Contaminants
Index
Missing
Figure 2-9. Comparison of NCA results for Northeast Coast NEP estuaries and all Northeast Coast estuaries (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 37
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CHAPTER 2 I U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
Fish Tissue Contaminants
Index
Figure 2-10. Comparison of NCA results for Southeast Coast NEP estuaries and all Southeast Coast estuaries (U.S. EPA/NCA).
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue Contaminants
Index
Figure 2-11. Comparison of NCA results for Gulf Coast NEP estuaries and all Gulf Coast estuaries (U.S. EPA/NCA).
38 National Estuary Program Coastal Condition Report
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CHAPTER 2 ! U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
Fish Tissue Contaminants
Index
Figure 2-12. Comparison of NCA results for West Coast NEP estuaries and all West Coast estuaries (U.S. EPA/NCA).
The 28 NEPs identify habitat loss or alteration of habitat in the NEP estuaries as a primary environmental concern (Ed Garland).
National Estuary Program Coastal Condition Report 39
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CHAPTER 2 U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
NEP Environmental Concerns
There are a number of major environmental
concerns that plague the nations 28 NEP estuaries
(ANEP, 2005; U.S. EPA, 2006d). As shown in Figure
2-13, several of these environmental concerns affect
almost all of the NEPs, while others are a concern for a
more limited number of NEPs and are related to site-
specific differences in the climatic conditions, geology,
or geomorphology of the individual estuaries. To
address these issues, the 28 NEPs have made many of
these environmental concerns the cornerstones of the
priority management activities for their respective
programs. The major environmental concerns for the
NEP estuaries include those discussed below.
Habitat Loss/Alteration (28 NEPs)
All 28 of the NEPs identify habitat loss or alteration
of habitat as a primary environmental concern.
Estuaries are the transitional zones that provide high-
quality habitat for a diverse array of organisms,
including food, shelter, migratory corridors, and
breeding and nursery areas for fish, shellfish, and water-
fowl. Healthy estuaries and their associated wetlands
and marshes protect water quality by sequestering toxi-
cants, filtering nutrients from runoff and storing water,
reducing flood potential, and protecting shorelines from
erosion during hurricane and storm-related events;
however, these areas are the habitats that are most
affected by human development, including dredging
and dredge-disposal activities; construction of groins,
seawalls, and other hardened structures; and hydrologic
modifications.
Declines in Fish and Wildlife
Populations (25 NEPs)
Human population growth and the associated activi-
ties of residential and commercial development threaten
the biological diversity, habitat quality, and productivity
of our nation's estuaries. Environmental degradation
associated with habitat loss, fragmentation or alteration,
water pollution from toxic chemicals and nutrients,
overexploitation of natural resources, and introduction
of invasive species have all led to major declines in some
of the native fish and wildlife populations that depend
upon estuaries for their existence. In addition to the 25
NEPs that identify declines in fish and wildlife species
as an environmental concern, 14 of these NEPs (-50%)
identify that these declines have occurred in some
recreationally or commercially valuable fish and shellfish
species.
Excessive Nutrients (21 NEPs)
Nutrients such as nitrogen and phosphorus are natu-
rally occurring and vital elements needed to support a
healthy ecosystem; however, excessive amounts of nutri-
ents can result in serious environmental problems. For
example, algal blooms rob the water column of
dissolved oxygen and diminish water clarity, reducing
the growth of SAV (e.g., seagrasses). Loss of SAV
acreage can result in loss of critical habitat needed to
sustain healthy communities of fish and shellfish. From
Delaware south to Florida's Atlantic arid Gulf Coast
estuaries, excessive nutrients have also been linked to
fish kills by toxic algae such as Pfiesteria piscicida (N.C.
Department of Health and Human Services, 2003).
Nutrients can enter estuaries via runoff of agriculturally
and residentially applied fertilizers and animal wastes,
discharges from wastewater treatment plants (WWTPs),
leaching from malfunctioning septic systems, and
discharges of sanitary wastes from recreational boats. It
is noteworthy that although excessive nutrients remain a
concern in many estuaries, $53 billion in funding has
been spent over the past 18 years to rebuild and
upgrade WWTPs, resulting in expanded capacity for
secondary and tertiary treatment of wastewater to
remove nutrients, heavy metals, and organic contami-
nants (U.S. EPA, 2006a).
Toxic Chemical Contaminants
(20 NEPs)
During the past 50 years, 70,000 synthetic chemicals
have been released into the nation's estuarine and
marine environments via stormwater runoff, industrial
discharges, agricultural runoff, and deposition of toxi-
cants from air pollution (ANEP, 2005). The chemical
contaminants of major concern include metals (e.g.,
mercury), PCBs, PAHs, a variety of organochlorine
pesticides (e.g., DDT, dieldrin, and chlordane), and
herbicides. These chemicals may become adsorbed
to estuarine sediments and affect the structure and
diversity of benthic communities. In addition, they
provide a conduit for chemical contaminants to move
up the food chain because fish and other wildlife feed
on benthic organisms living in areas with contaminated
sediments.
40 National Estuary Program Coastal Condition Report
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CHAPTER 2 U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
Pathogenic Microorganisms (19 NEPs)
Pathogenic microorganisms (pathogens) include
bacteria, viruses, and algae that produce diseases in
plants, animals, and humans. In addition to human
health risks from recreational contact with contami-
nated seawater and consumption of contaminated fish
and shellfish, pathogen contamination in estuaries can
result in economic losses due to shellfish-harvesting
closures. Pathogens can cause disease conditions, such as
gastroenteritis, salmonellosis, hepatitis A, and, in the
case of the bacteria Vibrio vulnificus, can even cause
death in some individuals (Rippey, 1994). Pathogen
sources may include WWTP discharges, malfunctioning
septic systems, land runoff from confined animal
feeding operations (CAFOs) or concentrations of
migratory waterfowl, and sanitary wastes from recre-
ational boats.
Alteration of Freshwater Flows
(11 NEPs)
In many parts of the United States, fresh water is an
increasingly scarce natural resource. Human activities
have altered the timing and volume of freshwater flows
into some estuaries through dam construction and
extensive withdrawals of water for irrigation or munic-
ipal drinking water use. Alteration in the timing and
volume of freshwater flows can have devastating reper-
cussions for estuarine plants and animals, especially in
regions where rainfall is minimal. Alterations in fresh-
water discharges can result in changes in salinity, nutrient,
and sediment levels in estuarine waters, which can affect
seasonal fish-spawning activities, shellfish condition,
avian nesting activities, and the health of wildlife that
are dependent on the estuaries (ANEP, 2005).
Habitat Loss/Alteration
Species Loss/Decline
Nutrients
Toxics
Pathogens
Freshwater Inflow
Introduced/Pest Species
Sedimentation
Contaminated Seafood
Human Population Growth
Conventional Pollutants
Land Use
Dredging/Disposal
Floatable Debris
HABs and/or Red/Brown Tides
Non-point Source Pollution
Hypoxia (Low Oxygen)
Stormwater
Drinking Water Problems
Hydrologic Alteration
Oil Spills
Swimming Area Closings
Wastewater
Flooding
0
National Estuary Program Environmental Concerns
28
HZ5
H2I
19
UM
Jio
_h
10 15 20
Number of Estuary Programs
—T~
25
30
Figure 2-13. List of environmental concerns of the nation's 28 individual NEPS (U.S. EPA, 2006d).
National Estuary Program Coastal Condition Report 41
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CHAPTER 2 U.S. NATIONAL ESTUARY PROGRAM COASTAL CONDITION—A NATIONAL SNAPSHOT
Introduction of Invasive Species
(11 NEPs)
Invasive species can be plants, animals, and other
organisms such as microorganisms (e.g., bacteria,
viruses, algae) that are typically introduced through
human activities. An invasive species is one that is non-
native to the ecosystem under consideration and whose
introduction causes economic or environmental harm
or human health concerns (USDA, 2006). The food
webs of some NEP estuaries have been altered by the
introduction of non-indigenous, exotic species,
including both plants and animals. These invading,
opportunistic species have, through predation of and
competition with native species, led to the alteration or
eradication of many native plants and animals. Invasive
species can also affect commercial and recreational
fishing, recreational boating, and beach ecology; inter-
fere with industrial processes and navigation; cause
wetlands loss; and modify nutrient cycling and soil
fertility (ANEP, 2005). Many invasive species are
transported by cargo ships, which discharge millions of
gallons of ballast water at large commercial shipping
ports in the United States. Other species are imported
intentionally into the United States through the
aquarium or water garden trade (USGS, 2006a). The
European milfoil (Myriophyllum spicatuni) is a prime
example of an invasive SAV species that can become
permanently established where it is introduced. In many
estuarine rivers and bays along the Atlantic, Gulf, and
Pacific coasts, water milfoil has thrived and has become
the dominant SAV.
Although some environmental concerns are universal
among the NEP estuaries, others are restricted to only a
few NEPs. Each individual NEP must address, monitor,
and effectively manage a slightly different suite of
environmental concerns relative to their own estuary.
Further information on some of the more important
environmental concerns confronting each of the
28 NEP estuaries is described in the latter half of each
NEP profile (Chapters 3 through 7) in the section
entitled Indicators of Estuarine Condition.
42 National Estuary Program Coastal Condition Report
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CHAPTER 3
NORTHEAST COAST NATIONAL ESTUARY PROGRAM
COASTAL CONDITION
.t:
-------
CHAPTER 3
NORTHEAST COAST NATIONAL ESTUARY PROGRAM
COASTAL CONDITION
Background
The Northeast Coast region extends from Maine
southward to Virginia and contains the largest number
of NEP estuaries (12) per region in the United States
(Figure 3-1). Tides throughout the Northeast Coast
region occur twice a day and range from highs of
18 feet in areas of northern Maine to 10 feet in
southern Maine, diminishing to less than 3 feet in
southern Virginia (NOAA, 1985).
Within the Northeast Coast region, there are two
distinct and unique geological areas. The first area,
referred to as the Gulf of Maine, extends from the
I. Casco Bay
2. New Hampshire Estuaries
3. Massachusetts Bays
4. Buzzards Bay
5. Narragansett Bay
6. Long Island Sound
7. Peconic Estuary
8. New York/New Jersey Harbor
9. Barnegat Bay
10. Delaware Estuary
11. Delaware Inland Bays
12. Maryland Coastal Bays
Figure 3-1. The Northeast Coast region is home to 12 NEP
estuaries.
Canadian border south to Cape Cod, MA. Estuaries in
the Gulf of Maine were formed by ancient glaciers that
scoured much of the soil cover from the land, leaving
rocky shorelines, thin soils, and deeply carved channels
through which rivers today flow out to the ocean. These
estuarine systems are similar in many ways to fjords. As
a result of the strong tidal flows and the shape of the
basins in the Gulf of Maine estuaries, circulation within
these systems is tidally dominated (NO.AA, 1985).
The Northeast Coast region's second geological area
extends from Cape Cod, MA, south to Virginia. The
topography of this area was less affected by ancient
glaciers; rather, rising sea level resulting from melting
glaciers drowned the mouths of ancient rivers flowing
across the continental shelf, which created coastal plain
estuaries. In these coastal plain estuaries, the volume of
water introduced by tidal action is large compared to
freshwater river inflow, with tides in the estuaries
serving as the dominant force influencing circulation
(NOAA, 1985). In addition to its basin and coastal
plain estuaries, the Northeast Coast region also has
several shallow lagoon systems where circulation is
largely wind-dominated (Day et al., 1989).
The 12 Northeast Coast NEP estuaries are very
different in their geological and physical characteristics.
On average, water depth is greater than 56 feet from
Maine to New York, but only 20 feet from New York to
Delaware. Light can penetrate to 33 feet or more in the
northern waters of the region, where there is less
suspended sediment, but to less than 7 feet south of
New Jersey, where thicker soils in the mid-Atlantic
contribute greater amounts of sediment to coastal
waters. As a result, seagrass communities in the south-
ernmost waters of this region are often light-limited and
more sensitive to human development (Thayer et al.,
1984; Roman et al., 2000).
44 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Freshwater inflows into the Northeast Coast NEP
estuaries typically carry low amounts of sediment
because of the extensive stretches of heavy forest and the
rocky nature of the soils that predominate in the region's
estuarine drainage areas. Sediment loading to Northeast
Coast estuaries increases southward as the coastal plain
widens and agricultural activity increases. Precipitation
patterns also influence freshwater input from rivers
flowing into these estuaries, and annual precipitation
(averaging 40 to 44 inches) increases only slightly from
north to south. Freshwater inflows to the Northeast
NEP estuaries tend to coincide with variations in winter
snow melt, with high-flow periods occurring from
March through May in the northern portions of the
region and slightly earlier in the year in the central and
southern portions of the region. Freshwater inputs to
the NEP estuaries throughout the region are lowest
from July through September. Along the East Coast, the
Northeast NEP estuaries contribute about 65% of all
freshwater discharges to coastal waters (NOAA, 1985).
Population Pressures
The population of the 75 NOAA-designated coastal
counties coincident with the NEP study areas of the
Northeast Coast region increased by 24% during a
40-year period, from 30.5 million people in I960 to
37.9 million people in 2000 (Figure 3-2) (U.S. Census
Bureau, 1991; 2001). This increase resulted in a popu-
lation density of 1,055 persons/mi2 in 2000 for these
coastal counties; however, the population densities of
the region's individual NEP study areas varied consider-
ably in 2000, from a high of 3,097 persons/mi2 for
the New York/New Jersey Harbor to a low of 98
persons/mi2 for the Maryland Coastal Bays (U.S.
Census Bureau, 2001). The population density of the
Northeast Coast region was much higher than the den-
sities exhibited the Southeast Coast (168 persons/mi2),
Gulf Coast (287 persons/mi2), and West Coast (421
persons/mi2) regions. Development and population
pressures are especially strong surrounding most of the
Northeast NEP estuaries, which are close to some of the
oldest cities in the United States. These cities—located
along the nation's most heavily populated corridor
between Washington, D.C., and Boston, MA—are
historic and current centers of commerce and industry,
and the nearby NEP estuaries are popular areas for
commercial and recreational fishing and other activities
for city residents.
NCA Indices of Estuarine
Condition—Northeast Coast
Region
Based on data collected for the NCA, the overall
condition of the collective NEP estuaries of the
Northeast Coast region is rated poor (Figure 3-3). EPA
summarizes conditions in the 12 Northeast Coast NEP
estuaries, and these statistical summaries facilitate
coastal condition comparisons among different NEP
estuaries within the region. As part of the NCA, more
than 550 Northeast sites were assessed during 2000 and
2001, and 18 sites in the Peconic Estuary were also
surveyed in 2002. Each site was visited once during the
summer season; therefore, the picture that emerges from
the NCA study is a "snapshot" rather than a description
of long-term conditions. The NCA approach provides
an accurate assessment of conditions in the relatively
stable realm of the sediments and biological communi-
ties; however, it does not address short-term water
40
o 30
e 20
"5 10
I960
2000
Figure 3-2. Population of NOAA-designated coastal counties
of the Northeast Coast region's NEP study areas, 1960-2000
(U.S. Census Bureau, 199 I; 2001).
National Estuary Program Coastal Condition Report 45
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
quality conditions, such as changes in the water column
that may occur weekly or daily during the summertime
survey period.
EPA assessed the Northeast Coast NEP estuaries
using four indices that respectively evaluate water
quality, sediment quality, benthic condition (i.e., the
status of the invertebrate community that lives in or on
the sediments), and fish tissue contaminant levels.
These indices were rated good, fair, or poor based on
the criteria outlined in Chapter 1 (Tables 1-24, 1-25,
and 1-26), and a category of missing was applied when
data were unavailable. Figure 3-4 shows the percent of
NEP estuarine area in the Northeast Coast region rated
good, fair, poor, or missing for each parameter consid-
ered. For all parameters except the fish tissue contami-
nants index, results were expressed as the percentage of
estuarine area falling within a category for each NEP.
The fish tissue contaminants index was not weighted by
area, but was reported as the percentage of fish
analyzed.
The water quality index for the collective NEP estu-
aries of the Northeast Coast region is rated fair, and the
sediment quality, benthic, and fish tissue contaminants
indices for this region are rated poor based on the
criteria used in this report. These regional-scale ratings
facilitate comparisons among NEP estuaries in different
regions of the country.
Natural and anthropogenic features and pressures in
the Northeast Coast region strongly influence the
manner in which pollutants accumulate and are
processed in estuaries, as well as the structure and
condition of estuarine fish and benthic communities.
The major estuaries of the Northeast Coast region—
those associated with the Connecticut, Hudson, and
Delaware rivers—have watersheds that are relatively
small compared with estuaries along the Southeast
Coast and Gulf Coast regions; therefore, estuaries of the
Northeast Coast are more affected by local sources of
pollution and stresses than estuaries in the other
regions. In addition, NEP estuaries in the Northeast
Coast region are situated along the most densely popu-
lated coastline in the country (U.S. Census Bureau,
2001). Estuarine sediment contamination levels tend to
be highest where sediments deposit near urban centers,
and nutrient concentrations in developed areas are
greater than in pristine areas. In New England, the
dominant nutrient input is from WWTPs in urban
centers and from atmospheric deposition of nitrogen for
non-urban sites. In the mid-Atlantic, agricultural runoff
and animal operations are important sources of nutri-
ents, in addition to atmospheric deposition and urban
sources.
Overall Condition
Northeast Coast
NEP Estuaries
(1.5)
Fair
Water Quality Index (3)
Sediment Quality Index (I)
Benthic Index (I)
Fish Tissue Contaminants
Index (I)
Figure 3-3. The
overall condition of
the Northeast Coast
NEP estuarine area is
poor (U.S. EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Estuarine Area
Missing
Figure 3-4. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Northeast Coast
region (U.S. EPA/NCA).
46 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Water Quality Index
The water quality index for the collective NEP estu-
aries of the Northeast Coast region is rated fair (Figure
3-5). The index was based on five component indicators
measured in the NCA: three indicators that estimate the
extent of estuarine eutrophication (DIN, DIP, and
chlorophyll a concentrations) and two that evaluate
conditions that are key to estuarine health (water clarity
and dissolved oxygen concentrations). Generally, there
was a north to south pattern in the Northeast region's
water quality index, which degraded southward.
Dissolved Nitrogen and Phosphorus The
Northeast Coast region is rated fair for both DIN and
DIP concentrations. Based on the thresholds indicating
impairment, 10% of the Northeast Coast NEP estu-
arine area was rated poor for DIN concentrations, and
data were unavailable for 23% of the estuarine area.
A north to south gradient was generally evident in the
DIN data, with large areas of the Delaware Estuary,
Delaware Inland Bays, and Maryland Coastal Bays
exhibiting poor or fair condition for this component
indicator.
Eleven percent of the Northeast Coast NEP estuarine
area was rated poor for DIP concentrations, and data
for this component indicator were unavailable for 11 %
of the estuarine area. More than 62% of the region had
poor or fair DIP levels; however, there was no clear
pattern with latitude for DIP. There are important
questions regarding the process by which nutrients
cause phytoplankton blooms and what levels of these
nutrients are detrimental in estuaries; however, neither
the frequency nor the location of measurements in the
NCA survey were sufficient to address these questions.
Chlorophyll a \ The Northeast Coast region is
rated good for chlorophyll a concentrations. Only 4%
of the region's NEP estuarine area was rated poor for
this component indicator, and 31 % of the area was
rated fair. Chlorophyll a data were unavailable for 11 %
of the Northeast Coast NEP estuarine area. The north
to south gradient observed for DIN data was also gener-
ally evident in the chlorophyll a data, with large areas of
the Delaware Estuary, Delaware Inland Bays, and
Maryland Coastal Bays exhibiting poor or fair condition
for this component indicator.
This report discusses two different approaches for
characterizing estuarine condition:
Approach I -The NCA provides unbiased, quality-
assured data that can be used to make consistent
"snapshot" comparisons among the nation's NEP
estuaries. These comparisons are expressed in terms
of the percent of NEP estuarine area in good, fair,
or poor condition.
Approach 1 - Each individual NEP collects site-
specific estuarine data in support of local problem-
solving efforts. These data are difficult to compare
among NEPs, within regions or nationally, because the
sampling and evaluation procedures used by the
NEPs are often unique to their individual estuaries.
However, these evaluations are important because
NEP-collected data can evaluate spatial and temporal
changes in estuarine condition on a more in-depth
scale than can be achieved by the NCA snapshot
approach.
Water Quality Index - Northeast Coast
Site Criteria: Number of component
indicators in poor or fair condition
• Good — No more than I is fair
OFair ac | is poor, or 2 or
more are fair
• Poor = 2 or more are poor
O Missing
I
Fair
45%
Figure 3-5. Water quality index data for the Northeast Coast
NEP estuarine area (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 47
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Water Clarity I The Northeast Coast region is
rated good for water clarity. NCA data show that poor
water clarity occurred in only 6% of the Northeast NEP
estuarine area; however, data from 23% of the area were
unavailable. Poor water clarity was prevalent only in the
more southernly NEP estuaries of the Northeast Coast
region, including Barnegat Bay, Delaware Estuary, the
Delaware Inland Bays, and the Maryland Coastal Bays.
Diminished water clarity is commonly observed in these
estuarine systems, to some extent because of natural
processes such as tidal resuspension of fine sediments.
Dissolved Oxygen I The Northeast Coast region
is rated good for dissolved oxygen concentrations.
Seventy-five percent and 17% of the regions NEP
estuarine area were rated good and fair, respectively, for
dissolved oxygen concentrations, and only 3% of the
estuarine area was rated poor. Depleted dissolved
oxygen concentrations were measured in portions of
Long Island Sound, Narragansett Bay, New York/
New Jersey Harbor, and Buzzards Bay.
Sediment Quality Index
Sediment quality for the Northeast Coast region was
calculated using three component indicators of sedi-
ment condition measured by the NCA: sediment
toxicity, sediment contaminants, and sediment TOC.
The sediment quality index for the collective estuaries
of the Northeast Coast region is rated poor (Figure
3-6), primarily because 21% of the NEP estuarine area
monitored was rated poor due to sediment toxicity or
sediment contaminants concentrations.
The Northeast Coast NEP estuaries with the poorest
sediment quality condition were generally situated near
major urban centers (e.g., New York/New Jersey
Harbor, western Long Island Sound, upper Narragan-
sett Bay, and the waters of the Delaware Estuary in the
vicinity of Philadelphia). At these locations, impaired
ratings were usually triggered by sediment contamina-
tion, such as high concentrations of metals, PCBs,
and/or DDT.
Sediment Toxicity I The Northeast Coast region is
rated poor for sediment toxicity because 9% of the
region's NEP estuarine area was rated poor. Eighty-four
percent of the area was rated good for this component
indicator, and NCA data on sediment coxicity were
unavailable for 7% of the Northeast Coast NEP
estuarine area.
Sediment Contaminants I The Northeast Coast
region is rated fair for sediment contaminant concentra-
tions because 15% of the region's NEP estuarine area
was rated poor for this component indicator. In addi-
tion, 15% of the area was rated fair, and 64% of the
area was rated good. NCA data on sediment contami-
nant concentrations were unavailable for 6% of the
Northeast Coast NEP estuarine area.
Total Organic Carbon The Northeast Coast
region is rated good for sediment TOC. Only 1.% of
the Northeast Coast NEP estuarine area was rated poor
for TOC concentrations, whereas 48% of the area was
rated good and 20% of the area was rated fair. NCA
data on TOC concentrations were unavailable for 31 %
of the estuarine area.
Sediment Quality Index - Northeast Coast
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
O Fair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Fair
13%
Figure 3-6. Sediment quality index data for the Northeast
Coast NEP estuarine area (U.S. EPA/NCA).
48 National Estuary Program Coastal Condition Report
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CHAPTER 3 ! NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Benthic Index
Sixty-one percent of the Northeast Coast NEP estu-
arine area exhibited acceptable benthic condition, but
26% did not; therefore, the benthic index for the collec-
tive NEP estuaries of the Northeast Coast region is
rated poor (Figure 3-7). The extent of impairment was
relatively uniform at all NEP sites, slightly exceeding a
third of the estuarine area only in Long Island Sound,
New York/New Jersey Harbor, and the Delaware Inland
Bays. The benthic index for the Northeast Coast region
was calculated by two methods: an established benthic
index created specifically for the Virginian Province was
used to evaluate conditions south of Cape Cod (Paul et
al., 2001), whereas the Shannon-Weiner Diversity Index
was used to evaluate locations north of Cape Cod. By
both measures, greater diversity is indicative of a
healthier community. Currently, a new benthic index
for the waters north of Cape Cod is being developed
that will account for the effects of natural habitat varia-
tions that affect species diversity.
Fish Tissue Contaminants Index
The fish tissue contaminants index for the collective
NEP estuaries of the Northeast Coast region is rated
poor (Figure 3-8). Thirty-eight percent of all fish
samples analyzed had concentrations of chemical conta-
minants that exceeded EPA Advisory Guidance values
for fish consumption; another 25% of the fish samples
analyzed were rated fair for fish tissue contaminant
levels; and only 37% were rated good. In addition, wide
differences in contaminant levels were noted among the
individual NEP estuaries. All of Narragansett Bay and
New York/New Jersey Harbor achieved a poor or fair
rating for fish tissue contaminant concentrations, as did
large portions of the New Hampshire Estuaries,
Buzzards Bay, Massachusetts Bays, and Delaware
Estuary. In contrast, nearly all of the Delaware Inland
Bays and Maryland Coastal Bays were rated good for
this index, and NCA data were unavailable for Casco
Bay. These results reflect concentrations in whole fish;
whereas the EPA Advisory Guidance refers to edible
portions of fish. Contaminant levels in whole fish can
Benthic Index - Northeast Coast
Site Criteria:
Shannon-Weiner Diversity
Index Score
• Good = > 0.63
• Poor = s 0.63
0 Missing
Site Criteria:
Virginian Province
Benthic Index Score
• Good = > 0.0
• Poor = s 0.0
O Missing
61%
Figure 3-7. Benthic index data for the Northeast Coast NEP
estuarine area (U.S. EPA/NCA).
In some areas of the Northeast, lobster tissue was analyzed for
contaminants (NOAA).
National Estuary Program Coastal Condition Report 49
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Fish Tissue Contaminants Index - Northeast Coast
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
O Fair = Falls within Guidance range
• Poor = Exceeds Guidance range
Poor
38%
Fair
25%
Figure 3-8. Fish tissue contaminants index data for the
Northeast Coast NEP estuarine area (U.S. EPA/NCA).
be higher or lower than levels in fillets, depending on
the fish species and contaminant assessed; however, the
guidelines used for this report are appropriate for some
populations that consume whole fish.
NEP Estuaries and the Condition
of the Northeast Coast Region
The purpose of the NEP is to identify, restore, and
protect the nationally significant estuaries of the United
States. Most of the 12 NEP estuaries of the Northeast
Coast region need this extra protection, in part because
their size and societal significance have led to intense
human development and a diversity of uses, including
industrial and agricultural production and international
commerce and shipping, resulting in associated environ-
mental concerns throughout their watersheds. Does the
condition of the Northeast Coast NEP estuaries
accurately reflect the condition of all Northeast Coast
estuaries (both NEP and non-NEP)? Based on the
NCA survey results, the collective Northeast Coast NEP
estuaries and all Northeast Coast estuaries combined are
both rated poor for overall condition, with the group of
NEP estuaries receiving an overall condition score of
1.5, just slightly higher than the overall condition score
of 1.25 for all Northeast Coast estuaries (Figure 3-9).
Both groups of estuaries also have similar regional
ratings for most of the NCA estuarine indices and
component indicators.
A comparison of the NCA data shows that the
collective Northeast Coast NEP estuaries are rated fair
for the water quality index and poor for the sediment
quality, benthic, and fish tissue contaminants indices.
The group of all Northeast Coast estuaries combined
are rated fair to poor for the water quality index and
poor for the sediment quality, benthic, and fish tissue
contaminants indices. The two groups of estuaries are
rated comparably for a number of the water and sedi-
ment quality component indicators, with both groups
rated good for sediment TOC concentrations, fair for
DIN and sediment contaminant concentrations, and
poor for sediment toxicity. However, the collective NEP
estuaries are rated good for water clarity and chlorophyll
a and dissolved oxygen concentrations and rated fair for
DIP concentrations, whereas the group of all Northeast
Coast estuaries are rated poor for water clarity, fair for
chlorophyll a and dissolved oxygen concentrations, and
good for DIP concentrations. Based on these ratings,
the condition of the Northeast Coast NEP estuaries is
relatively representative of the condition of all Northeast
Coast estuaries, with the exception of water quality
condition, where the group of NEP estuaries received
better or equal ratings for the index and most of the
component indicators.
With respect to the individual Northeast Coast NEP
estuaries, 11 of the 12 estuaries received higher or
comparable overall condition scores than the overall
condition score for than the collective Northeast Coast
NEP estuaries (1.5, rated poor). Casco Bay (5.0) and
Peconic Estuary (4.33) are both rated good for overall
condition; the New Hampshire Estuaries (3.5),
Barnegat Bay (3.5), the Maryland Coastal Bays (3.5),
Buzzards Bay (3.25), the Delaware Inland Bays (2.5),
50 National Estuary Program Coastal Condition Report
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CHAPTERS NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue Contaminants
Index
Missing
Figure 3-9. Comparison of NCA results for Northeast Coast NEP estuaries and all Northeast Coast estuaries (U.S. EPA/NCA).
and the Massachusetts Bays (2.5) are each rated fair;
and Narragansett Bay (1.75), Delaware Estuary (1.75),
and Long Island Sound (1.5) are each rated poor. Only
one Northeast Coast NEP estuary, New York/New
Jersey Harbor, received an overall condition score (1.0,
rated poor) that is lower than the overall score for the
collective Northeast Coast NEP estuaries.
A review of the NCA data for the water quality
index and component indicators shows that this index
is rated good for Casco Bay, the Massachusetts Bays,
Buzzards Bay, and Peconic Estuary; good to fair for
Barnegat Bay; fair for the New Hampshire Estuaries,
Narragansett Bay, Long Island Sound, and Delaware
Inland Bays; and poor for New York/New Jersey
Harbor, Delaware Estuary, and the Maryland Coastal
Bays. The poor water quality ratings were caused
primarily by elevated DIN and/or DIP concentrations
in all three estuaries and by degraded water clarity and
elevated chlorophyll a concentrations in Delaware
Estuary and the Maryland Coastal Bays. A north to
south gradient was generally evident in the DIN data
for the Northeast Coast NEP estuaries, with Casco Bay,
the New Hampshire Estuaries, the Massachusetts
Bays, Buzzards Bay, Narragansett Bay, Long Island
Sound, Peconic Estuary, and Barnegat Bay rated good
for this component indicator; New York/New Jersey
Harbor and the Delaware Inland Bays rated fair; and
Delaware Estuary and Maryland Coastal Bays rated
poor. No clear pattern was observed with latitude for
DIP concentrations in the Northeast Coast NEP estu-
aries, with Casco Bay, the Massachusetts Bays, and
Barnegat Bay rated good for this component indicator;
the New Hampshire Estuaries, Buzzards Bay,
Narragansett Bay, Long Island Sound, Peconic Estuary,
Delaware Estuary, and the Delaware Inland Bays rated
fair; and New York/New Jersey Harbor and the
Maryland Coastal Bays rated poor. Casco Bay, the
New Hampshire Estuaries, the Massachusetts Bays,
Buzzards Bay, Long Island Sound, Peconic Estuary,
New York/New Jersey Harbor, and Barnegat Bay are
rated good for chlorophyll a concentrations. Narragan-
sett Bay, Delaware Estuary, the Delaware Inland Bays,
and the Maryland Coastal Bays are rated fair. None of
the Northeast Coast NEP estuaries are rated poor for
National Estuary Program Coastal Condition Report 51
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
chlorophyll a concentrations. A north to south gradient
was generally evident in the chlorophyll a data, with
large areas of Delaware Estuary, the Delaware Inland
Bays, and the Maryland Coastal Bays exhibiting fair
condition for this component indicator. Narragansett
Bay was the only estuary rated fair for this component
indicator that exhibited an exception to this latitudinal
trend.
Although the water clarity rating is good for the
Northeast Coast NEP estuarine area and for 9 of the
12 individual NEP estuaries, the Delaware Estuary is
rated fair and Barnegat Bay and the Maryland Coastal
Bays are rated poor for this component indicator. Poor
water clarity was prevalent only in the more southernly
NEP estuaries of the Northeast Coast region.
Diminished water clarity is commonly observed in these
estuarine systems, to some extent because of natural
processes such as tidal resuspension of fine sediments.
Accordingly, the reference levels used to rate water
clarity are different for the naturally turbid Delaware
Estuary, where greater turbidity was required to merit a
fair or poor rating than the criteria for neighboring
estuaries. An important determination involving water
clarity is the level of turbidity due to excess soil erosion
or phytoplankton blooms caused by human activity;
however, the NCA data alone were not sufficient to
answer this question. Dissolved oxygen concentrations
are rated good for 11 Northeast Coast NEP estuaries,
but are rated fair for Long Island Sound. Depleted
dissolved oxygen concentrations were measured in areas
of Long Island Sound, Narragansett Bay, New
York/New Jersey Harbor, and Buzzards Bay.
The sediment quality index and component indi-
cator ratings for the individual Northeast Coast NEP
estuaries range from good to poor. The sediment quality
index is rated good for Casco Bay and the Maryland
Coastal Bays; good to fair for the New Hampshire
Estuaries, Barnegat Bay, and Delaware Estuary; fair for
Buzzards Bay; and poor for the Massachusetts Bays,
Narragansett Bay, Long Island Sound, New York/New
Jersey Harbor, and the Delaware Inland Bays. Typically,
sediment toxicity and/or sediment contaminant concen-
trations were responsible for a poor sediment quality
index rating because all of the Northeast Coast NEP
estuaries are rated good for sediment TOG None of the
sediment quality component indicators were assessed for
the Peconic Estuary.
The north to south pattern of degraded condition
seen with some of the water quality component indica-
tors was not apparent with the sediment quality compo-
nent indicators. Rather, the NEP sites with the poorest
condition were generally situated near major urban
centers (e.g., New York/New Jersey Harbor, western
Long Island Sound, upper Narragansett Bay, and the
portion of Delaware Estuary near Philadelphia). At
these locations, the impaired ratings were usually trig-
gered by sediment contamination, most often high
concentrations of metals (in particular, mercury, silver,
and nickel), PCBs, and DDT. With respect to the sedi-
ment quality component indicators, sediment toxicity is
rated good for Casco Bay, the New Hampshire
Estuaries, Barnegat Bay, and the Maryland Coastal Bays
and poor for the Massachusetts Bays, Buzzards Bay,
Narragansett Bay, Long Island Sound, New York/New
Jersey Harbor, Delaware Estuary, and the Delaware
Inland Bays. Sediment toxicity was generally not
observed in more than 11 % of an NEP's estuarine area,
with the exception of New York/New Jersey Harbor,
where sediments were rated poor in 25% of the NEP
estuarine area. The NCA survey did not assess sediment
toxicity in the Peconic Estuary. Sediment contaminant
concentrations are rated good for Casco Bay, the New
Hampshire Estuaries, Barnegat Bay, Delaware Estuary,
the Delaware Inland Bays, and the Maryland Coastal
Bays; fair for the Massachusetts Bays, Buzzards Bay, and
Narragansett Bay; and poor for Long Island Sound and
New York/New Jersey Harbor. The NCA did not assess
sediment contaminants in the Peconic Estuary. Finally,
all of the Northeast Coast NEP estuaries are rated good
for sediment TOC concentrations, although relatively
large areas of Casco Bay and the New Hampshire
Estuaries are rated fair for this component indicator.
The northern NEP estuaries of the Northeast Coast
region generally had the greatest occurrence of high
TOC concentrations; however, some analysts caution
that high TOC levels are not necessarily a definitive
indication of sediment degradation. The NCA survey
did not assess sediment TOC for the Peconic Estuary.
52 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
The benthic index ratings for the Northeast Coast
NEP estuaries range from good to poor. The benthic
index is rated good for Casco Bay; good to fair for
Buzzards Bay; fair for the New Hampshire Estuaries,
Peconic Estuary, Barnegat Bay, and the Maryland
Coastal Bays; fair to poor for Narragansett Bay; and
poor for the Massachusetts Bays, Long Island Sound,
New York/New Jersey Harbor, Delaware Estuary, and
the Delaware Inland Bays. Some of the estuaries north
of Cape Cod (e.g., Acadian Province) did not score well
based on the NCA method used to determine the
health of benthic communities south of Cape Cod;
therefore, the Shannon-Weiner Diversity Index of
benthic community health was used for estuaries in the
Acadian Province (see Chapter 1, Benthic Index)
The final estuarine index, the fish tissue contami-
nants index, is rated good for Peconic Estuary, the
Delaware Inland Bays, and the Maryland Coastal Bays;
good to fair for the New Hampshire Estuaries; fair for
the Massachusetts Bays and Barnegat Bay; and poor for
Buzzards Bay, Narragansett Bay, Long Island Sound,
New York/New Jersey Harbor, and Delaware Estuary.
NCA data were unavailable to evaluate fish tissue
contaminant levels in Casco Bay.
The overall condition score for the collective NEP
estuaries of the Northeast Coast region (1.5) was lower
than the overall condition scores for the collective NEP
estuaries of the Southeast Coast (4.0), Gulf Coast
(2.75), or West Coast (2.5) regions and comparable to
the score for Puerto Rico (1.5). This low overall condi-
tion score is not unexpected because many Northeast
Coast NEP estuaries were designated to the program
because of their societal importance to the nation as
major centers of commerce and international trade and
as commercial or recreational fishery areas since the
1700s. In addition, the counties surrounding the
Northeast Coast NEP estuaries have some of the
highest population densities in the country.
Population pressures, measured as population density
(number of persons/mi2), correlated fairly well with the
overall condition scores for the individual Northeast
Coast NEP estuaries. For example, the study areas of
the New York/New Jersey Harbor and Long Island
Sound had the highest population densities of 3,097
and 2,170 persons/mi2, respectively, and are both rated
poor for overall condition, receiving the lowest overall
condition scores of 1.0 and 1.5, respectively. The three
Northeast Coast NEP study areas with the lowest
population densities— Maryland Coastal Bays (98
persons/mi2), Casco Bay (138 persons/mi2), and the
New Hampshire Estuaries (216 persons/mi2)— are
rated fair (3.5), good (5.0), and fair (3.5) for overall
condition, respectively. However, Peconic Estuary, with
a moderately high population density (1,558
persons/mi2), had one of the highest overall condition
scores (4.3, rated good) for the Northeast Coast NEPs,
although sediment quality was not evaluated for this
estuary.
Slater Mill Pawtucket, Rl, is considered the birthplace of the
American industrial revolution (NBEP).
National Estuary Program Coastal Condition Report 53
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Casco Bay Estuary Partnership
Casco Bay Estuary Partnership
PARTNERSHIP
www.cascobay.usm.maine.edu
Background
The watershed of Casco Bay contains only 3% of
Maine's land mass, but about a quarter of the state's
population. This NEP study area encompasses 41
municipalities and extends over a 985 mi2 area. The
Bay itself has 578 miles of shoreline, including 758
islands (CBEP, 2000). Three major rivers—the Royal,
Presumpscot, and Fore— flow into the Bay. Casco Bay
has relatively low water temperatures and high flushing
rates, compared to some other estuaries of the
Northeast Coast region (Pearce et al., 1996). A 1994
Portland
Atfontic Ocean
Fore River
study estimated the annual value of Casco Bay's fishing
industry at $120 million, with tourism and recreation
around the Bay generating another $250 million each
year (CBEP, 2000).
Starting in 1990, a diverse coalition began to shape a
plan for Casco Bay's future as part of EPA's NEP. The
Casco Bay Plan (CBEP, 1996) now fuels collaborative
projects around the watershed involving municipal and
state officials, community groups, businesses, and
citizens. The Casco Bay Estuary Partnership (CBEP;
formerly the Casco Bay Estuary Project) coordinates
these efforts. Since the plan was adopted, area residents
54 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Cosco Bay Estuary Partnership
and groups have taken measures to protect wildlife
habitat, improve water quality, reduce pollution from
stormwater runoff and combined sewer overflows
(CSOs), reduce toxic pollution, and protect and restore
clam flats and swimming areas.
Environmental Concerns
Although Casco Bay's waters may appear relatively
pristine to the casual observer, toxic pollution in the
Bay is a concern. Casco Bay still contains toxics from
industries that operated more than a century ago,
contaminating sediments, fish, shellfish, and wildlife
(CBEP, 1994). Volunteer water quality monitoring has
taken place since 1993, and data show that the Bay's
water quality is generally good, although cause for
concern remains in certain areas. Low dissolved oxygen
has been identified in a few areas, and the CBEP is
conducting further studies to determine the nature and
causes of these hypoxic events.
Population Pressures
The population of the 5 NOAA-designated coastal
counties (Androscoggin, Cumberland, Oxford,
Sagadahoc, and York) coincident with the CBEP study
area increased by about 48% during a 40-year period,
from 0.44 million people in 1960 to 0.65 million
people in 2000 (Figure 3-10) (U.S. Census Bureau,
1991; 2001). This rate of population growth for the
CBEP study area is higher than the population growth
0.7
-^ 0.6
(A
| 0.5
1
c
o
0.4
0.3
£ 0.2
a
o.i
o.o
I960
2000
Figure 3-10. Population of NOAA-designated coastal counties
of the CBEP study area, 1960-2000 (U.S. Census Bureau, 1991;
2001).
rate of 24% for the collective NEP-coincident coastal
counties of the Northeast Coast region. In 2000, the
population density of the CBEP's 5 NEP-coincident
coastal counties was 138 persons/mi2, dramatically
lower than the population density of 1,055 persons/mi2
for the collective NEP-coincident coastal counties of the
Northeast Coast region (U.S. Census Bureau, 2001).
The CBEP-coincident coastal counties had the second-
lowest population density of any of the Northeast Coast
NEP estuaries (only the coastal counties coincident with
the Maryland Coastal Bays Program were lower at 98
persons/mi2).
NCA Indices of Estuarine
Condition—Casco Bay
The overall condition of Casco Bay is rated good
based on three of the four indices of estuarine condition
used by the NCA (Figure 3-11). All three indices (water
quality index, sediment quality index, and benthic
index) are rated good for Casco Bay. No data were
available to calculate a fish tissue contaminants index
for this estuary. Figure 3-12 provides a summary of the
percentage of estuarine area rated good, fair, poor, or
missing for each parameter considered. This assessment
is based on data from 30 NCA sites sampled in the
CBEP estuarine area in 2000 and 2001. Please refer to
Tables 1-24, 1-25, and 1-26 (Chapter 1) for a summary
of the criteria used to develop the rating for each index
and component indicator.
Overall Condition
Casco Bay (5.0)
Water Quality Index (5)
Sediment Quality Index (5)
Benthic Index (5)
Fish Tissue Contaminants
Index (missing)
Figure 3-11. The
overall condition of
the CBEP estuarine
area is good (U.S.
EPA/NCA).
National Estuary Program Coastal Condition Report 55
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Casco Bay Estuary Partnership
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Estuarine Area
Missing
Figure 3-12. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Casco Bay
(U.S. EPA/NCA).
Water Quality Index
Based on data from the NCA survey, the water
quality index for Casco Bay is rated good (Figure 3-13).
This index was developed using NCA data on five
component indicators: DIN, DIP, chlorophyll a, water
clarity, and dissolved oxygen. Casco Bay has one of the
best ratings for water quality among the Northeast
Coast NEP estuaries. DIN and chlorophyll a concentra-
tions were uniformly low, less than 0.1 mg/L and
5 ug/L, respectively, and DIP concentrations were less
than 0.01 mg/L in all areas of Casco Bay. Water clarity
was satisfactory everywhere in the Bay, and there were
no incidences of depleted dissolved oxygen.
Dissolved Nitrogen and Phosphorus I Casco
Bay is rated good for both DIN and DIP concentra-
tions. Eighty-seven percent of the estuarine area was
rated good for DIN concentrations, and 6% of the area
was rated fair. No area of Casco Bay was rated poor for
DIN concentrations. Fifty-four percent of the Bay's
estuarine area was rated good for DIP concentrations,
and no area of Casco Bay was rated poor for this
component indicator. NCA data on DIN and DIP
concentrations were unavailable for 7% of the CBEP
estuarine area.
Water Quality Index - Casco Bay
Site Criteria: Number of component
indicators in poor or fair condition
• Good = No more than I is fair
O Fair = I is poor, or 2 or more are fair
• Poor = 2 or more are poor
O Missing
82%
Figure 3-13. Water quality index data for Casco
(U.S. EPA/NCA).
56 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Casco Bay Estuary Partnership
Chlorophyll a Casco Bay is rated good for chloro-
phyll a concentrations. Eighty-six percent of the estu-
arine area was rated good for this component indicator,
4% was rated fair, and none of the area had poor
chlorophyll a concentrations. NCA data on chlorophyll
a concentrations were unavailable for 10% of the CBEP
estuarine area.
Water Clarity The water clarity rating for Casco
Bay is good. Water clarity was rated poor at a sampling
site if light penetration at 1 meter was less than 10% of
surface illumination. None of the estuarine area was
rated poor or fair for water clarity, and 88% of the area
was rated good. NCA data on water clarity were
unavailable for 12% of the CBEP estuarine area.
Dissolved Oxygen I Casco Bay is rated good for
dissolved oxygen concentrations, with 93% of the Bay's
estuarine area rated good for this component indicator.
No area of Casco Bay was rated poor for dissolved
oxygen concentrations, and NCA data on this compo-
nent indicator were unavailable for 7% of the CBEP
estuarine area.
Sediment Quality Index
The sediment quality index for Casco Bay is rated
good, with about 3% of the estuarine area rated poor
for sediment quality and 39% rated fair (Figure 3-14).
This index was developed using NCA data on three
component indicators: sediment toxicity, sediment
contaminants, and sediment TOC. The Casco Bay sites
classified as impaired showed both a moderate degree of
sediment contamination by metals or PCBs and
moderate levels of TOC.
Sediment Toxicity I Casco Bay is rated good for
sediment toxicity. No area of Casco Bay had sediments
that were toxic to amphipods, although NCA data on
sediment toxicity were unavailable for 14% of the
CBEP estuarine area.
Sediment Quality Index - Casco Bay
Site Criteria: Number and condition of component indicators
• Good = None are poor, and sediment contaminants is good
OFair = None are poor, and sediment contaminants is fair
• Poor = I or more are poor
O Missing
I
Fair
39%
Figure 3-14. Sediment quality index data for Casco Bay
(U.S. EPA/NCA).
Sediment Contaminants I The sediment conta-
minants rating for Casco Bay is good. Approximately
3% of the estuarine area was rated poor for sediment
contaminant concentrations, and 39% of the CBEP
estuarine area was rated fair.
Total Organic Carbon \ Casco Bay is rated good
for sediment TOC, with 36% of the estuarine area
rated good for TOC concentrations and 50% of the
area was rated fair. No area of Casco Bay was rated poor
for TOC.
National Estuary Program Coastal Condition Report 57
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Cosco Boy Estuary Partnership
&
Benthic Index
Casco Bay Estuary Partnership
Only 8% (five sites) of the estuatine area of Casco
Bay had unsatisfactory benthic condition, as measured
by the Shannon-Weiner Diversity Index (Figure 3-15);
therefore, Casco Bay is rated good for benthic condi-
tion. Seventy-eight percent of the area was rated good
for benthic condition, indicating that Casco Bay exhib-
ited a relatively high degree of species diversity for the
Northeast Coast region. Most NCA sites that received a
poor rating for benthic condition were also moderately
contaminated with pollutants and exhibited moderate
TOC levels.
Fish Tissue Contaminants Index
No fish were collected as part of the NCA surveys in
2000 and 2001; therefore, a fish tissue contaminants
index for Casco Bay was not developed for this report.
Benthic Index - Casco Bay
Site Criteria:
Shannon-Weiner Diversity Index Score
• Good = > 0.63
• Poor = s 0.63
O Missing
Good
78%
Figure 3-15. Benthic index data for Casco Bay (U.S. EPA/NCA).
Water and Sediment Quality
The group Friends of Casco Bay, with support from
the CBEP, has monitored surface waters at 106 sites
throughout the Bay since 1993. Through Friends of
Casco Bay, 300 trained volunteers have tested water
samples annually from April through October for water
temperature, dissolved oxygen, pH, salinity, and water
clarity. This sampling effort represents the only long-
term collection of Casco Bay water quality data,
providing an invaluable resource for municipal and state
planners, as well as local conservation and shellfish
commissions (CBEP, 2000). The results of this
sampling indicate that the water quality in Casco Bay is
good; however, low dissolved oxygen levels are a
concern in some areas. These areas include locations
with restricted circulation or with potentially heavy
nutrient loadings from point or non-point sources
(CBEP, 2005). Test results help communities around
the Bay clean up existing pollution sources and prevent
future contamination from occurring. Consistent use of
water quality tests can also help address environmental
concerns, such as red tide outbreaks and elevated bacte-
rial counts, which can cause area closures for swimming,
fishing, and shellfish harvesting.
The CBEP has also studied chemical contamination
in the surface sediments of Casco Bay, including heavy
metals, PCBs, pesticides, tributyltin (TBT), dioxins and
furans, and PAHs. In general, some toxic pollutants
were found in Bay sediments far from waterborne
sources, suggesting deposition from the air as dry parti-
cles or in rain and snow. Elevated heavy metal concen-
trations were most commonly found near Portland,
ME. PCBs were found in Fore River sediments, and
TBT levels were highest near boating centers. Dioxins
and furans were measured in low levels throughout the
Bay, with the highest concentrations detected in sedi-
ments near the Presumpscot River. PAHs were the most
prevalent contaminant in Casco Bay sediments and
often occurred at high concentrations when compared
to PAH levels in sediments from other bays around the
United States (CBEP, 2000).
58 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Ccrsco Bay Estuary Partnership
Habitat Quality
Casco Bay hosts a variety of habitats, including salt
marshes, eelgrass beds, tidal creeks, islands, rocky
shores, and estuarine waters. The most prevalent habitat
in the study area is intertidal mudflats. In 1995, up to
one-third of the Bay's wildlife habitat was endangered
by human development; however, it appeared that few
of the highest-value habitats faced imminent threats
(CBEP, 2000). As a response, the CBEP began tracking
the acreage of protected lands in the Bay area. Since
1997, the acres of protected land in the Casco Bay
watershed have increased by almost 50%. These
protected lands provide habitat for a variety of birds,
fish, and other wildlife. For example, Flag Island is a
protected 41-acre island in Casco Bay and provides
habitat to more than 600 nesting pairs of common
eiders (CBEP, 2005).
The CBEP also tracks the number of acres in large
tracks of undeveloped, natural land located within the
study area as an indicator of habitat quality. This indi-
cator provides insight into the degree of habitat frag-
mentation in the Bay area. Larger habitat blocks are
more likely to support healthy, genetically diverse
wildlife populations and are especially important to
such animals as the bobcat, Northern goshawk, or wood
thrush, which require larger areas of uninterrupted
habitat. Overall, large tracts of unfragmented, natural
lands do exist in the CBEP study area, although they
are growing increasingly scarce due to development.
Most of these tracts are located in the upper watershed;
however, substantial tracts do exist in more developed
areas (CBEP, 2005).
Eelgrass, a type of seagrass, is an important habitat
for fish, shellfish, and waterfowl. Casco Bay has the
largest and densest concentration of eelgrass beds
mapped along the coast of Maine (CBEP, 2000). The
extent of eelgrass in Casco Bay has increased in recent
years, with the overall acreage of eelgrass in the Bay
increasing from 7,056 to 8,248 acres between 1993 and
2001; however, several areas have experienced substan-
tial local losses in eelgrass coverage during this time
period (CBEP, 2005).
Living Resources
Casco Bay is home to a variety of waterbirds,
including common eiders, gulls, and great blue herons.
In addition, the Bay contains 50 seabird-nesting islands
and 6 heron nurseries (CBEP, 2000). The CBEP tracks
the number of waterbirds in Casco Bay as an environ-
mental quality indicator to assess environmental
impacts on the birds. In 2000, the Maine Department
of Inland Fisheries and Wildlife, FWS, and CBEP
worked together to conduct a series of waterbird surveys
in the Bay. The data collected from this survey series
will provide the baseline for future waterbird population
evaluations of Casco Bay (CBEP, 2005).
The CBEP has studied contamination levels in the
tissues of blue mussels and lobsters, and the Maine
Department of Environmental Protection (DEP) and
the Gulf of Maine Program also sample mussels at
additional sites in Casco Bay. Through this long-term
testing, the CBEP can assess whether toxic contaminant
levels in the Bay are increasing or decreasing. Shellfish
are filter feeders and concentrate pollutants from the
water. By testing the tissues of mussels and lobsters for
chemical contaminants, scientists can evaluate the
presence of toxics that may affect human health.
The CBEP has monitored mussels at eight locations
and lobsters at two sites and found that the contami-
nant levels in mussel tissues from some locations
exceeded the state level for posting health advisories
(based on eating shellfish once a week). Elevated levels
of the contaminants lead, PAHs, PCBs, dioxins, and
furans were detected in some mussels, and further tests
are being performed to confirm these results (CBEP,
2000).
National Estuary Program Coastal Condition Report 59
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Casco Bay Estuary Partnership
Trends in Toxic Chemicals in Casco
Bay Sediments
The presence of toxic chemicals in the sediments of
Casco Bay serves as an indicator of overall contamina-
tion of the Bay's marine ecosystem. When toxic chemi-
cals are introduced to the Bay from rivers, stormwater
runoff, point-source discharges, and atmospheric depo-
sition, many do not readily degrade or disperse. Instead,
these chemicals adsorb to sediment particles and settle
to the bottom of the Bay, where they may persist for a
long time. Even when clean sediments are deposited on
top of contaminated sediments, dredging and biological
activity can bring the contaminants back to die surface.
Bottom-dwelling (benthic) animals play an impor-
tant role in the food chain, recycling organic matter and
serving as a food source for groundfish (e.g., flounder,
cod, and haddock), lobsters, and crabs. These benthic
organisms can suffer adverse effects from their exposure
to and ingestion of contaminated sediments and, as
prey of groundfish, may provide a conduit for intro-
ducing diese contaminants into the food chain. Fish
and large crustaceans that feed on contaminated benthic
organisms may experience inhibited growth and repro-
duction, disease vulnerability, and even death. As the
contaminants move up the food chain, humans who eat
seafood contaminated by toxic chemicals can also be at
risk. For example, the presence of dioxins in Casco
Bay—largely a byproduct of pulp and paper mills—has
resulted in elevated dioxin concentrations in the liver
(tomalley) of lobsters. A public health advisory against
eating lobster tomalley has been in effect in Maine since
1992 (Maine DEP, 2004). The Maine Department of
Health and Human Services has also issued guidelines
for the consumption of saltwater fish contaminated by
mercury and organic chemicals, such as PCBs.
When scientists first studied the sediments of Casco
Bay in 1980, they were surprised to find a wide array of
toxic contaminants, including heavy metals and organic
chemicals. In 1991, die CBEP commissioned a baseline
study to assess sediment contamination levels at 65 sites
in the Bay using state-of-the art analytical methods.
Sampling sites were selected based on depth, circulation,
sediment type, and historical contaminants data, such as
the locations of industrial facilities and other point-
source discharges. Samples were analyzed for heavy
metals, PAHs, PCBs, and pesticides (Kennicutt et al.,
1992). In 1994, sediments from 28 of the original study
sites and 5 new sites were analyzed for butyltins,
dioxins/furans, and coplanar PCBs (Wade et al., 1995).
In 2000 and 2001, in partnership with EPA's NCA
survey, the CBEP resampled the sediments at the orig-
inal sampling locations. Scientists from Texas A&M
University compared the results of the 1991-1994
sampling to the 2000-2001 studies and concluded that
most toxic chemical concentrations have decreased or
remained the same over time, indicating that pollution-
control strategies are working in Casco Bay (see table).
In some heavily polluted areas, such as the flats of the Fore
River (near Portland, ME), mollusks, small crustaceans, and
other expected benthic species were absent in a 1989 sampling.
Some of the hardy worms that were found had oil on their
"feet" (parapodia), probably from petroleum-related contami-
nants (Personal communication, Doggett, 200.5).
60 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Cosco Bay Estuary Partnership
Changes in Chemical Concentrations in Sediments from the 1991-1994 to
2000-2001 Sampling Efforts in Casco Bay (Wade and Sweet, 2005)
Increased
Silver
High molecular-weight PAHs
No Overall Change
Arsenic
Copper
Lead
Zinc
Planar PCB 77
PAHs2
Dioxins/furans
Decreased
Cadmium
Chromium
Mercury
Nickel
Selenium
Total pesticides
4,4-DDE
4-4-DDD
Total DDTs
TBT1 and butyltin
Total PCBs
Planar PCB 126
Low molecular-weight PAHs
' The overall decline of TBT concentrations in the Bay's sediments reflects the effectiveness of federal and
Maine laws that now ban the use of paints with TBT for all uses except for vessels longer than 25 meters
or those having aluminum hulls (Maine DEP, 1999). The continued use of TBT paints on large commercial
vessels may explain the presence of elevated concentrations of TBT in the sediments of Inner Bay sites.
2Overall, the total concentration of PAHs in Casco Bay sediments has remained unchanged. This suggests
that increased use of fossil fuels is balanced by environmental controls that lower the PAH inputs to the
Bay (Wade and Sweet, 2005).
The Texas A&M University comparison examined
the concentrations of a variety of contaminants in sedi-
ments, including metals, PAHs, PCBs, and pesticides.
Heavy metal concentrations in Casco Bay are lower than
levels known to cause harmful effects to organisms. Even
the elevated concentrations of metals seen in Casco Bay
are lower than concentrations found in the highly con-
taminated sediments of urban areas, such as Long Island
Sound and Boston Harbor. Although concentrations are
highly elevated above natural background levels, the
PAH concentrations seen in the sediments of the inner
part of Casco Bay ranged between the ERL and ERM
concentrations (Long et al.,1995). The majority of
PAHs detected in the Bay are high molecular-weight,
combustion-related PAHs that sequester in fine parti-
cles, which may reduce their toxicity. PCB concentra-
tions at almost all Casco Bay sites were below the toxic
response threshold, and concentrations of pesticides
were low compared to concentrations considered toxic.
Butyltins, dioxins/furans, and planar PCBs were not
present at toxic concentrations, and in general, the
highest concentrations of toxic chemicals were found
near known sources. For example, elevated butyltin
concentrations (a constituent of marine anti-fouling
paints) were found near boat anchorages and marinas,
whereas dioxins and furans were found in elevated
concentrations downstream of pulp and paper mills
(Wade and Sweet, 2005).
National Estuary Program Coastal Condition Report 61
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Casco Bay Estuary Partnership
Environmental Stressors
The CBEP uses a variety of human indicators to
assess the environmental quality of Casco Bay, including
the volume and frequency of CSOs, population
changes, the amount of impervious cover in the water-
shed, and the amount of air pollution near the Bay.
Annually, CSOs contribute millions of gallons of
polluted water to Casco Bay; however, the volume and
frequency of these overflows have decreased since 1996
(CBEP, 2005).
The human population in the Casco Bay watershed
is expected to increase by 6% between 2005 and 2015.
The CBEP uses population growth as an indicator of
environmental stress because of the impact that related
activities, such as transportation or housing construc-
tion, have on the Bay's ecosystem. For example, vehicle
registrations in Cumberland County increased from
about 215,000 to more than 283,000 between 1998
and 2003. Such an increase in the number of vehicles
can contribute to urban sprawl patterns and increased
impervious surface area (CBEP, 2005). The amount of
impervious surfaces in a watershed is important because
high levels of these surfaces can reduce groundwater
recharge and increase flooding, erosion, and stream
channel alteration. Impervious surface coverage can also
be used as an indicator of stream degradation. Recent
studies suggest that, when impervious surface coverage
exceeds 6% to 10% of the watershed, the ability of
Maine's streams to support aquatic ecological communi-
ties becomes degraded. Approximately 5.9% of the
entire Casco Bay watershed is composed of impervious
surfaces. It should be noted that this percentage was
calculated for a large area and is not directly applicable
to the 6% to 10% threshold calculated for very small
watersheds (CBEP, 2005).
With grant funding from EPA and the Maine DEP,
the CBEP established a coastal air monitoring site at
Wolfe's Neck in Freeport, ME. Data from this site,
along with results collected by the Maine DEP at an
inland site in Bridgton, are helping these agencies deter-
mine patterns of air pollution in the watershed. The
monitoring program has tracked the deposition of
PAHs; mercury, cadmium, and other trace metals; and
nitrogen, as well as the concentration of fine particu-
lates. Data from this program and from the National
Atmospheric Deposition Program suggest that the
atmosphere is a significant source of pollution for Casco
Bay. Rainfall sampled in Freeport, ME, contained PAHs
at concentrations equal to an urban air monitoring site
near Boston. These elevated levels were more common
Tern on Outer Green Island, ME (Matthew Craig).
62 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Cosco Bay Estuary Partnership
in samples collected during the wetter seasons of spring
and summer; however, the dry deposition of PAHs was
much lower in samples from Freeport than from the
urban site, suggesting that dry deposition is related to
local sources (Golumb et al., 2001). The atmosphere is
the dominant source of both nitrogen and mercury to
the Bay (Figure 3-16) (Ryan et al., 2003).
Current Projects,
Accomplishments, and
Future Goals
Since 1990, the CBEP has had numerous accom-
plishments, including the following recent accomplish-
ments:
• Initiated a coordinated habitat-restoration effort
and catalyzed on-the-ground projects through
seed funding, grant-writing, and technical support
• Facilitated a 14-municipality interlocal collabora-
tion (Interlocal Stormwater Working Group) on
the management of stormwater
• Facilitated the reopening of more than 300 acres
of clam flats to harvesting
• Helped protect more than 3,000 acres of high-
value habitat through conservation
• Presented experts on marine invasive species and
stormwater management in cold climates during
local and regional conferences.
• Compiled and analyzed available data on 14 indi-
cators of the health of Casco Bay to publish the
report State of the Bay 2005, which was released at
the State of the Bay 2005 conference on
November 3, 2005 (CBEP, 2005).
Conclusion
Casco Bay's overall condition appears to be rated
good based on three of the NCA indices of estuarine
condition and on assessment work done by the CBEP;
however, some concerns have been identified as a result
of monitoring work conducted during the 1990s and
into the 21st century. Toxic pollution, thought to origi-
nate from legacy sources and atmospheric deposition, is
a primary concern for stakeholders. In addition, rela-
tively localized hypoxic conditions are being carefully
studied, and other concerns, such as red tide outbreaks,
algal blooms, and elevated bacterial counts, are also
being monitored.
o
<
160
140
120
100
80
60-
40-
20-
Wastewater treatment plants
Dry deposition
Wet deposition
Low - Surface High - Surface Low-Watershed High-Watershed
Figure 3-16. Atmospheric deposition (wet and dry) may account for 84% to 92% of the
overall mercury loading to Casco Bay. The overall contribution of dry deposition to the
total mercury loading on the surface of Casco Bay and on the Casco Bay watershed is
estimated, and the high and low ranges of this estimate are presented on the graph
(Ryan et al., 2003).
National Estuary Program Coastal Condition Report 63
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New Hampshire Estuaries Project
New Hampshire Estuaries Project
Estuaries
www.nhep.unh.edu
At/antic Ocean
Seabrook Estuary
Background
New Hampshire has more than 230 miles of sensi-
tive tidal shoreline, in addition to 18 miles of open-
ocean coastline on the Gulf of Maine (NHEP, 2003).
The Great Bay and Hampton-Seabrook estuaries are the
largest distinct estuaries in New Hampshire. Other estu-
aries of importance are Little Bay, Little Harbor, and
Rye Harbor, as well as portions of their tidal tributaries
(NHEP, 2005).
The Great Bay Estuary covers 17 mi2, with nearly
150 miles of tidal shoreline (NHEP, 2003). Great Bay is
unusual because it is located inland, more than five
miles up the Piscataqua River from the ocean. Due to
this location, Great Bay's tidal exchange with the ocean
is slow, requiring up to 18 days (or 36 tide cycles) for
water entering the head of the Bay to move to the ocean
(Jones, 2000). Oysters, clams, striped bass, bluefish,
herring, smelt, lobsters, and eels are harvested from
Great Bay for both recreational and commercial
purposes. In addition, Great Bay is New Hampshire's
principal waterfowl overwintering site and a focus area
for the North American Waterfowl Management Plan
(NHEP, 2005).
64 National Estuary Program Coastal Condition Report
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CHAPTER 3 ! NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New Hampshire Estuaries Project
Hampton-Seabrook Harbor encompasses 480 acres
of open water at high tide. This coastal estuary is char-
acterized by extensive salt marshes and is separated from
the ocean by a series of barrier beaches. The Harbor is
surrounded by a 5,000-acre salt marsh, which is the
largest contiguous salt marsh in the state, and Hampton
Beach is one of the busiest tourist attractions in New
Hampshire (NHEP, 2003). Several thousand residents
purchase shellfish licenses each year, primarily to dig
softshell or steamer clams locally.
Environmental Concerns
After a long history of industrial and sewage pollu-
tion, water quality in the New Hampshire Estuaries has
shown significant improvements during the past two
decades (Jones, 2000); however, bacterial and nutrient
contamination, toxic contaminants, the loss or fragmen-
tation of wildlife habitat, degraded salt marshes, and
declines in oyster and clam populations continue to be
high-priority problems for water quality, habitat, fish,
and wildlife.
Population Pressures
The population of the 3 NOAA-designated coastal
counties (Carroll, Rockingham, and Strafford) coinci-
dent with the New Hampshire Estuaries Project (NHEP)
study area increased by more than 148% during a
40-year period, from 0.17 million people in 1960 to
almost 0.43 million people in 2000 (Figure 3-17) (U.S.
0.5
0.4
£ 0.3
O 0.2
9- O.I
0.0
I960 1970 1980 1990 2000
Year
Figure 3-17. Population of NOAA-designated coastal counties
of the NHEP study area, 1960-2000 (U.S. Census Bureau, 1991;
2001).
Census Bureau, 1991; 2001). This rate of population
growth for the NHEP study area is almost 6 times the
population growth rate of 24% for the collective NEP-
coincident coastal counties of the Northeast Coast
region. In 2000, the population density of these 3 NEP-
coincident coastal counties was 216 persons/mi2, almost
5 times lower than the population density of 1,055
persons/mi2 for the collective NEP-coincident coastal
counties of the Northeast Coast region (U.S. Census
Bureau, 2001).
NCA Indices of Estuarine
Condition—New Hampshire
Estuaries
The overall condition of the New Hampshire
Estuaries is rated fair based on the four indices of estu-
arine condition used by the NCA (Figure 3-18). Two of
the assessed indices (sediment quality and fish tissue
contaminants) received good to fair ratings for the New
Hampshire Estuaries, whereas the other two indices
(water quality and benthic) received fair ratings. Figure
3-19 provides a summary of the percentage of estuarine
area rated good, fair, poor, or missing for each para-
meter considered. This assessment is based on data from
76 NCA sites sampled in the NHEP estuarine area in
2000 and 2001. Please refer to Tables 1-24, 1-25, and
1-26 (Chapter 1) for a summary of the criteria used to
develop the rating for each index and component
indicator.
I
Overall Condition
New Hampshire Estuaries
(3.5)
Water Quality Index (3)
Sediment Quality Index (4)
Benthic Index (3)
Fish Tissue Contaminants
Index (4)
Figure 3-18. The
overall condition of the
NHEP estuarine area is fair
(U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 65
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New Hampshire Estuaries Project
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Estuarine Area
I I I Missing
Figure 3-19. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — New Hampshire
Estuaries (U.S. EPA/NCA).
Water Quality Index
Based on data collected by the NCA surveys, the
water quality index for the New Hampshire Estuaries is
rated fair. This index was developed using NCA data on
five component indicators: DIN, DIP, chlorophyll a,
water clarity, and dissolved oxygen. About half of the
estuarine area of the New Hampshire Estuaries was
rated fair for water quality, and less than 1 % was rated
poor (Figure 3-20). Nutrient concentrations were
moderately high, particularly for DIP, and 16% of the
estuarine area had moderate chlorophyll a concentra-
tions, primarily in the tributaries. The water quality
condition of the New Hampshire Estuaries was rela-
tively poor as compared to other NEPs in the Acadian
Province, from Massachusetts to Maine. The larger of
the New Hampshire Estuaries, the Great Bay and
Piscataqua Pviver system, formed as a drowned river
valley and therefore displays different characteristics
from other, more oceanic-influenced systems in the
Acadian Province. There were no indications of
dissolved oxygen depletion or poor water clarity in the
New Hampshire Estuaries during the NCA assessment
period (2000-2001).
Dissolved Nitrogen and Phosphorus I The
New Hampshire Estuaries are rated good for DIN
concentrations because 52% of the estuarine area was
rated good and 46% of the area was rated fair for this
component indicator. None of the NHEP estuarine area
was rated poor for DIN concentrations. The Estuaries
are rated fair for DIP concentrations, with 7% of the
estuarine area rated good, 88% of the area rated fair,
and 3% of the area rated poor for this component
indicator.
Water Quality Index - New Hampshire Estuaries
J_
Site Criteria; Number of component
indicators in poor or fair condition
• Good = No more than I is fair
OFair = I is poor, or 2 or more are fair
• Poor = 2 or more are poor
O Missing
Missing p0or
Fair
54%
Figure 3-20. Water quality index data for the New Hampshire
Estuaries, 2000-2001 (U.S. EPA/NCA).
66 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New Hampshire Estuaries Project
Chlorophyll a I The New Hampshire Estuaries are
rated good for chlorophyll a concentrations. Of the
estuarine area assessed, 77% and 16% was rated good
and fair, respectively, and none of the area was rated
poor. NCA data on chlorophyll a concentrations were
unavailable for 7% of the NHEP estuarine area.
Water Clarity Water clarity in the New
Hampshire Estuaries is rated good. None of the estu-
arine area was rated poor for water clarity, and 74% of
the area was rated good; however, NCA data on water
clarity were unavailable for 26% of the NHEP estuarine
area.
Dissolved Oxygen I The New Hampshire Estuaries
are rated good for dissolved oxygen concentrations.
Ninety-eight percent of the estuarine area was rated
good for dissolved oxygen concentrations, and none of
the area was rated poor. NCA data on dissolved oxygen
concentrations were unavailable for 2% of the NHEP
estuarine area.
Sediment Quality Index
The sediment quality index for the New Hampshire
Estuaries is rated good to fair, with 7% of the estuarine
area rated poor, 27% rated fair, and 56% rated good for
sediment quality (Figure 3-21). This index was devel-
oped using NCA data on three component indicators:
sediment toxicity, sediment contaminants, and sediment
TOC. One site in Portsmouth Harbor proved to be
toxic to amphipods; however, sediments were sandy at
this site, which may have contributed to the low
amphipod survival. Most of the survey sites character-
ized as impaired had sediments with moderate to high
concentrations of metals, PAHs, and DDT, and nearly
all of the contaminated sites also had moderate levels of
TOC.
Sediment Toxicity I The New Hampshire
Estuaries are rated good for sediment toxicity, with only
3% of the estuarine area rated poor for this component
indicator. NCA data on sediment toxicity were unavail-
able for 10% of the NHEP estuarine area.
Sediment Quality Index - New Hampshire Estuaries
Site Criteria: Number and condition of
component indicators
»Good = None are poor, and sediment
contaminants is good
O Fair = None are poor, and sediment
contaminants is fair
• Poor = lor more are poor
O Missing
Missing Poor
10% 7%
Fair
i 27%
I
Figure 3-21. Sediment quality index data for the New
Hampshire Estuaries, 2000-2001 (U.S. EPA/NCA).
Sediment Contaminants The New Hampshire
Estuaries are rated good for sediment contaminant
concentrations. Approximately 2% of the estuarine area
was rated poor for sediment contamination, and 32%
of the area was rated fair.
Total Organic Carbon I Another measure of
sediment quality is sediment TOC, and the New
Hampshire Estuaries are rated good for this component
indicator. Forty-eight percent of the estuarine area was
rated good for TOC concentrations, and 40% of the
area was rated fair. Only 1 % of the estuarine area was
rated poor, and NCA data on sediment TOC concen-
trations were unavailable for 11% of the NHEP
estuarine area.
National Estuary Program Coastal Condition Report 67
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New Hampshire Estuaries Project
Benthic Index
The benthic index for the New Hampshire Estuaries
is rated fair, with 16% of the estuarine area showing
poor benthic condition as measured by the Shannon-
Weiner Diversity Index (Figure 3-22). This rating indi-
cates a level of diversity comparable with other NEP
estuaries in the Northeast Coast region. Most of the
sites with a poor benthic index rating also had moderate
or high concentrations of sediment contaminants. In
addition, some of the low diversity sites occurred in
waters where salinity was relatively fresh (less than 20
ppt), which indicates a site where natural salinity fluctu-
ations could be a natural stressor, causing a reduction in
benthic species diversity.
Benthic Index - New Hampshire Estuaries
J_
Site Criteria:
Shannon-Weiner Diversity Index Score
• Good = > 0.63
• Poor = sO.63
O Missing
Missing Poor
10% 16%
Figure 3-22. Benthic index data for the New Hampshire
Estuaries, 2000-2001 (U.S. EPA/NCA).
Fish Tissue Contaminants Index
The fish tissue contaminants index lor the New
Hampshire Estuaries is rated good to fair (Figure 3-23).
Seventeen fish and six shellfish (e.g., lobster) samples
from the New Hampshire Estuaries were analyzed for
chemical contaminants. Twelve percent of the samples
had high concentrations of at least one toxicant and
were rated poor, and 63% had moderate levels of
contaminants and were rated fair.
Fish Tissue Contaminants Index - New Hampshire
Estuaries
_L
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
OFair = Falls within Guidance range
• Poor = Exceeds Guidance range
Figure 3-23. Fish tissue contaminants index data for the
New Hampshire Estuaries, 2000-2001 (U.S. EF'A/NCA).
68 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New Hampshire Estuaries Project
New Hampshire Estuaries
Project Indicators of Estuarine
Condition
The NHEP tracks the health of the New Hampshire
Estuaries through 34 environmental indicators that are
defined in the NHEP Monitoring Plan 2004, Version 4
(Townbridge, 2004). Every 3 years, the NHEP
produces a report that highlights results from the key
environmental indicators. The most recent report
(NHEP, 2003) was issued in 2003, coincident with a
State of the Estuaries conference. The 12 indicators
identified in the 2003 State of the Estuaries report are
summarized in the sections below. The full report and
conference proceedings are available at
http://www.nhep.unh.edu.
Some of the NHEP indicators are based on data
from the NCA's 2000—2001 probabilistic survey, which
were used for the EPA National Indicators of Estuary
Condition and will be included in the 2006 State of the
Estuaries report. The NHEP uses different standards or
analysis methods for some indicators than EPA; there-
fore, the NHEP's conclusions will differ from the EPA
report. For example, the NHEP evaluates sediment
quality using a triad approach with sediment toxicity,
sediment chemistry, and benthic community data,
whereas EPA calculates the sediment quality index using
data on sediment contaminants, sediment toxicity, and
TOG. The New Hampshire Department of Environ-
mental Services and the University of New Hampshire
(UNH) have analyzed the 2000-2001 NCA data to
calculate NHEP indicators and document other obser-
vations (NHDES, 2005).
Water and Sediment Quality
The NHEP reported on four indicators of water
quality: bacteria concentrations, toxic contaminants in
mussel tissue, nitrogen concentrations, and violations of
the dissolved oxygen standard. Overall, these four indi-
cators show that water and sediment quality in the New
Hampshire Estuaries is generally good; however, there is
concern about rising nitrogen concentrations.
Dry-weather fecal coliform contamination is used
as an indicator of sewage contamination in the New
Hampshire Estuaries. In the middle of Great Bay at
Adams Point, fecal coliform concentrations decreased
by 30% between 1992 and 2002 (Figure 3-24).
Stronger declining trends were found at the tributary
sampling sites, where decreases of 75% were observed
for the same period. Despite these improvements, many
shellfish bed closures still exist due to bacterial pollution
(NHEP, 2003).
Blue mussels (Mytilus edulis) are used as a water
quality indicator species for toxic contaminants from
polluted waters because these shellfish accumulate
contaminants in their tissues. Between 1993 and 2000,
none of the samples collected from the 13 mussel-
sampling sites in the New Hampshire Estuaries had
toxic contaminant levels greater than U.S. Food and
Drug Administration (FDA) guidelines. Levels of PCBs
and the pesticide DDT are declining at the Portsmouth
Harbor station, and PAH levels are increasing. The
decreasing PCB and DDT concentrations are probably
due to the decreased use of these chemicals following an
EPA ban enacted in 1979 and 1972, respectively. PAHs
are present as petroleum constituents and as residuals of
the combustion of petroleum products and other
organic compounds. Increased stormwater runoff from
impervious surfaces (e.g., parking lots) and fuel spills
into the Estuaries are two of many possible reasons for
the increasing PAH concentrations in blue mussel
tissues (NHEP, 2003).
Great Bay at Adams Point
10000.0 E
E 1000.0
o
o
L_
|
O
U
o
0)
100.0 r
Figure 3-24. Fecal coliform concentrations between 1988
and 2002 in Great Bay at Adams Point (NHER2003).
National Estuary Program Coastal Condition Report 69
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New Hampshire Estuaries Project
Mapping Impervious Surfaces in
New Hampshire's Coastal
Watershed
Stormwater runoff from pavement and other imper-
vious surfaces is a major factor that affects water quality
in the New Hampshire Estuaries. Shellfish beds are
often closed after rain storms due to bacteria that have
been washed into the Estuaries via impervious surfaces,
which are a marker for high-impact human develop-
ment in the watershed. To address this issue, the NHEP
set out to obtain a watershed-wide map of impervious
surfaces to better understand the extent of impervious
surface and the possible water quality impacts.
The NHEP contracted with the UNH Complex
Systems Research Center to generate maps of imper-
vious surfaces in 1990 and 2000 from satellite imagery
(Justice and Rubin, 2002). UNH used a subpixel
analysis routine on Landsat Thematic Mapper data,
coupled with ground-truthing surveys, to generate the
maps. The NHEP totaled the area of impervious
surfaces in each of the 42 coastal towns located within
the NHEP study area and calculated the percent of land
area covered by impervious surfaces. The map on the
next page shows the 42 coastal watershed towns and
their percent of imperviousness in 2000.
Eleven of the 42 towns had more than 10% of their
land area covered by impervious surfaces. Studies
conducted in other regions of the country have demon-
strated water quality deterioration where impervious
surfaces cover greater than 10% of the watershed area
(Schueller, 1995); therefore, it is the goal of the NHEP
to keep the coverage of impervious surfaces in the
coastal subwatersheds to less than 10% (Townbridge,
2003). However, additional factors, such as the
o.s
0.4
0.3
0.2
O.I
0.0
0.0
O.I
0.4
0.5
0.2 0.3
1990 (acres/person)
Comparison of imperviousness per capita in 1990 to 2000
(Townbridge, 2003).
proximity of the impervious surfaces to waterbodies and the
extent of buffer, may be more important: than percent
imperviousness.
The impervious surface data was also used to study the
pattern of "sprawl-type" development in the coastal water-
shed. A commonly accepted definition of sprawl is
increasing rates of land consumption per person. Using the
impervious surface data from 1990 and 2000, the NHEP
was able to show that all of the 42 towns used more imper-
vious surface per person in 2000 than in 1990 (the differ-
ence was statistically significant for 25 of the 42 towns). On
average, the acres of impervious surface lor each person in
the towns increased from 0.15 acres/person in 1990 to 0.20
acres/person in 2000 (Townbridge, 2003). The figure above
shows the general increase in imperviousness per capita for
each town in 1990 versus 2000. All of the towns are
plotted above the red line, which shows that impervious-
ness per capita is increasing in all the towns, even if the
change is not statistically significant.
70 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New Hampshire Estuaries Project
After the NHEP presented the impervious surface
data at the 2003 State of the Estuaries Conference,
many town officials requested detailed information for
their towns. As a result, the NHEP produced a
customized map of impervious surfaces and water
resources for each of the 42 towns. The towns also
received a fact sheet summarizing what is known about
the effects of impervious surfaces on water quality. The
NHEP distributed this information at a workshop for
conservation commissions and planning boards in
October 2004. The NHEP plans to update these
impervious surface maps in 2005 and again in 2010.
I
li. Tidal Waters
Town boundaries
Imperviousness in
HUC12 Watersheds
• 0-2.5%
• 2.5-5.0%
5.0-7.5%
7.5- 10.0%
10.0-15.0%
_J 15.0-20.0%
• 20.0-30.0%
V
Lower Cocheco River I
Lower Salmon Falls River I
Portsmouth Harbor I
"
Berrys Brook-Rye Harbor (
Hampton Harbor I
Taylor River-Hampton River I
Percent impervious surface in New Hampshire's coastal watershed in 2000
(NHEP, based on data from UNH Complex Systems Research Center).
National Estuary Program Coastal Condition Report 71
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New Hampshire Estuaries Project
Excessive nitrogen concentrations in estuaries can
cause blooms of algae that change the species composi-
tion of important habitats. Monthly measurements at
three long-term water quality monitoring sites have
documented changes in nitrogen (as nitrate+nitrite)
concentrations in the Great Bay between 1992 and
2001. Statistical tests have shown that nitrate+nitrite
concentrations have increased during this period at the
sites at Adams Point in Great Bay and in the Lamprey
River; however, there were no statistically significant
trends at the Squamscott River station. Despite the
increasing concentrations of nitrate+nitrite in the New
Hampshire Estuaries, there have not been any signifi-
cant trends observed in the typical indicators of
eutrophication (e.g., dissolved oxygen and chlorophyll a
concentrations); therefore, the load of nitrate+nitrite to
the Great Bay appears to have not yet reached the level
at which the undesirable effects of eutrophication occur.
The major sources of nutrient contamination to the
Estuaries are WWTP effluents, malfunctioning septic
systems, atmospheric deposition, and runoff from urban
and agricultural areas, which are all related to popula-
tion growth and the associated land development
patterns (NHEP, 2003).
Fish and many other aquatic organisms need
dissolved oxygen in the water to survive. The strong
tidal flushing through the Estuaries and inflow from
freshwater streams keeps the water well mixed and
oxygenated. Dissolved oxygen levels in Great Bay and
the Squamscott River consistently meet state standards.
Although the standard has also been met at the
Lamprey River sites 90% of the time, there have been a
few instances where the standard was not met. The
causes of these sporadic hypoxic events are not known.
Blooms of algae, respiration of benthic organisms, and
oxygen demand from WWTP effluent can deplete
oxygen in the water; however, in some cases, these low
concentrations may be a natural phenomenon (NHEP,
2003).
Habitat Quality
The NHEP tracks six indicators to determine habitat
quality: eelgrass abundance, unfragmented forest blocks,
salt marsh restoration, protected lands, impervious
surfaces, and sprawl-type growth. Only the first two of
these indicators are presented in this section. The other
four indicators are discussed in the Current Projects,
Accomplishments, and Future Goals section of this profile
and in the NHEP Highlight article.
Eelgrass (Zostera marina) is an essen rial part of the
Estuaries' ecology because it provides food for wintering
waterfowl and habitat for juvenile fish (Thayer et al.,
1984). The UNH Seagrass Ecology Group has mapped
the distribution of eelgrass in Great Bay every year from
1986 to 2001. Eelgrass cover in Great Bay has been
relatively constant for the past 10 years at approximately
2,000 acres. In 1989, there was a dramatic 85% decline
in eelgrass acreage to 300 acres; however, the eelgrass
beds made a rapid recovery the following year. Water
clarity and water depth are the main factors affecting
the presence of eelgrass, although eelgrass can also be
affected by other factors (e.g., disease) on a rapid
temporal scale (NHEP, 2003). For example, the
dramatic density decline in 1989 was caused by an
infestation of a slime mold, Labryrinthula zosterae,
commonly called "wasting disease" (Muehlstein et al.,
1991).
The fragmentation of open lands due to new roads
and sprawling patterns of development can have signifi-
cant consequences for habitat and hydrologic functions
within the coastal watershed. As of 2001, there were
282 unfragmented blocks greater than 250 acres in the
coastal watershed, the majority of which were less than
1,000 acres. In addition, there were only 4 blocks
greater than 5,000 acres, and only 10% of the
remaining blocks are protected from development
(NHEP, 2003).
Living Resources
The NHEP reported on two wildlife indicators—
oyster and clam populations—in the 2003 State of the
Estuaries report, citing both species as declining in the
New Hampshire Estuaries.
Oysters are economically important because they
support valuable recreational fisheries and have tremen-
dous potential as an aquaculture species. They are also
excellent bioindicators of estuarine condition because
they are relatively long lived, remain stationary, and
filter large volumes of estuarine water to feed.
Additionally, as filter feeders, oysters play an important
role in cycling nutrients, improving water clarity, and
removing significant quantities of nitrogen and
phosphorus from the water (NHEP, 2003). Since 1993,
the oyster harvest in Great Bay has suffered a serious
72 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New Hampshire Estuaries Project
decline (Figure 3-25). In 2002, the standing stock in
beds open for harvesting was 3,579 bushels, about 7%
of the goal of 50,000 bushels. Most of the remaining
standing stock is in the Adams Point, Nannie Island,
and Woodman Point beds in Great Bay. The major
cause of this decline is thought to be the protozoan
pathogens MSX and Dermo, which have caused similar
declines in oyster fisheries in Chesapeake Bay and other
mid-Atlantic estuaries (NHEP, 2003).
Soft shell clams are an economic, recreational,
cultural, and natural resource for the seacoast region.
Recreational shellfishing in Hampton-Seabrook Harbor
is estimated to contribute more than $3 million a year
to the local and state economies (Jones, 2000). Soft
shell clam densities in 2001 were well below the most
recent 10-year average (1990-1999) and were declining
in all three main clam flats. The 2001 densities at
Common Island and Middle Ground were also lower
than the long-term baseline densities recorded between
1974 and 1989. The source of the current decline in
harvestable clam populations is unknown (NHEP,
2003); however, an NHEP study in 2001-2002
concluded that predation of juvenile clams by green
crabs and strong currents in the harbor were potential
factors in the juvenile clam population decline (Beal,
2002). Other observers have expressed concern that
over-harvesting may also be contributing to the decline.
00
'5
_c
"S
-C
vt
£
o
01
-C
CO
Major Oyster Beds
D Adams Point
Nannie Island
• Oyster River
D Piscataqua River
Squamscott Rive
D Woodman Point
25,000
1992
2004
Figure 3-25. Standing stock of harvestable-size oysters in Great
Bay between 1992 and 2004 (NHER 2003).
Current Projects,
Accomplishments, and Future
Goals
The NHEP has been successful at implementing
many projects to protect and enhance die New
Hampshire Estuaries. Data from two environmental
indicators show that the NHEP has achieved on-the-
ground results for land conservation and salt marsh
restoration.
For the past 5 years, the NHEP has supported the
Great Bay Resource Protection Partnership to conserve
land in the coastal watershed. As of 2002, there were
42,585 acres of protected land in New Hampshire's
coastal watershed, which represented 8.4% of the entire
watershed land area (Figure 3-26). In coastal communi-
ties, 18,116 acres were protected lands in 2002, which
is 13.1% of the total area of these communities. In
order to reach the NHEP's goal of protecting 15% of
the watershed land area by 2010, an additional 33,827
acres need to be protected in the watershed, including
at least 2,685 acres in the 17 coastal communities
(NHEP, 2003).
80,000
I
Watershed
Coastal towns
Figure 3-26. Acres of protected lands in New Hampshire's
coastal watershed and coastal towns (NHER 2003).
National Estuary Program Coastal Condition Report 73
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CHAPTER 3 ' NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New Hampshire Estuaries Project
Filling, ditching, draining, and restricting tidal flow
degrades salt marshes, which can disrupt the marsh
ecology and can result in mosquito problems, flooding,
and reduced biological diversity. Restoration efforts seek
to remedy these problems by improving tidal hydrology
and reestablishing healthy marsh habitats. The NHEP
has a goal to restore 300 acres of tidal wetlands through
tidal restriction removal. Through the leadership of the
New Hampshire Coastal Program (NHCP), 176.5 acres
of salt marsh have been restored through tidal restric-
tion removal (59% of the goal) since January 2000. The
NHCP is currently planning another 129 acres of salt
marsh restoration by tidal restriction removal, which, if
completed, will surpass the NHEP goal (NHEP, 2003).
Conclusion
In the 2003 State of the Estuaries report, the NHEP
concluded that the New Hampshire Estuaries are in
generally good condition. During the past decade, water
quality has improved and land conservation efforts and
salt marsh restoration projects have been successful;
however, shellfish resources are declining in the
Estuaries, and development pressures are growing
throughout the watershed. In contrast, the overall
condition of the New Hampshire Estuaries is rated fair,
based on NCA data from 76 sites surveyed in
2000-2001.
Prescott Park and Fishermen's cooperative along the Piscataquog River in Portsmouth, NH (NHEP).
74 National Estuary Program Coastal Condition Report
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CHAPTER 3 ! NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Massachusetts Bays Program
Massachusetts Bays Program
tester
Massachusetts Bay
North Shore
www.mass.gov/envir/massbays
Background
The Massachusetts Bays cover more than 800 miles
of coastline, from the tip of Cape Cod Bay to the New
Hampshire border, and serve 50 coastal communities.
The Bays' NEP study area encompasses about 1,650
mi2 and is located at the southern end of the Gulf of
Maine, a large coastal sea characterized by relatively cool
water and large tidal ranges (MBP, 2004b). The Bays'
NEP study area includes Cape Cod Bay, Massachusetts
Bay, Boston Harbor, the Merrimack River, the North
and South shores, and the portion of Ipswich Bay in
Massachusetts. The watershed of the Massachusetts Bays
covers more than 7,000 mi , with the majority of fresh-
water that flows into the Bays coming from the Charles
and Merrimack rivers (Martin et al., 1996; MBP,
2004b).
Natural habitats in the Massachusetts Bays' water-
shed include freshwater and saltwater marshes, tidal
flats, barrier island beaches, eelgrass meadows, rocky
intertidal shores, and numerous small lakes and salt
ponds. Outside of Boston Harbor, the Massachusetts
Bays support a rich, healthy marine ecosystem. Local
wildlife refuges and marine sanctuaries are home to
whales, fish, and more than 300 species of birds
National Estuary Program Coastal Condition Report 75
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Massachusetts Bays Program
(Martin et al., 1996). Finfish caught in the Bays include
bluefin tuna, Atlantic cod, winter flounder, Atlantic
flounder, and Atlantic herring, and harvested shellfish
species include soft shell clams, oysters, bay scallops,
American lobster, and blue mussels.
More than 3.8 million people live in the Massachu-
setts Bays' watershed, and this number is growing.
Pressures from human development exacerbate environ-
mental problems by increasing stormwater runoff,
sewage-related pollution, and the effects on fragile
coastal habitats. In addition, the number of housing
units on Cape Cod more than doubled between 1970
and 1990, from 65,676 to 135,192. This population
growth is the equivalent of adding almost 10 new
housing units a day for 20 years (ANEP, 200 Ic). Such
development is producing more impervious surfaces,
and as a result, increasing the stormwater volumes and
velocities that the Bays must absorb.
Boston, the major shipping port in this estuary,
generates $8 billion in annual revenues and supports
9,000 jobs (MBP, 2004b). Water-based economies for
this NEP study area include tourism, commercial fish-
eries, and local marinas, which depend directly on the
resources provided by the Massachusetts Bays. Boston
Harbor is a center for numerous public resources,
including the shipping industry, marine research institu-
tions, whale-watching activities, and the Harbor Island
Park system. The Massachusetts coast attracts visitors
from all over New England to enjoy kayaking, sailing,
surfing, and hiking. The Massachusetts Department of
Public Health (MDPH) posts annual beach reports at
http://www.mass.gov/dph/beha/tox/reports/beach/
beaches.htm.
The Massachusetts Bays Program (MBP) was
launched in 1988 to address threats to the health of the
Massachusetts and Cape Cod bays. In 1990, EPA
accepted the MBP into the NEP. To ensure that each of
the MBP's 50 communities receives its share of atten-
tion, the program partners with watershed associations
and regional planning agencies to provide regional coor-
dinators in five subregions: Upper North Shore, Salem
Sound, Metro Boston, South Shore, and Cape Cod
(MBP, 2004b).
Environmental Concerns
The Massachusetts Bays face a variety of environ-
mental concerns, including increasing stormwater
runoff, sewage-related pollution, and the effects of
human development on fragile coastal habitats. These
pressures threaten the health of the Massachusetts Bays
and cause approximately 1,000 acres of the Bays' coastal
and inland wetlands to be lost each year. Boston Harbor
and the North Shore have historically also been affected
by toxic contamination problems, including elevated
levels of PAHs, copper, arsenic, lead, cadmium,
mercury, chromium, nickel, zinc, PCBs, and pesticides.
The status and trends of exploited fish stocks in the
Massachusetts Bays is another primary concern of the
MBP. Trawl surveys have helped identify declining
trends in a variety of commercially important finfish
(Martin et al., 1996). In addition, invasive species have
caused significant economic impacts to industries that
are dependent upon shellfish, groundfish, and coastal
recreation. These impacts include the fouling of aqua-
culture facilities and the spread of diseases among native
species.
Population Pressures
The population of the 6 NOAA-designated coastal
counties (Barnstable, Essex, Middlesex, Norfolk,
Plymouth, and Suffolk) coincident with the MBP study
area increased by more that 23% during a 40-year
period, from 3.4 million people in 1960 to almost
4.2 million people in 2000 (Figure 3-27) (U.S. Census
Bureau, 1991; 2001). This rate of population growth
for the MBP study area is equivalent to the population
growth rate of 24% for the collective NEP-coincident
coastal counties of the Northeast Coast region. In 2000,
the population density of these 6 coastal counties was
1,493 persons/mi2, about 40% higher than the popula-
tion density of 1,055 persons/mi2 for the collective
NEP-coincident coastal counties of the Northeast Coast
region (U.S. Census Bureau, 2001). Population pres-
sures for this NEP are likely to be high because this
estuary serves a major metropolitan area, and center for
commerce, including major commercial fishing
activities in these coastal communities.
76 National Estuary Program Coastal Condition Report
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CHAPTER 3 ; NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
/Massac/iusetfs Bays Progran
9 4 -
£ 3 -
2000
Figure 3-27. Population of NOAA-designated coastal counties
of the MBP study area, 1960-2000 (U.S. Census Bureau, 1991;
2001).
NCA Indices of Estuarine
Condition—Massachusetts Bays
The overall condition of the Massachusetts Bays is
rated fair based on the four indices of estuarine condi-
tion used by the NCA (Figure 3-28). The water quality
index for the Bays is rated good; the sediment and
benthic indices are rated poor (although fair may be
more appropriate, see later discussions); and the fish
tissue contaminants index is rated fair. Figure 3-29
provides a summary of the percentage of estuarine area
rated good, fair, poor, or missing for each parameter
considered. This assessment is based on data from 44
NCA sites sampled in the MBP estuarine area in 2000
and 2001. Please refer to Tables 1-24, 1-25, and 1-26
(Chapter 1) for a summary of the criteria used to
develop the rating for each index and component
indicator.
Overall Condition
Massachusetts Bays
(2.5)
Water Quality Index (5)
Sediment Quality Index (I)
Benthic Index (I)
Fish Tissue Contaminants
Index (3)
Figure 3-28. The overall
condition of the MBP
estuarine area is fair (U.S.
EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
I
20 40 60 80
Percent NEP Estuarine Area
100
|| | Missing
Figure 3-29. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Massachusetts
Bays (U.S. EPA/NCA).
Water Quality Index
The water quality index for the Massachusetts Bays is
rated good (Figure 3-30). The Massachusetts Bays have
one of the best ratings for water quality among the
Northeast Coast NEP estuaries, with 93% of the
Massachusetts Bays' estuarine area receiving a good
rating for water quality. This index was developed using
NCA data on five component indicators: DIN, DIP,
chlorophyll a, water clarity, and dissolved oxygen.
Dissolved Nitrogen and Phosphorus I The
Massachusetts Bays are rated good for DIN concentra-
tions. Ninety percent of the estuarine area was rated
good for DIN concentrations, 10% was rated fair, and
none of the area was rated poor. The Massachusetts
Bays are also rated good for DIP concentrations because
83% of the estuarine area was rated good for this
component indicator and 17% of the area was rated
fair. None of the estuarine area was rated poor for DIP
concentrations.
National Estuary Program Coastal Condition Report 77
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Massachusetts Bays Program
Chlorophyll a \ The Massachusetts Bays are rated
good for chlorophyll a concentrations. Of the estuarine
area, 99% and 1% were rated good and fair, respec-
tively, and none of the estuarine area was rated poor for
chlorophyll a concentrations.
Water Clarity The water clarity rating for the
Massachusetts Bays is good. None of the estuarine area
was rated poor for water clarity, and 94% of the area
was rated good. NCA data on water clarity were
unavailable for 6% of the MBP estuarine area
Dissolved Oxygen The Massachusetts Bays are
rated good for dissolved oxygen because 99% of the
estuarine area was rated good for this component
indicator. No area of the Bays was rated poor for
dissolved oxygen concentrations, and NCA data on
dissolved oxygen concentrations were unavailable for
only 1% of the MBP estuarine area.
Water Quality Index - Massachusetts Bays
Site Criteria: Number of
component indicators in poor or fair
condition
- •Good = No more than I is fair
OFair = I is poor, or 2 or more
are fair
• Poor = 2 or more are poor
O Missing
Sediment Quality Index
The sediment quality index for the Massachusetts
Bays is rated poor, with 16% of the Bays' estuarine area
classified as poor, just slightly higher than the 15%
threshold used to define this category (Figure 3-31).
This index was developed using NCA data on three
component indicators: sediment toxicity, sediment
contaminants, and sediment TOC. Sediment toxicity
was evident at four sites (11% by area); however, these
sites did not coincide with areas of sediment contamina-
tion. High concentrations of sediment contaminants
were found at just two Boston Harbor sites, reflecting a
legacy of pollution that stems from several decades of
abuse. Moderate sediment contaminant: concentrations
were found at three additional sites, in total comprising
about 5% of the Bays' estuarine area—a relatively
minor record of contamination compared with other
Northeast Coast NEP estuaries. TOC levels for the Bays
were typical for the Northeast Coast region. The sedi-
ment quality rating of poor for the Massachusetts Bays
largely reflects the absence of overlap in sites impaired
for each of the three component indicators. A fair rating
for the Massachusetts Bays may be a better assessment
of sediment quality.
Sediment Toxicity The sediment toxicity rating
for the Massachusetts Bays is poor. Eleven percent of
the estuarine area was rated poor, and NCA data on this
component indicator were unavailable for 8% of the
MBP estuarine area.
Sediment Contaminants I The Massachusetts
Bays are rated fair for sediment contaminant concentra-
tions. Approximately 5% of the estuarine area was rated
poor, 1% of the area was rated fair, and 90% of the area
was rated good for this component indicator.
Total Organic Carbon I The Massachusetts Bays
are rated good for sediment TOC. Sixty-two percent of
the estuarine area was rated good for TOC concentra-
tions, 12% of the area was rated fair, and none of the
area was rated poor. NCA data on this component
indicator were unavailable for 26% of the MBP
estuarine area.
Figure 3-30. Water quality index data for the Massachusetts
Bays, 2000-200 \ (U.S. EPA/NCA).
78 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Massachusetts Bays Progran
Sediment Quality Index - Massachusetts Bays
Site Criteria: Number and condition
of component indicators
• Good = None are poor, and sediment
contaminants is good
OFair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
OMissing
Mics*nS Poor
16%
Fair
Figure 3-31. Sediment quality index data for the Massachusetts
Bays, 2000-2001 (U.S. EPA/NCA).
Digging for clams (Rick Balla).
Benthic Index
The benthic index for the Massachusetts Bays is
rated poor. As measured by the Shannon-Weiner
Diversity Index, 21% of the Massachusetts Bays estu-
arine area received a poor rating because of an unsatis-
factory degree of benthic diversity, just slightly greater
than the threshold used to define this category (Figure
3-32); therefore, a designation of fair for the
Massachusetts Bays may be a better assessment for
benthic quality.
Fish Tissue Contaminants Index
The fish tissue contaminants index for the
Massachusetts Bays is rated fair (Figure 3-33). Of the
20 fish samples analyzed, 17 were collected from Cape
Cod Bay, and nearly 80% of the analyzed samples had
moderate or high levels of PCBs.
Benthic Index - Massachusetts Bays
Site Criteria:
Shannon-Weiner Diversity
Index Score
• Good = > 0.63
»Poor = s 0.63
OMissing
Figure 3-32. Benthic index data for the Massachusetts Bays,
2000-2001 (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 79
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CHAPTER 3 NORTHEAST COAST NAT'ONAL ESTUARY PROGRAM COASTAL CONDITION
Massachusetts Bays Program
Fish Tissue Contaminants Index - Massachusetts Bays
Site Criteria: EPA Guidance
concentration
9 Good = Below Guidance range
OFair = Falls within Guidance
range
• Poor = Exceeds Guidance range
Figure 3-33. Fish tissue contaminants index data for the
Massachusetts Bays, 2000-2001 (U.S. EPA/NCA).
Massachusetts Bays Program
Indicators of Estuarine Condition
Water and Sediment Quality
The Massachusetts Water Resources Authority
(MWRA) has collected water quality data in
Massachusetts and Cape Cod bays for the Harbor and
Outfall Monitoring Program since 1992. This water
quality monitoring program includes continuous
vertical profiles of temperature, salinity, dissolved
oxygen, chlorophyll a (fluorescence), beam attenuation,
and irradiance, ranging from the water surface to within
1.6 feet of the bottom at each site. Discrete samples
from three to five different depths were collected for
nutrient analyses (all forms of nitrogen and phos-
phorus), total suspended solids, chlorophyll a, and
dissolved oxygen. Samples were also collected for
phytoplankton and zooplankton species enumeration at
representative sites throughout the Massachusetts Bays
(Libby et al., 2005).
In September 2000, the MWRA terminated effluent
discharges to Boston Harbor outfalls and redirected the
discharges offshore via a 9.5-mile outfall to the Massa-
chusetts Bays. Total nitrogen has decreased by 34%
since the discharges to Boston Harbor were redirected,
and there has been a 6% increase in mid-summer
dissolved oxygen levels in near-bottom areas. Chloro-
phyll a levels decreased slightly during 2001 after the
outfall relocation offshore, but increased slightly in
2002 (MBP, 2004b).
Significantly high levels of mercury have been found
in sediments collected from Gloucester, Salem, and
Boston harbors (MBP, 2004b). In 2004, mercury was
detected in fish at levels warranting a statewide fish
consumption advisory for both marine fish and fresh-
water fish in Massachusetts' lakes and ponds (U.S. EPA,
2005a). Public health concerns related to consumption
of fish and shellfish are also being addressed through the
measurement of trace metal and organic chemical
concentrations in winter flounder and lobster. In addi-
tion, an ongoing project evaluates the bioaccumulation
of contaminants using caged mussels deployed each
summer at key locations in the Boston Harbor/Massa-
chusetts Bay system (Wisneski et al., 2004). The impact
of contaminants on the soft-bottom benthic commu-
nity in the Bays is analyzed through a sampling
program in both Boston Harbor and Massachusetts Bay,
with annual sampling conducted at 8 sites in the
Harbor and more than 20 sites in the E>ay. In addition
to conventional benthic community analysis, sediment-
penetrating camera systems and video imagery are used
to evaluate bottom conditions (Williams et al., 2005).
Habitat Quality
The MBP and the Massachusetts Office of Coastal
Zone Management (Massachusetts CZM) are
conducting research routinely to measure conditions in
coastal wetlands on Cape Cod. In 1997, the Wetland
Health Assessment Toolbox (WHAT) multi-metric
protocol was developed to help estimate the overall
ecological quality of wetlands habitat. The WHAT tech-
nique is a comprehensive evaluation of wetlands health
80 National Estuary Program Coastal Condition Report
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CHAPTER 3 ! NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Massachusetts Bays Program
before and after constructed improvements are imple-
mented. Indicators used to evaluate wetlands habitat
include water chemistry, adjacent land use, tidal influ-
ence, vegetation, aquatic macroinvertebrates, avifauna,
and fish. The data collected are synthesized by the
Massachusetts CZM research team to produce an
overall wetlands health rating for each salt marsh site
(MBP, 2000).
Many tidal marshes in this estuary system are
impacted by road and highway construction and main-
tenance activities. Because of these impacts, the MBP's
Wetland Restoration Program has attempted to coordi-
nate with the Massachusetts Highway Department on
construction and maintenance operations in coastal
areas. Since 1994, nearly 35 wetland-restoration projects
have been completed in the watershed, totaling more
than 450 acres of wetlands. The MBP has a variety of
ongoing efforts to restore wetland acreage, which
provides valuable nursery and spawning grounds for
fisheries and helps improve water quality. Most habitat-
restoration projects have focused on restoring tidal
flows, removing fill, regrading marsh topography,
building creeks and pools, and suppressing the invasive
reed Phragmites australis. The Great Marsh region along
the northern shore of Massachusetts contains a tremen-
dous wealth of aquatic habitats. Human activities that
have degraded habitat value in the Great Marsh include
the channelization of streams, restriction of tidal flows,
and obstruction offish passages (MBP, 2004b). The
MBP has been working with other agencies and private
partners to help restore and incorporate fishways in the
Bays to allow river herring and shad to travel upstream
for spawning. The MBP has also helped write several
successful grants that have generated hundreds of thou-
sands of dollars for fishway repair and restoration on the
South Shore (NSRWA, 2005).
The MBP is helping the Massachusetts CZM
develop an eelgrass health assessment index to expand
monitoring of this productive habitat within the Bays.
Mooring-chain scarring and dredging are two primary
causes of eelgrass habitat loss in the Massachusetts Bays.
The extent of nutrient over-enrichment and the subse-
quent reduction in water clarity impacting eelgrass habi-
tats is another important stressor that the MBP is
currently evaluating with its partners; however, there is
insufficient data on eelgrass coverage to truly quantify
changes over time within the Bays' system. Eelgrass is
expected to recolonize Boston Harbor due to substantial
improvements in water quality (MBP, 2004b).
Permanently protected open space in the watershed
provides valuable remaining habitat areas because these
spaces cannot be developed or converted for other uses
in the future. The Massachusetts Office of Geographic
and Environmental Information collects data on how
much open space is maintained in the watershed.
Nearly 25% of land within the 50 communities of the
MBP are protected from development (MBP, 2004b).
The MBP's Healthy Habitats Initiative is a multi-
faceted approach to resource management that links
habitat protection with land-use planning. The goal of
this 3-year initiative is to protect critical habitat and
unique community character by helping towns preserve
open space, protect wetlands, prevent stormwater
impacts to water quality, and manage coastal resources
(MBP, 2000). The MBP has also helped develop the
Green Neighborhoods Program, which promotes
habitat protection through development clustering and
implementation of good local and subregional land-use
practices.
©
Human activities are restricted in some areas that provide nesting
habitat for threatened bird species (Jamal Kadri).
National Estuary Program Coastal Condition Report 81
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Massachusetts Bays Program
Monitoring and Ecological
Assessment of the Massachusetts
Bays Ecosystem
The Massachusetts Bays are part of the larger Gulf of
Maine; therefore, many of the conditions that prevail in
the Gulf proper are significant to setting the conditions
for Massachusetts Bay, and subsequently, Cape Cod
Bay. Details about the influence of the Gulf of Maine
on the physical setting of the Bays were published in an
early 1990s report to the MBP (Geyer et al., 1992). The
results of the probabilistically based sampling effort help
to provide the regional context necessary for under-
standing the integrity of the Massachusetts Bays. The
good NCA water quality index rating for the Bays
reflects, in part, the extensive flushing by the Gulf of
Maine.
This regional perspective is important for under-
standing the fate and transport of contaminants, as
well as for evaluating the strength of local impacts. For
die past 15 years, the MBP and Massachusetts CZM
have monitored concentrations of chemicals in blue
mussel (Mytilus edulis) tissue as part of the larger Gulf of
Maine Gulfwatch Program. Organized and adminis-
tered by the Gulf of Maine Council on the Marine
Environment, Gulfwatch has mussel-sampling sites
around the Gulf of Maine, from Nova Scotia to Cape
Cod. Some contaminants measured by the program,
such as mercury, show a broad regional input (e.g.,
atmospheric deposition), whereas odier contaminants
show clear, localized impacts (e.g., PAHs in blue mussel
tissue from selected sites in Boston Harbor). Gulfwatch
data are accessible at http://www.gomoos.org/
chameleon/gulfwatch.
Wetland condition is another indicator of ecological
integrity that the MBP and Massachusetts CZM are
currently developing for application in the Massachu-
setts Bays. To date, there has been little systematic effort
to measure, document, and describe the condition of
coastal and inland wetlands in Massachusetts; however,
since 1995, the MBP and Massachusetts CZM have
been actively working on projects to advance wetland-
assessment methods and approaches. Currently, die
MBP and Massachusetts CZM are working with EPA
on a three-phase coastal wetlands assessment project in
selected study areas of Massachusetts and Rhode Island,
exploring die potential for a more comprehensive
national effort and possible alignment with the NCA
surveys. An important component of the project is the
development and application of a Rapid Assessment
Method (RAM). Requiring both remotely sensed and
on-site procedures and taking about half a day to
conduct, the RAM generates data on some 22 indica-
tors. In 2004, 23 randomly selected sites were evaluated
with the RAM (see map), and another 24 sites are being
examined. Some of the initial project findings indicate
that increased development and land-use intensity in
the 500-foot buffer zone around a salt marsh site corre-
spond with higher abundances of invasive species, lower
extent of high marsh, increased marsh fragmentation,
and decreased connectivity to associated habitats
(Personal communication, Carlisle, 2005). Volunteer
groups are also employing assessment methods to
understand the condition of selected estuarine marshes
in their regions. Salem Sound Coastwatch and the
Association to Preserve Cape Cod use the methods
contained in a Volunteer's Handbook for Monitoring New
England Salt Marshes (developed by the Massachusetts
CZM and MBP, and available on the Web at
http://www.mass. gov/czm/volunteermarshmonitoring.
htm).
82 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Massachusetts Bays Program
Lastly, the Merrimack River to the north of
Massachusetts Bay is important to the biology,
chemistry, and mixing within the estuarine system
(Manohar-Maharaj and Beardsley, 1973). Menzie-Cura
& Associates (1991; 1995) demonstrated the impor-
tance of contaminant loading from the Merrimack
River to the Bays. The USGS is currently leading a
team of partners that includes MBP/Eight Towns and
the Bays (a Local Governance Committee for the Bays),
the U.S. Army Corps of Engineers (USAGE), and the
Massachusetts DEP to characterize the dispersion of
wastewater discharges from the Merrimack Estuary into
Massachusetts Bay.
I
Study area and salt marsh sites randomly selected and
evaluated in 2004 for the current MBP and Massachusetts
CZM wetland assessment project (Massachusetts CZM and
MBP, 2004).
National Estuary Program Coastal Condition Report 83
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Massachusetts Bays Program
Living Resources
The MBP does not use a formal set of indicator
species to evaluate the health of fish and wildlife ecosys-
tems in the Massachusetts Bays, but it does support the
monitoring efforts of state agencies for both indigenous
and invasive species populations across the system.
Several endangered and threatened species are depen-
dent on the Bays' habitats, including the North Atlantic
right whale, blue whale, fin whale, sei whale, humpback
whale, Kemp's ridley sea turtle, shortnose sturgeon,
roseate tern, loggerhead sea turtle, and piping plover
(Martin et al., 1996). The right whale population has
been slow to rebound, with only a 2.5% growth rate
per year (MBP, 2004b). The Stellwagen Bank National
Marine Sanctuary is one of the most critical areas in the
North Atlantic for whales, dolphins, and porpoises.
Other areas of the Massachusetts Bays attract a large
diversity of bird species; the Parker River National
Wildlife Refuge is a barrier island habitat for more than
300 avian species, including snowy owls, Canada geese,
egrets, storm petrels, and cormorants (Martin et al.,
1996). Despite modest efforts at restoration, it appears
that river herring population levels are substantially
below historic levels and well below the production
capacity of spawning habitats in lakes and ponds of the
Massachusetts Bays' watershed (Purintan et al., 2003).
Populations of smelt and alewives have also declined in
recent years. Landings of shellfish have declined in
several towns along the Massachusetts Bays' coastline,
and 15 towns north of Boston Harbor are closed to
shellfishing (MBP, 2004a).
Two invasive species of particular concern in the Bays
are the Asian shore crab and the Pacific tunicate, which
can impact the health of the scallop fishery (MBP,
2004b). Recent activities to help control marine inva-
sive species have included surveys of marine habitats
and pathways for the introduction of invasive species;
public awareness campaigns; analyses of regional legisla-
tion for invasive species; and workshops on response
strategies for aquatic pests. More than 26 invasive
species of plants and invertebrates were found in a 2000
survey of the Massachusetts Bays (MBP, 2004b).
Environmental Stressors
Some of the major sources of pathogens in the
Massachusetts Bays include marine sanitation devices,
CSOs, and urban stormwater runoff. E>isease-causing
viruses and bacteria from these sources regularly close
bathing beaches and shellfish-harvesting areas. An
average of 44 beach closures occurred each year between
1988 and 1991 at South Shore, North Shore, and
Boston Harbor due to pathogen contamination. Each
year, an estimated 10,000 people become ill from inges-
tion of the bacteria-contaminated waters of this estuary
(Martin et al., 1996). In recent years, there has been a
significant reduction in the number of CSOs in the
MBP estuarine area (MBP, 2004b).
Wastewater discharges can also introduce contami-
nants to the Bays. The number of permitted discharges
to the Bays has decreased in the past 14 years as a result
of local water conservation programs (MBP, 2004a), but
overall discharge flow increased between 1991 and 2004
due to cooling-water use by area power plants (MBP,
2004b).
Ferries in Boston, MA (Ben Fertig).
84 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Massachusetts Bays Program
Current Projects,
Accomplishments, and Future
Goals
The MBP has had a number of successful programs
and uses benchmarks that measure progress toward the
goal of restoring and maintaining the health of the
Bays. To combat stormwater pollution, the MBP
installed high-tech "StormTreat" systems for stormwater
discharge at two sites, which has been very successful.
The Shellfish Clean Waters Initiative is currently moni-
toring the effectiveness of these treatment systems for
possible use at other sites. In 1996, the town of
Duxbury completed construction of a shared
sewer/septic system with a $32,000 grant from the
MBP. This project reduced bacteria levels to a safe
range, leading to the reopening of 99 acres of produc-
tive shellfish beds (MBP, 2000). Another method used
by the MBP to reduce pathogen pollution involved
initiating a Betterment Bill, which provides loans to
landowners to replace failing septic systems (Martin et
al., 1996).
In 2003, the COASTSWEEP Program organized
cleanups with local coordinators and more than 3,000
volunteers, cleaning up 35,000 pounds of trash and
marine debris from 155 locations estuary-wide (APNS,
2005). In August 2003, the MBP worked with 7 other
NEPs and the Massachusetts Institute of Technology
Sea Grant Program to conduct a rapid survey for
marine invasive species in the northeastern United
States, focusing on fixed docks and piers at 20 different
sites between Casco Bay, ME, and the New York/New
Jersey Harbor (MBP, 2004b).
Currently, the MBP is working with EPA and the
Massachusetts Watershed Initiative to develop a
Wetlands Restoration Atlas for tidally restricted coastal
wetlands from Winthrop to Quincy, which will be used
to aid in the assessment of anadromous fish runs. The
MBP is also pursuing No-Discharge Zone designations
and is developing guidelines for personal watercraft use
on Cape Cod (MBP, 2000).
Conclusion
Some of the most significant environmental chal-
lenges facing the Massachusetts Bays are wetlands loss
and degradation, increased stormwater runoff in
developing areas, contamination of Bay sediments with
toxic contaminants, contamination of shellfish beds and
recreational waters with bacteria, declines in fisheries
stocks, and the impact of invasive species on the estuary.
The actions of EPA and the MBP, with support from
the MWRA and Massachusetts CZM, have been
successful in addressing many of the priority environ-
mental concerns facing the Massachusetts Bays. One of
the notable successes in the region has been the restora-
tion of 450 acres of wetlands. In addition, eelgrass
populations have stabilized since the 1990s, partly due
to improvements in water quality. Wastewater impacts
in the Bays, specifically in Boston Harbor, are much less
than historic levels. Total nitrogen levels have decreased,
and dissolved oxygen levels in bottom waters have
increased since 2000. Remediation of contaminated
sediments in Boston Harbor is still a work in progress
because the inner harbor area has had some of the
highest concentrations of sediment contaminants
compared to other sites in the Bays. For the
Massachusetts Bays, the NCA estuarine survey rates
water quality as good, fish tissue contamination as fair,
and sediment quality and benthic condition as poor.
Humpback whales are found in the MPB study area (Robin
Hunter FWS).
National Estuary Program Coastal Condition Report 85
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Buzzards Bay National Estuary Program
Buzzards Bay National Estuary Program
^* ^^
National Estuary
Program
www.buzzardsbay.org
Background
Buzzards Bay is a moderately large estuary located
between the western part of Cape Cod and the
Elizabeth Islands in Massachusetts. The Bay is approxi-
mately 269 mi2 in size and 28 miles long, averages
about 8 miles wide, and has an average depth of 36 feet
(NOAA, 1985; BB NEP, 2005). The coastline stretches
over 280 miles and includes inner harbors, the bayward-
facing portions of the Elizabeth Islands, the portions of
the Cape Cod Canal that are in the watershed, and
11 miles of public beaches that lure thousands of
tourists from Massachusetts and neighboring states
(BBNEP, 1992). In addition, the world-renowned
Woods Hole Oceanographic Institution and the Marine
Biological Laboratory are located near a passage to
Buzzards Bay.
Buzzards Bay exchanges water with Rhode Island
Sound to the southwest, with Vineyard Sound through
the Elizabeth Islands, and with Cape Cod Bay via the
Cape Cod Canal at the northern end. A number of trib-
utaries provide freshwater flows to the Bay, including the
Agawam, Wankinco, Wewantic, Mattapoisett, Acushnet,
86 National Estuary Program Coastal Condition Report
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CHAPTER 3 ! NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Buzzards Bay National Estuary Prograr,
Paskamanset, and Westport rivers. Buzzards Bay is rich
in shellfish resources and has a $4 million annual shell-
fish industry, representing 25% of Massachusetts'
annual fisheries total. Shellfish species harvested in
Buzzards Bay include soft shell clams, quahogs, scallops,
oysters, and lobster. Shellfish-harvesting is a popular
pastime for many tourists, and more than 500 commer-
cial permits and 12,800 recreational permits are sold
annually (BB NEP, 2005).
The Buzzards Bay coastline features a wealth of habi-
tats, including salt marshes, tidal flats, barrier beaches,
eelgrass beds, and subtidal zones. The Buzzards Bay
National Estuary Program (BB NEP) is an advisory and
planning unit of the Massachusetts CZM and receives
funding from EPA as part of the NEP.
Environmental Concerns
The most significant threats to Buzzards Bay and
its watershed include toxic contamination of the
ecosystem, closures of shellfish beds due to bacterial
contamination, non-point source pollution, habitat loss,
and nitrogen loading and resulting coastal eutrophica-
tion. In general, environmental degradation from
pollutant inputs is localized in the more than 30
embayments along the periphery of Buzzards Bay,
whereas water and habitat quality in the central Bay are
very good (CBB, 2003).
Population Pressures
The population of the 4 NOAA-designated coastal
counties (Barnstable, Bristol, Dukes, and Plymouth)
coincident with the BB NEP study area increased by
72% during a 40-year period, from 0.72 million people
in 1960 to about 1.24 million people in 2000 (Figure
3-34) (U.S. Census Bureau, 1991; 2001). This rate of
population growth for the BB NEP study area is almost
three times the population growth rate of 24% for the
collective NEP-coincident coastal counties of the
Northeast Coast region. In 2000, the population
density of the BB NEP's 4 coastal counties was 726
persons/mi2, slightly lower than the population density
of 1,055 persons/mi2 for the collective NEP-coincident
coastal counties of the Northeast Coast region (U.S.
Census Bureau, 2001).
1.4
1.2
1.0
0.8
0.6
_o
4S 0.4
Q.
£ 0.2
0.0
I960
2000
Figure 3-34. Population of NOAA-designated coastal counties of
the BB NEP study area, 1960-2000 (U.S. Census Bureau, 199 I;
2001).
NCA Indices of Estuarine
Condition—Buzzards Bay
The overall condition of Buzzards Bay is rated fair
based on the four indices of estuarine condition used by
the NCA (Figure 3-35). The water quality index for
Buzzards Bay is rated good, the sediment quality index
is rated fair, the benthic index is rated good to fair, and
the fish tissue contaminants index is rated poor. Figure
3-36 provides a summary of the percentage of estuarine
area rated good, fair, poor, or missing for each param-
eter considered. This assessment is based on data from
30 NCA sites sampled in the BB NEP estuarine area in
2000 and 2001. Please refer to Tables 1-24, 1-25, and
1-26 (Chapter 1) for a summary of the criteria used to
develop the rating for each index and component
indicator.
Overall Condition
Buzzards Bay
(3.25)
Fair
Water Quality Index (5)
Sediment Quality Index (3)
Benthic Index (4)
Fish Tissue Contaminants
Index (I)
Figure 3-35. The
overall condition of
the BB NEP estuarine
area is fair (U.S.
EPA/NCA).
National Estuary Program Coastal Condition Report 87
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Buzzards Bay National Estuary Program
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80
Percent NEP Estuarine Area
100
Missing
Figure 3-36. Percentage of estuarine area achieving each rating
for all indices and component indicators — Buzzards Bay
(U.S. EPA/NCA).
Water Quality Index
Based on the NCA survey results, the water quality
index for Buzzards Bay is rated good, although water
quality data were unavailable for nearly a third of the
estuary (Figure 3-37). This index was developed using
NCA data on five component indicators: DIN, DIP,
chlorophyll a, water clarity, and dissolved oxygen.
Fourteen percent of Buzzards Bay had moderate DIN
values, but DIN measurements were not available for
almost half of the Bay. Nearly the entire Bay displayed
moderately high DIP levels—not an unusual finding in
Northeast Coast estuarine waters. Chlorophyll a
concentrations were uniformly low for Buzzards Bay.
Water clarity was satisfactory everywhere in Buzzards
Bay, and there was only one incidence of oxygen
depletion.
Dissolved Nitrogen and Phosphorus I The
DIN concentrations rating for Buzzards Bay is good,
with 37% of the estuarine area rated good and 14%
of the area rated fair for this component indicator. None
of the estuarine area was rated poor for DIN; however,
DIN concentrations were not assessed in 49% of the BB
NEP estuarine area. DIP concentrations in Buzzards Bay
were rated fair, with 6% of the estuarine area rated good
for DIP and 80% of the area rated fair. Three percent of
the estuarine area was rated poor for this component
indicator, and NCA data on DIP concentrations were
unavailable for 11 % of the BB NEP estuarine area.
Water Quality Index - Buzzards Bay
Site Criteria: Number of component
indicators in poor or fair condition
• Good = No more than I is fair
OFair = I is poor, or 2 or
more are fair
• Poor = 2 or more are poor
O Missing
Figure 3-37. Water quality index data for Buzzards Bay,
2000-2001 (U.S. EPA/NCA).
88 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Buzzards Bay National Estuary Program
Chlorophyll fl Buzzards Bay is rated good for
chlorophyll a. concentrations. Seventy-nine percent of
the estuarine area was rated good for chlorophyll a
concentrations, and none of the area was rated poor or
fair; however, NCA data on chlorophyll a concentra-
tions were unavailable for 21% of the BB NEP
estuarine area.
Water Clarity I Buzzards Bay is rated good for
water clarity. Water clarity was rated poor at a sampling
station if light penetration at 1 meter was less than 10%
of surface illumination. Eighty-nine percent of the
Buzzards Bay estuarine area was rated good for water
clarity, 2% was rated fair, and none of the area was
rated poor. NCA data on water clarity were unavailable
for 9% of the BB NEP estuarine area.
Dissolved Oxygen \ Buzzards Bay is rated good for
dissolved oxygen concentrations. Ninety-six percent of
the estuarine area was rated good for dissolved oxygen
concentrations, and only 4% of the estuarine area was
rated poor.
Sediment Quality Index
The sediment quality index for Buzzards Bay is rated
fair, with 11 % of the estuarine area rated poor and less
than 1% of the area rated fair for sediment quality
condition (Figure 3-38). There were relatively few indi-
cations of sediment contamination in Buzzards Bay.
Sediments proved to be toxic to amphipods at four sites
(11% by area), including one contaminated site, and
there were no indications of high TOC concentrations.
Sediment Toxicity I Buzzards Bay is rated poor for
sediment toxicity. Eleven percent of the Buzzards Bay
estuarine area was rated poor for sediment toxicity, and
NCA data on this component indicator were unavail-
able for 4% of the BB NEP estuarine area.
Sediment Contaminants I Buzzards Bay is rated
fair for sediment contaminant concentrations. Approxi-
mately 10% of the estuarine area was rated poor for this
component indicator, and 86% of the area was rated
good.
Sediment Quality Index - Buzzards Bay
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
OFair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Figure 3-38. Sediment quality index data for Buzzards Bay,
2000-2001 (U.S. EPA/NCA).
Total Organic Carbon I Buzzards Bay is rated
good for sediment TOC. Seventy-nine percent of the
estuarine area was rated good for TOC concentrations,
9% of the area was rated fair, and none of the area was
rated poor. NCA data on TOC concentrations were
unavailable for 12% of the BB NEP estuarine area.
National Estuary Program Coastal Condition Report 89
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Buzzards Bay National Estuary Program
Benthic Index
Fish Tissue Contaminants Index
The benthic condition rating for Buzzards Bay is
good to fair, as evaluated by the Virginian Province
Benthic Index (Figure 3-39). Eighty percent of the
estuarine area was rated good for benthic condition, and
11 % of the area was rated poor. Only one Buzzards Bay
site designated as impaired for benthic condition also
had an impaired rating for sediment contamination.
Benthic Index - Buzzards Bay
Based on the NCA survey data collected in
2000-2001, the fish tissue contaminants index for
Buzzards Bay is rated poor. Eighty-three percent of fish
samples analyzed exceeded EPA Advisory Guidance
values for at least one contaminant and were rated poor
for this index (Figure 3-40).
Fish Tissue Contaminants Index - Buzzards Bay
Site Criteria:
Virginian Province Benthic Index Score
• Good = > 0.0
• Poor = <; 0.0
O Missing
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
OFair = Falls within Guidance range
• Poor = Exceeds Guidance range
Good
80%
Figure 3-39. Benthic index data for Buzzards Bay, 2000-2001
(U.S. EPA/NCA).
Figure 3-40. Fish tissue contaminants index data for
Buzzards Bay, 2000-2001 (U.S. EPA/NCA).
90 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Buzzards Bay National Estuary Program
Buzzards Bay National Estuary
Program Indicators of Estuarine
Condition
To assess environmental results for improving
habitat, living resources, and water quality, the BB NEP
relies on direct measures of water quality and acres of
shellfish-harvesting closures. For other environmental
assessments, the BB NEP relies on documentation of
human behavioral impacts (e.g., number of gallons
pumped at boat pump-out facilities). The following
specific indicator measures are used by the BB NEP to
evaluate environmental conditions in Buzzards Bay.
Water and Sediment Quality
In order to encompass the many different water
quality measurements monitored by the BB NEP, the
program created a eutrophication index, the Buzzards
Bay Health Index, to score each cove and harbor on a
scale of 0 to 100. The BB NEP uses this index as a
compilation of five individual indicators: dissolved
oxygen, DIN, total organic nitrogen, chlorophyll a, and
Secchi disk depth. Dissolved oxygen measures used by
the program are an average of the lowest 20% of read-
ings collected by a citizens' water quality monitoring
group, The Coalition for Buzzards Bay (CBB). Each
embayment (harbors and coves) within the Buzzards
Bay watershed has its own suite of nutrient sources and
potential management solutions. Embayments with
scores less than 35 are labeled eutrophic, whereas those
with scores of 35 to 65 are designated as fair. Those
embayments with scores greater than 65 are labeled
good to excellent. Water quality measurements are
collected by CBB, with roughly 10 to 15 samples
collected at 2 to 4 sites at each of 30 different Buzzards
Bay embayments (Costa et al., 1999). Central Buzzards
Bay, which exhibits excellent water quality, has scored
close to 100 on the Buzzards Bay Health Index, whereas
the Nasketucket River, Agawam River, Eel Pond, and
Westport River exhibited the lowest scores of any areas
within the watershed between 1997 and 2003. In
contrast, Quissett Harbor, Aucoot Cove, and Penikese
Island received excellent scores (between 90 and 100)
for their water quality (CBB, 2003).
The number of shellfish-harvesting closures is a good
indicator of bacterial contamination problems in
Buzzards Bay. Shellfish-harvesting closures reached their
peak in 1990, when more than 16,500 acres were closed
to harvesting due to bacteria contamination. In 2003,
almost 41% (roughly 9,300 acres) of the 23,000 acres
of Buzzards Bay's most productive nearshore shellfishing
areas were closed to harvesting (CBB, 2003). The
Massachusetts Division of Marine Fisheries (DMF) and
the MDPH test surface waters or shellfish to track
bacteria contamination, and the BB NEP creates a
thumbnail sketch of the change in number of acres of
shellfish beds closed over time, using data collected on
July 1 of each year.
Habitat Quality
The widespread distribution of eelgrass in Buzzards
Bay and its sensitivity to pollution make it an ideal indi-
cator species for changes in water quality and for
tracking overall ecosystem health. For these reasons, the
BB NEP funded a study of eelgrass distribution in
Buzzards Bay (Figure 3-41) that was based on historical
aerial photographs, field surveys, and sediment cores.
The ratio of existing eelgrass habitat area to potential
eelgrass habitat area has been evaluated, and although
there is considerable variability in response among the
embayments, a clear trend overall of declining eelgrass
coverage with increased nitrogen loadings was observed.
Additionally, the decline in the catch of bay scallops in
Waquoit Bay (Cape Cod Lagoon) has coincided with
declines in eelgrass (BB NEP, 2005).
30,000
1600 1900 1930s 1950s 1960s 1970s 1985 1996
Years
Figure 3-41. Eelgrass abundance measured by the BB NEP
(BBNER2005).
National Estuary Program Coastal Condition Report 91
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Buzzards Bay National Estuary Program
Protecting the Endangered Roseate
Tern
Roseate terns (Sterna dougallii) are a federally endan-
gered species recognized under the Migratory Bird
Treaty Act. These birds breed in North America on the
coasts and islands of the Atlantic Ocean, winter along
the northern coast of South America, and nest in associ-
ation with other tern species, such as the common tern.
Although the population of roseate terns in north-
eastern North America has increased slowly since 1987,
more than 90% of this species' population is concen-
trated in five predator-controlled sites in the United
States. The largest North American colony of this
species is found in Buzzards Bay, with half of North
America's breeding pairs found on two of the Bay's tiny
islands (Bird Island and Ram Island) (see bar graph).
Roseate terns returned to Ram Island in the 1990s after
a 20-year absence, and the island now hosts more
breeding pairs than Bird Island.
The Massachusetts Division of Fisheries and Wildlife
(MassWildlife) reports on the numbers of roseate tern
nests by individual island. The New Bedford Superfund
trustees have awarded more than a million dollars to
protect and preserve tern habitat on Bird Island through
beach replenishment and restoration, while Penikese
Island, located near the southern tip of the Elizabeth
Island chain, is the focus of new efforts to expand
roseate tern habitat onto additional islands in the
estuary.
A century ago, roseate terns were a favorite target of
hunters selling feathers to the millinery industry and
egg collectors. Human exploitation (trapping for
market) of the roseate tern on its South American
wintering grounds, where no public protection is
offered, is currently the main limiting factor for the
species. Predation at breeding colonies by gulls, crows,
marsh hawks, short-eared owls, and other wildlife poses
a constant threat and seems to be the main reason for
the selection of islands and inlets as nesting sites. Other
concerns include competition for nest sites from other
species (e.g., larger gulls) and the reproductive effects
(e.g., thinning of eggshells, premature breakage of eggs,
reduced reproductive success) of toxic chemicals that
pass through the food chain. In addition, a shortage of
males may limit the productivity of roseate terns at
some colonies in northeastern North America, where
20% of breeding females do not find mates.
Roseate tern (Ted D Eon. http://www.geocities.com/teddeon509/
gallery.html )
92 National Estuary Program Coastal Condition Report
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CHAPTER 3 I NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Buzzards Bay National Estuary Program
As a result of an oil spill in April 2003 that severely
affected Ram Island, "hazing" operations using cannons
and lights were put into effect to discourage the arrival
and nesting of birds to the island until the oil was
cleaned up. Some breeding pairs delayed nesting on
Ram Island because of the cleanup activities, whereas
other pairs nested on Penikese Island. One account of
the impact included an estimate that at least 350 roseate
tern chicks had been lost because of the delayed nesting;
this number represents roughly 10% of annual chick
production for the species. The impact to roseate terns
and other species and habitat from the spill is being
addressed through the Natural Resource Damage
Assessment (NRDA) process. Separate from the NRDA
process, a $ 10 million criminal settlement was finalized
in November 2004.
Additional information about roseate terns in
Buzzards Bay is available at http://www.buzzardsbay.
org/roseates.htm.
a
Q_
to
-D
£
2000-
1500
• Other
• Bird Island
D Ram Island
1000
1975
1980
1985
1990 1995
2000
Year
Buzzards Bay roseate tern breeding pairs (Data courtesy of Brad Blodget and Carolyn Mostello,
former and current State Ornithologist, MassWildlife).
National Estuary Program Coastal Condition Report 93
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Buzzards Boy National Estuary Progran
Acres of forest cover serve as a useful indicator of the
ability of the Buzzards Bay system to support healthy
ecosystems. Forest growth along streambanks is critical
for maintaining freshwater quality, filtering nitrogen
and sediments, stabilizing erodible soils, and providing
fish and wildlife habitat. A target threshold suggested
for forest cover is approximately 70%, based on obser-
vations in similar coastal watersheds. Forest cover in the
Bay watershed has increased since 1850 as pastures and
farm fields were abandoned; however, about 23,000
acres (13%) of forests have been lost since 1973,
primarily due to residential and commercial develop-
ment. In 2003, more than half the Buzzards Bay water-
shed was covered by forests (CBB, 2003).
The BB NEP also uses the acreage of protected open
space in the watershed as a useful indicator of potential
habitat area. Open space areas that are critical for
protection include coastal and freshwater wetlands, river
and stream corridors, and watersheds to nitrogen-sensi-
tive embayments and public drinking water supplies.
More than 50,000 acres (or 20% of the total land area)
in the Buzzards Bay watershed, from Fall River to
Falmouth, is permanently protected open space (BB
NEP, 2005).
Although it is not currently assessed, the number of
anadromous (migratory) fish runs restored in the Bay
will be used as an indicator by the BB NEP in the
future. Populations of anadromous fish species such as
the alewife and blueback herring have declined dramati-
cally in Buzzards Bay during the past century. Not only
are these two species part of an important commercial
fishery, they are also an important forage food for other
fish, whales, and coastal birds, such as the roseate tern
(BBPNEP, 1999).
Living Resources
River herring populations are an important natural
resource in Buzzards Bay, and their numbers have
declined over time to a fraction of their historic levels.
Currently, only the Mattapoisett and Sippican rivers are
surveyed for river herring on a routine basis using elec-
tronic counters. In an effort to help restore the river
herring population, the BB NEP has assisted with the
removal of fish passage obstructions and the construc-
tion or repair offish ladders (BB NEP, 2005). In addi-
tion, alewives and blueback herring populations have
decreased dramatically in the Bay, whereas populations
of shad, sturgeon, and Atlantic salmon have been elimi-
nated (CBB, 2003).
The bay scallop population in Buzzards Bay is under
close study by the Massachusetts DMF because pollu-
tion and declines in eelgrass bed coverage have hindered
scallop colonization. Scallop populations in the Bay
have declined dramatically during the past 30 years
(CBB, 2003); therefore, the BB NEP is; supporting
physical restoration efforts to stimulate eelgrass and
scallop recovery in areas of the Bay with good water
clarity.
Environmental Stressors
Measurements of human activity (e.g., population
growth rates, number of marine vessels in the Bay) can
also be used as indicators of estuarine condition. Like
most coastal areas, the Buzzards Bay watershed
continues to lose open land to development. The 2000
U.S. Census confirmed that the Buzzards Bay watershed
remains a fast-growing area. Although the City of New
Bedford experienced a population decline, population
growth averaged 8.8% during the last decade among
other towns in the watershed (U.S. Census Bureau,
2001). More than 236,000 people live in the Buzzard
Bay watershed, and nearly 20,000 marine vessels pass
through the Bay annually (Martin et al., 1996).
Current Projects,
Accomplishments, and Future
Goals
Some of the major environmental accomplishments
of the BB NEP include the following:
• The number of acres of shellfish beds closed
because of bacterial contamination has declined
nearly 25% since the Buzzards Bay Comprehensive
Conservation and Management Plan was
completed in 1991 (BB NEP, 1992; BBP NEP,
1999; CBB, 2003).
• The BB NEP assisted in the construction of a test
center to evaluate and promote advanced septic
treatment solutions for use in watersheds where
limits have been established on the discharge of
nitrogen, and the designation of Buzzards Bay as a
No-Discharge Area has helped to reduce bacteria
inputs to the Bay from vessel traffic.
94 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Buzzards Bay National Estuary Program
In 1989, the BB NEP gave $35,000 in grants to
the City of New Bedford and the Barnstable
County Health Department to upgrade their
laboratories and to pay for the analysis of extra
samples collected by the Massachusetts DMF.
DMF staff also trained local officials to assist with
the sanitary surveys in their communities (BBP
NEP, 1999).
CBB has created a nature trail for local schools,
organized beach cleanups, and promoted bilingual
stenciling of storm drains that discharge directly
into Buzzards Bay.
The BB NEP has developed two atlases to assist
with wetland-restoration efforts. One atlas identi-
fies 172 tidally restricted salt marshes and will be
helpful in efforts to remove tidal restrictions and
to improve and restore wetland health (Costa et
al., 2002). The development of this atlas has
already led to the restoration of 10 of these sites
(Personal communication, Costa, 2006). The
second atlas identifies filled and impaired wetlands
on public and conservation lands and is used to
identify wetland-restoration sites to meet mitiga-
tion requirements from other programs (Rockwell
et al., 2004; Rockwell and Williams, 2005).
The BB NEP recently completed an $85,000
grant entitled Managing Nitrogen Sensitive
Embayments through Land Conservation for work
in the Slocums River and Onset Bay (Wareham)
watersheds. The Massachusetts Environmental
Trust provided $29,000 in matching funds to this
project.
Nitrogen-analysis work begun in the mid-1990s
by the BB NEP for West Falmouth Harbor led to
the construction of a tertiary WWTP in 2005
that is designed to reduce nitrogen inputs to the
harbor (BB NEP, 2005).
New Bedford assessed its open space needs and
incorporated a Greenway Plan for the city.
Ongoing cleanup of New Bedford Harbor sedi-
ments represents one of the most promising
restoration efforts in the Buzzards Bay watershed.
The BB NEP Web site was used by state and
federal agencies to disseminate information about
the impacts of the 2003 oil spill in the Bay and
about ongoing cleanup activities. The BB NEP
also conducted an analysis of the volume of oil
spilled during the accident, and this analysis
contributed to the 98,000-gallon estimate adopted
by state and federal agencies. The BB NEP
continues to assist federal agencies in the NRDA
efforts related to the 2003 oil spill and in the
identification of potential restoration sites
(BB NEP, 2005).
In 2003, the BB NEP completed an atlas of
stormwater discharges and stormwater drainage
networks discharging to Buzzards Bay (Costa and
Bissette, 2003). This atlas has helped municipali-
ties achieve the mapping requirements for Phase II
National Pollution Discharge Elimination System
(NPDES) stormwater permits and identify
problem discharges that contribute to shellfish bed
closures. In partnership with a vocational high
school and a non-profit composed of municipal
officials, this effort expanded inland during 2005
to map all known discharges to wetlands located
in the watershed. An updated stormwater atlas
will be published in 2006 (BB NEP, 2005).
Since 1992, the BB NEP has awarded millions of
dollars in federal and state funds through their
ongoing municipal mini-grant program to assist
area municipalities and non-profits with the
implementation of recommendations contained in
the BB NEP CCMP. These mini-grants have
helped leverage other funds. The BB NEP also
assists municipalities in developing successful
grant applications to other programs (BB NEP,
2005).
National Estuary Program Coastal Condition Report 95
-------
Buzzards Bay National Estuary Program
The Buzzards Bay estuarine area is rated fair for
overall condition based on the NCA's four indices of
estuarine condition. The BB NEP findings show that
the four most significant environmental challenges
facing the Buzzards Bay estuarine area are toxic contam-
ination and oil spills, nitrogen loading and the effects of
eutrophication, natural habitat loss, and bacterial con-
tamination of Bay waters and shellfish-harvesting areas.
The Buzzards Bay Health Index is used to evaluate
water quality changes, with a scoring system based on
oxygen depletion, excess nutrient levels, transparency,
and algal blooms. Some of the key habitat indicators
used to monitor environmental changes in Buzzards
Bay include acres of eelgrass bed coverage, forest
coverage, and the amount of protected open space. In
addition, populations of several wildlife species are used
as primary indicators of environmental quality, including
the river herring and bay scallop. Populations of these
species have decreased due to human activities in the
watershed. New Bedford Harbor remains one area of
special concern for the BB NEP, but substantial progress
has been made in the remediation of contaminated
sediments. Buzzards Bay has avoided many estuary-wide
problems that plague other watersheds around the
country, but land-use practices and the growing local
population have impacted natural resources in the
32 small embayments in the Buzzards E>ay area.
96 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Narragansett Bay Estuary Program
Narragansett Bay Estuary Program
I
NARRAGANSETT BAY
ESTUARY PROGRAM
www.nbep.org
Background
Narragansett Bay is located primarily in Rhode
Island; however, 60% of the Bay's watershed area is
located in Massachusetts. The Narragansett Bay water-
shed area covers 1,650 mi2 and is one of the most
densely populated watersheds in the United States, with
almost 1,000 people/mi2 (RIDEM et al., 2000; U.S.
Census Bureau, 2001). Worcester and Fall River, MA,
and Providence, RI, are major cities within this water-
shed, and the Blackstone, Taunton, and Pawtuxet rivers
provide the majority of fresh water that flows into the
Bay. Narragansett Bay has approximately 147 mi2 of
surface water, with an average depth of 30 feet (NOAA,
1985). The Bay supports approximately 3,600 acres of
various types of salt marshes and 570 acres of tidal flats
(RIDEM et al., 2000) and contributes billions of dollars
to Rhode Island's economy through fisheries, tourism,
and marine industries. Quahog (hard clam), lobster,
bluefish, striped bass, and flatfish are sought after as
recreational and commercial fisheries species in
Narragansett Bay (Martin et al., 1996).
Between 1985 and 1992, more than 100 people
representing 45 federal, state, and local government
National Estuary Program Coastal Condition Report 97
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Narrogansett Boy Estuary Program
agencies; non-profit organizations; universities; marine
trade organizations; industry; communities; and citizens
met under the direction of the Narragansett Bay
Estuary Program (NBEP) to develop ways to preserve
and restore Narragansett Bay. The Narragansett Bay
Conservation & Management Plan (RIDEM, 1992) was
completed in 1993 and is being implemented by the
NBEP, which is now affiliated with the University of
Rhode Island (URI) Coastal Institute. In addition,
Rhode Island legislation created a Coordination Team
in 2004 for the management of Narragansett Bay. This
team formalizes the coordination among key state
agencies with respect to the Bay and its watershed.
Information on this and other Bay issues is available at
http://www.ci.uri.edu/RIBayTeam/default.html.
Environmental Concerns
Eutrophication, nutrient loading, and pathogens are
some of Narragansett Bay's major environmental
concerns. Although relatively well mixed and less
susceptible than other NEP estuaries to eutrophication,
Narragansett Bay is exhibiting an increasing array of
eutrophic-associated symptoms, including low dissolved
oxygen levels, fish kills, eelgrass loss, macroalgae
blooms, benthic community changes, and a shift in the
Bay's dominant fish community from bottom-dwelling
to water-column-dwelling species (RIDEM, 2003).
These symptoms have led the NBEP to focus on
nutrient inputs to the Bay, particularly nitrogen.
Currently, secondary treatment at WWTPs does not
reduce the high levels of nitrogen associated with
sewage (RIDEM et al., 2000). Excess nitrogen appears
to have caused episodes of oxygen depletion and fish
kills in fairly wide areas of the upper Bay, especially
during neap (very weak) summer tides, impairing
habitat quality and function (RIDEM, 2003). As for
pathogens, CSOs have been the major source of fecal
coliforms to the Bay in recent years, contributing
annual coliform loads nearly 4 orders of magnitude
higher than those from WWTPs and approximately
200 times the estimated annual loading from separate
storm drains (Governor's Narragansett Bay and
Watershed Planning Commission, 2004a).
Communities with older, failing septic systems also
contribute significantly to bacterial and nutrient-
loading. Together, these sources leave approximately
20% of Narragansett Bay permanently or conditionally
closed to shellfish harvesting because of actual or
suspected contamination from sewage-derived bacteria
and viruses (RIDEM, 2002).
Population Pressures
The population of the 10 NOAA-designated coastal
counties coincident with the NBEP study area increased
by 28% during a 40-year period, from 3.8 million
people in 1960 to almost 4.9 million people in 2000
(Figure 3-42) (U.S. Census Bureau, 1991; 2001). This
rate of population growth for the NBEP study area is
equivalent to the population growth rate of 24% for the
collective NEP-coincident coastal counties of the North-
east Coast region. In 2000, the population density of
these 10 coastal counties was 984 persons/mi2, slightly
lower than the population density of 1,055 persons/mi2
for the collective NEP-coincident coastal counties of the
Northeast Coast region (U.S. Census Bureau, 2001).
Population pressures for this NEP are likely high
because this estuary serves as a major metropolitan area
and a center of commerce and industrial development.
I960
2000
Figure 3-42. Population of NOAA-designated coastal counties
of the NBEP study area, 1960-2000 (U.S. Census Bureau, 1991;
2001).
98 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Narragansett Bay Estuary Program
NCA Indices of Estuarine
Condition—Narragansett Bay
The overall condition of Narragansett Bay is rated
poor based on the four NCA indices of estuarine
condition (Figure 3-43). The water quality index for
Narragansett Bay is rated fair, the benthic index is rated
fair to poor, and the sediment quality and fish tissue
contaminants indices are both rated poor. Figure 3-44
provides a summary of the percentage of estuarine area
rated good, fair, poor, or missing for each parameter
considered. Please refer to Table 1-24, 1-25, and 1-26
(Chapter 1) for a summary of the criteria used to
develop the rating for each index and component indi-
cator. By several measures, Narragansett Bay is a transi-
tional estuary that is more similar to estuaries further
south in the region. The Bay is distinct from estuaries in
the Acadian Province (north of Cape Cod), which are
characterized by higher tidal amplitude and tidal
flushing rates. This environmental assessment is based
on data from 56 NCA sites sampled in the NBEP
estuarine area in 2000 and 2001.
Overall Condition
Narragansett Bay
(1.75)
Water Quality Index (3)
Sediment Quality Index (I)
Benthic Index (1)
Fish Tissue Contaminants
Index (I)
Figure 3-43. The
overall condition of
the NBEP estuarine
area is poor
(U.S. EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Estuarine Area
Missing
Figure 3-44. Percentage of estuarine area achieving each rating
for all indices and component indicators — Narragansett Bay
(U.S. EPA/NCA).
Wickford Harbor on the west shore of Narragansett Bay (NBEP).
National Estuary Program Coastal Condition Report 99
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Narragansett Bay Estuary Program
Water Quality Index
The water quality index for Narragansett Bay is rated
fair (Figure 3-45), with 78% of the Narragansett Bay
estuarine area rated fair for water quality condition.
This index was developed using NCA data on five
component indicators: DIN, DIP, chlorophyll a, water
clarity, and dissolved oxygen. Relatively large areas of
the Bay had elevated concentrations of nutrients and
chlorophyll a—greater than neighboring bays to the
north and similar to estuaries further south in the
region. Narragansett Bay's pronounced signs of eutroph-
ication are probably attributed in part to the confined
nature of the estuary and the extensive urbanization in
upper Narragansett Bay. Water clarity was satisfactory
everywhere in the Bay, and low dissolved oxygen levels
were identified in a third of the Bay, predominantly in
the deeper portions of upper Narragansett Bay.
Dissolved Nitrogen and Phosphorus I
Narragansett Bay is rated good for DIN concentrations,
with 31 % of the estuarine area rated fair and only 2%
of the area rated poor. NCA data on DIN concentra-
tions were unavailable for 5% of the NBEP estuarine
area. DIP concentrations for Narragansett Bay are rated
fair, with 69% of the estuarine area rated fair and 14%
of die area rated poor. NCA data on DIP concentra-
tions were unavailable for 5% of the NBEP estuarine
area.
Chlorophyll a I Narragansett Bay is rated fair for
chlorophyll a, concentrations, with 51 % of the estuarine
area rated fair and 4% rated poor for this component
indicator. NCA data on chlorophyll a concentrations
were unavailable for 5% of the NBEP estuarine area.
Water Clarity I Narragansett Bay is rated good for
water clarity. Water clarity was rated poor at a sampling
site if light penetration at 1 meter was less than 10% of
surface illumination. Only 1 % of the Bay's estuarine
area was rated poor for water clarity, and 99% of the
area was rated good.
Dissolved Oxygen I Narragansett Bay is rated good
for dissolved oxygen concentrations. Fifty-seven percent
of the estuarine area was rated good for dissolved
oxygen concentrations, and 34% of area was rated fair.
None of the NBEP estuarine area was rated poor for
this component indicator, and NCA data on dissolved
oxygen concentrations were unavailable for 9% of the
area. Although no area of the Bay was rated poor on the
NCA sample dates, transient episodes of dissolved
oxygen at concentrations less than 2 mg/L are known to
occur in upper Narragansett Bay, often following
periods of minimal tidal mixing. Such events have been
documented by programs other than the NCA surveys,
using moored instrumentation and targeted sampling.
Results of these targeted oxygen and chlorophyll a
monitoring programs are available through the links at
http://www.nbep.org.
Water Quality Index - Narragansett Bay
Site Criteria: Number of component
indicators in poor or fair condition
• Good ~ No more than I is fair
OFair = I is poor, or 2 or more are fair
• Poor = 2 or more are poor
O Missing
Missing Po£r
5% ^ l/0
Good
16%
Figure 3-45. Water quality index data for Narragansett
2000-2001 (U.S. EPA/NCA).
1 00 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Narraganselt Bay Estuary Program
Sediment Quality Index
The sediment quality index for Narragansett Bay is
rated poor, with 15.3% of the estuarine area classified as
poor, just slightly greater than the 15% threshold used
to define this category (Figure 3-46). Sediment toxicity
was observed at two sites in Narragansett Bay, both of
which displayed sediment contamination. Moderate
and high concentrations of metals and organochlorine
chemicals, such as DDT and PCBs, were measured in
about half the Bay's sediment samples, with the highest
levels evident in the upper Bay tributaries (e.g., Taunton
and Providence rivers) and Greenwich Bay. Moderate
levels of TOC were also measured, again predominantly
in upper Narragansett Bay.
Sediment Quality Index - Narragansett Bay
Sediment Toxicity The sediment toxicity rating
for Narragansett Bay is poor. Seven percent of the Bay's
estuarine area was rated poor for sediment toxicity, and
NCA data were unavailable for 3% of the NBEP
estuarine area.
Sediment Contaminants I Narragansett Bay is
rated fair for sediment contaminant concentrations,
with 45% of the estuarine area rated good for this
component indicator and approximately 12% of the
area rated poor.
Total Organic Carbon I Narragansett Bay is rated
good for sediment TOC. Forty-four percent of the estu-
arine area was rated good for TOC concentrations, 27%
of the area was rated fair, and only 1 % of the area was
rated poor. NCA data on TOC concentrations were
unavailable for 28% of the NBEP estuarine area.
Site Criteria: Number and condition of component indicators
• Good = None are poor, and sediment contaminants is good
OFair = None are poor, and sediment contaminants is fair
• Poor = I or more are poor
O Missing
Figure 3-46. Sediment quality index data for Narragansett
2000-2001 (U.S. EPA/NCA).
College students studying icthyology at a salt pond in Bristol, Rl
(NBEP).
National Estuary Program Coastal Condition Report 101
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Narraganseft Bay Estuary Program
Benthic Index
Benthic condition in Narragansett Bay is rated fair to
poor, with 20% of the area receiving a poor designation
using the Virginian Province Benthic Index (Figure
3-47). Similar to the results for the water quality and
sediment quality indices, the impaired sites in the Bay
were largely restricted to upper Narragansett Bay and
the Bay's tributary rivers. Most of the sites designated as
impaired also had elevated levels of contaminants in the
sediments and can experience intermittent, but severe,
hypoxic events.
Benthic Index - Narragansett Bay
Site Criteria:
Virginian Province Benthic Index Score
• Good = > 0.0
• Poor = sO.O
O Missing
Missing
8% Poor
20%
Figure 3-47. Benthic index data for Narragansett I
2000-2001 (U.S. EPA/NCA).
Fish Tissue Contaminants Index
The fish tissue contaminants index for Narragansett
Bay is rated poor because 91 % of all fish tissue samples
analyzed for this estuary were rated poor (Figure 3-48).
All fish samples surveyed contained quantities of PCBs
that exceeded or fell within EPA's Advisory Guidance
values for fish consumption. High concentrations of
PCBs are commonly observed in fish from estuaries in
the Northeast Coast region.
Fish Tissue Contaminants Index - Narragansett Bay
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
OFair = Falls within Guidance range
• Poor = Exceeds Guidance range
Figure 3-48. Fish tissue contaminants index data for
Narragansett Bay, 2000-2001 (U.S. EPA/NCA).
1 02 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Narragansett Bay Estuary Program
Narragansett Bay Estuary
Program Indicators of Estuarine
Condition
Water and Sediment Quality
Few long-term, Bay-wide data sets exist for assessing
water quality trends in Narragansett Bay. Until very
recently, Rhode Island limited its environmental moni-
toring to fish population and bacterial surveys, such as
those used to certify shellfish-harvesting waters.
Although federal and university scientists have also
engaged in research and monitoring, these efforts were
for purposes other than management decision-making.
This has resulted in a critical data gap in management-
oriented, long-term water quality data for the Bay, espe-
cially with respect to excess nutrients, low dissolved
oxygen levels, and shifts in phytoplankton blooms
(RIDEM et al, 2000).
A more comprehensive monitoring network was
initiated in 1999 and involves a collaborative effort
among the Rhode Island Department of Environmental
Management (RIDEM) Division of Fish and Wildlife,
RIDEM Office of Water Resources, NBEP, Narragan-
sett Bay Commission, NOAA's National Marine
Fisheries Service (NMFS), EPA, National Estuarine
Research Reserve (NERR) at Prudence Island, URI,
Brown University, and Roger Williams University
(RIDEM et al., 2000). Infrastructure development and
data collection for this network include the following:
• Monthly neap-tide water-column surveys of
dissolved oxygen levels, salinity, and temperature
during the summer season are being coordinated
by the NBEP and mapped using GIS by Brown
University researchers.
• Continuous water quality monitoring stations at
10 sites have been strategically positioned around
Narragansett Bay. These stations have two contin-
uous monitoring probes: one set at a depth just
off the bottom of the Bay and a second set just
below the surface. Both probes measure salinity,
temperature, dissolved oxygen concentrations,
pH, and tidal amplitude. The near-surface probe
also measures chlorophyll a to track phyto-
plankton blooms. Additional information on these
stations is available at: http://www.dem.ri.gov/
bart/stations.htm.
• Surface sediment samples have been collected
from 43 sites in the Bay and analyzed for concen-
trations of heavy metals and organic contaminants
(RIDEM et al., 2000). Bay-wide surveys of sedi-
ment contamination have been conducted by the
NBEP in 1988 and 1989, as well as by URI in
1992, 1995, and 1998. Researchers have
completed three major studies to determine the
extent of sediment contamination in the Bay and
the coastal salt ponds of Rhode Island's South
Shore. Maps of sediment contamination and
trend information have been developed for levels
of copper, lead, and mercury in surface sediments
and are available at http://www.narrbay.org/
d_projects/rised/default.html.
An important step in enhancing Rhode Island's water
quality information is the recent development of a state-
wide monitoring strategy. This strategy is being
prepared under the review of a legislatively mandated
environmental monitoring collaborative and a Science
Advisory Committee, both of which have provided
input to target monitoring priorities for new funding
in the state's budget. Additional information on this
environmental monitoring is available online at
http://www.ci.uri.edu/Projects/RI-Monitoring/
OnlineResources.html.
The current and historic concentrations of man-
made pollutants (e.g., metals, nutrients, organic waste,
and other constituents) in Narragansett Bay's water and
sediments have demonstrated a clear north to south
gradient, with levels in the main Bay channels
decreasing towards the mouth of Bay. The highest
pollutant levels are located in the urbanized Provi-
dence/Seekonk tidal rivers and the Fall River/Taunton
River area, although poorly flushed coves and harbors
sometimes experience localized impacts from pollutants.
Since 1988, metals concentrations have decreased in
surface sediment samples collected from the heavily
urbanized portions of the study area and have remained
constant or increased slightly in samples from the mid-
Bay region (RIDEM et al., 2000).
National Estuary Program Coastal Condition Report 1 03
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Narragansett Bay Estuary Program
Fact-Based Findings in
Narragansett Bay
Rhode Island residents awoke on August 20, 2003,
to reports of a mass die-off of more than one million
fish in the states Greenwich Bay. The stunning fish kill
affected not only menhaden, but also other finfish, eels,
crabs, and, in particular, soft shell clams. This kill—the
worst in 50 years—was the result of prolonged oxygen
depletion, and while it was unexpected, it was not a
surprise. A report to the Governor prepared by RIDEM
and the NBEP subsequently documented that the fish
kill was not a simple or isolated event. Rather, it was
part of a much larger event going on in Greenwich Bay
and other parts of Narragansett Bay that year, as well as
part of a continuing trend observed in many preceding
years (RIDEM, 2003).
Hypoxia, or low dissolved oxygen levels, is often
caused by blooms of phytoplankton. Rapid phyto-
plankton growth occurs in response to an increase in
nutrients, especially nitrogen, in estuarine systems and
can result in large algal blooms. Although heavy rainfall
can lead to significant increases in nutrient loading via
stormwater, WWTPs are typically the major nutrient
source in densely populated areas. Other weather
factors, such as water temperature and wind direction
and strength, also play a roll, either by providing favor-
able conditions under which blooms can develop and
persist, or by disrupting the process through the mixing
and oxygenating of the water. Shallow bays and coves
may have poor circulation and flushing rates. These
waters are more vulnerable to nutrient loading, phyto-
plankton blooms, and hypoxic conditions (RIDEM,
2003).
Hypoxia can have a wide range of negative impacts
on the biological community. Severe hypoxia is associ-
ated with fish kills and the mass mortality of benthic
invertebrates and can have a structuring influence on
depth-specific zones for benthic communities. Even
moderate hypoxia can reduce growth rates of marine
organisms, cause shifts in the bottom-dwelling and
water-column-dwelling community structure, and alter
predator-prey interactions. Where hypoxia is a recurrent
problem, marine communities tend to shift dominance
from large, long-lived species to more tolerant or oppor-
tunistic, short-lived species (Deacutis, 1999).
Dissolved
Oxygen (mg/L)
mm o-i
mm 1-2
2-3
3-4
Bottom dissolved oxygen levels measured during an evening neap
tide on July 31, 2001. Areas with dissolved oxygen concentrations
less than 3 mg/L were exhibiting hypoxia (Emily Saarman, Brown
University).
1 04 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Narragansett Bay Estuary Program
In the upper half of Narragansett Bay, low dissolved
oxygen levels have occurred nearly every summer for at
least the past 10 years. As early as 1998, scientists began
systematically collecting evidence that suggested that low
dissolved oxygen problems were more widespread than
previously believed (RIDEM, 2003). This discovery
went against conventional wisdom that tidal energies in
the Bay were strong enough to preclude the develop-
ment of hypoxic conditions beyond the confines of the
Providence River in upper Narragansett Bay. For
example, studies to predict the sensitivity of various U.S.
estuaries to nutrient inputs had concluded that Narra-
gansett Bay was only moderately susceptible to high
levels of nitrogen inputs, with few demonstrated
impacts, such as hypoxia and loss of SAV. These findings
were due to a lack of any historical oxygen monitoring
data or published evidence of loss of SAV. Recent work
coordinated by the NBEP has now filled in this gap.
To test the hypothesis that significant portions of the
Bay were experiencing summer hypoxic conditions, the
NBEP organized a team of scientists and technically
trained volunteers (the "Insomniacs") to conduct night-
time surveys of dissolved oxygen during the hours from
midnight to 7 a.m. in the upper half of the Bay.
Beginning in 1999 and extending through 2004, a
flotilla of borrowed work boats and research vessels
conducted the monitoring from the Providence hurri-
cane barrier in the north to the northern tip of
Conanicut (Jamestown) Island in the south. Survey
dates were chosen to coincide with projected weak neap
tides, when physical conditions were most conducive to
the onset of hypoxia (e.g., warm water, stratified water
column, evening hours). Station placement was deter-
mined based on bathymetry, and a mix of deep and
shallow water stations were sampled.
The results of these evening oxygen surveys
confirmed that broad areas of upper Narragansett Bay
are subject to intermittent periods of hypoxia during
summer months, with probable ecological consequences
to benthic communities in these areas (RIDEM, 2003).
It is now known that specific areas of the Bay are under
temporary, but extreme stress from low-oxygen condi-
tions. Although most of these events do not result in
fish kills, such conditions can become harmful to the
Bay's ecology, driving fish out of the upper Bay,
stunting juvenile fish growth, and killing sensitive,
bottom-dwelling organisms that cannot escape. Areas
such as the Providence River, which experiences
frequent low-oxygen events, end up with altered
benthic communities where only the hardiest species
survive (Deacutis, 2004).
The evidence provided by these surveys also indi-
cated that although the contributing factors are
numerous and complex, a primary cause of die problem
is excess nutrient loading to die Bay. An analysis of the
2001-2002 data by the NBEP and Brown University
scientists (see map) showed that high-runoff, low-
salinity surface water was not required to produce very
low dissolved oxygen values, only a low-energy situation
(i.e., very weak neap tide and low winds) was required.
Nutrients are the source of the problem; algae provide
the organic "fuel" to the bacteria; and the weak neap
tides maintain the layering (stratification) necessary to
decrease oxygen in the lower water layers. This is why
weak neap tides are the periods of maximum risk for
hypoxic events in Narragansett Bay (RIDEM, 2003).
Although researchers cannot control the tides or the
weather, they can use information documented dirough
meticulous monitoring to better manage nutrient
inputs and make hypoxic events less frequent. The fish
kill was the wake-up call, but it was the data from the
dissolved oxygen surveys that laid the foundation for
unprecedented state legislation requiring nutrient reduc-
tions of least 40% to 50% from WWTPs discharging to
upper Narragansett Bay (Governors Narragansett Bay
and Watershed Planning Commission, 2004b).
Without another fish kill, the challenge now is to
maintain this level of monitoring to document
improvements in dissolved oxygen concentrations.
National Estuary Program Coastal Condition Report 105
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Narraganseft Bay Estuary Program
Habitat Quality
Using aerial photography and GIS applications,
collaborative efforts are being undertaken to map and
restore seagrass beds, salt marshes, shellfish beds, and
other critical estuarine habitats. Eelgrass in the Bay has
declined since the early 1950s as a result of water
pollution, coastal development, harbor dredging, and
other factors. In 1996, less than 100 acres of eelgrass
remained in Narragansett Bay, and eelgrass has
decreased 41% in coastal ponds due to increased
nitrogen loads. No significant eelgrass beds occur north
of Southern Prudence Island or in Greenwich Bay or
the Palmer River (RIDEM et al., 2000). SAV in
Narragansett Bay is currently being monitored by a
partnership consisting of the NBEP, Save The Bay, the
U.S. National Resource Conservation Service (NRCS),
and URL Links to maps of eelgrass, including NBEP
maps of all significant beds in the Bay, can be found at
http://www.nbep.org.
Living Resources
A variety of living resources are used as indicators of
ecological condition in Narragansett Bay, including
invertebrate assemblages; the abundance and health of
finfish, oysters, scallops, colonial nesting birds,
mammals, amphibians, and reptiles; fish kills; and the
diversity of benthic organisms and macroinvertebrates
(Kleinschmidt Energy and Water Resource Consultants,
2003)
Several different types of finfish and shellfish are
monitored in Narragansett Bay. In recent years, the
populations of the Bay's native bottom-dwelling fish,
such as winter flounder and tautog, have demonstrated
declining trends. Other water-column-dwelling species
have shown population increases. Scup and striped bass
stock have increased since the 1980s (Ardito, 2003b).
Scallop landings in the Bay have decreased from
300,000 bushels per day to negligible levels due to
eelgrass declines (Ardito, 2003a). After reaching record
levels in the 1990s, lobster landings are also decreasing
(Ardito, 2003b). Quahogs collected from the
Providence River have exhibited a low meat-to-shell
ratio, which may indicate that these shellfish are
experiencing stress due to low dissolved oxygen levels
(RIDEM et al., 2000).
Since data collection began, fish kills have been
reported in Greenwich Bay every year, except for 2000.
In August 2002, despite a severe drought, low oxygen
levels covered almost half of the Bay, including the
Providence River, East Passage, Upper Bay, and West
Passage. Although Greenwich Bay was not directly
measured, researchers working in the area at the time
corroborate that a severe low oxygen event also occurred
at this location in 2002. The severe hypoxia in the 2002
event was clearly not due to rainfall, but to baseline
conditions driven by nutrients from the point sources
(e.g., WWTPs) and groundwater entering the Bay due
to low river flow (RIDEM, 2003).
Environmental Stressors
An estimated 160 private marinas, yacht clubs, boat
yards, town docks, and launching ramps operated in the
Bay in 1989, with more than 40,000 boats registered in
Rhode Island (RIDEM, 1992; NBEP, 2002). Recogniz-
ing the need for additional pump-out facilities to main-
tain water quality standards, improve water quality, and
protect open shellfish beds, NBEP staff developed the
Marina Pumpout Siting Plan for Narragansett Bay, RI
(NBEP, 1993). The result of this plan was the 1998
designation of Rhode Island's coastal waters as a No-
Discharge Zone for boat sewage and the development of
30 additional pump-out facilities in the Bay for marine
toilets (up from 14 in 1993), with several more under
development (RIDEM et al., 2000).
Wetlands and yachts in Wickford Harbor (NBEP).
106 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
NarraganseH Bay Estuary Program
Current Projects,
Accomplishments, and Future
Goals
The upgrading of municipal WWTPs has reduced
biochemical oxygen demand (RIDEM et al., 2000),
and construction of a giant storage system (at a cost
of more than $300 million) is underway and will
eventually prevent the discharge of some 62 million
gallons of untreated sewage to the Bay via CSOs during
heavy rains (NBEP, 2005). Pretreatment requirements
have radically reduced the amount of metals discharged
in wastewater, as has the elimination of lead from
gasoline (RIDEM et al., 2000). In addition, a law was
passed in 2004 committing the State of Rhode Island
to a 50% decrease in recorded 1995—1996 levels of
nitrogen loads from major WWTPs to the Bay by 2008
(An Act Relating to Waters and Navigation—Water Pollu-
tion, H-8638). Finally, Rhode Island has committed to
the initiation of a comprehensive monitoring program
and adoption of a suite of indicators for the Bay and its
watersheds that will track such ecosystem characteristics
as land cover/use, demographics, water and sediment
quality, hydrology, habitat quality and quantity, produc-
tivity, and species assemblages and relative abundance
(RIDEM et al., 2000; Kleinschmidt Energy and Water
Resource Consultants, 2003).
The NBEP will continue to serve as a coordinating
entity for Bay actions and for organizing and creating
collaborative efforts to meet common goals. The
program will focus on expanding its partnership
activities with municipalities, agencies, and non-profit
organizations; securing the scientific data needed to
support policy initiatives and develop effective manage-
ment strategies; providing outreach on the Bay and
watershed ecosystem through workshops, conferences,
and educational events; securing additional funding for
CCMP implementation; addressing priority water
quality and living resource issues in the Bay; and
identifying and analyzing emerging Bay issues (e.g.,
introduced species).
Conclusion
Based on the four indices of estuarine condition used
by the NCA, the overall condition of Narragansett Bay
is rated poor. Although relatively well mixed and less
susceptible than other estuaries to eutrophication,
Narragansett Bay is exhibiting an increasing array of
eutrophic-associated symptoms, including low dissolved
oxygen levels, fish kills, eelgrass loss, macroalgae
blooms, benthic community changes, and a shift in the
Bay's dominant fish community from bottom-dwelling
to water-column-dwelling species. Workshops held in
2001 concluded that monitoring in Narragansett Bay
remains under funded, that significant data gaps exist,
and that there is a lack of coordination of monitoring
efforts and a lack of integration and analysis of existing
data. Since the workshops, the process of addressing
these concerns is well underway, with a significant
investment in both Bay monitoring and in the reduc-
tion of nutrients entering the Bay.
High school students having fun while cleaning up a beach at
Conimicut Point on upper Narragansett Bay (NBEP).
National Estuary Program Coastal Condition Report 107
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Long Island Sound Study
Long Island Sound Study
PLONG
ISLAND
SOUND
STUDY
www.longislandsoundstudy.net
Background
Long Island Sound is one of the most significant
coastal areas in the nation, with a watershed that
includes an area of more than 16,000 mi2 and that
traverses all of Connecticut and parts of New York,
Massachusetts, New Hampshire, Rhode Island, and
Vermont (LISS, 1994). Four major rivers (Connecticut,
Housatonic, Quinnipiac, and Thames) deliver fresh
water to the Sound, which is approximately 110 miles
long and is bounded by Connecticut and New York's
Westchester County to the north, by New York City to
the west, and by Long Island to the south.
Research shows that at least $5 billion is generated
annually in this region from boating, commercial and
sport fishing, and beach tourism (LISS, 1994). More
than 170 species of finfish can be found in the Sound,
including at least 50 species that spawn in the Sound
and 21 tropical species that stray into this region on a
seasonal basis (LISS, 2006). Species such as winter
flounder, tautog, bluefish, diamondback terrapins, and
many others have been over-harvested to the point
where resource management is critical to maintaining
stocks (LISS, 2003c).
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Long Island Sound Study
The Long Island Sound Study (LISS) began in 1985
as an innovative effort by EPA, New York, and
Connecticut to restore and protect Long Island Sound.
Two years later, under the newly established NEP,
Congress designated Long Island Sound as an Estuary
of National Significance. In its early years, the LISS
Management Conference, composed of EPA scientists,
representatives from other federal agencies, New York
and Connecticut state partners, citizens, and local busi-
ness representatives, worked together to draft a CCMP
to guide efforts to manage the Sound. Completed in
1994, LISS's The Comprehensive Conservation and
Management Plan (LISS, 1994) identified specific
priority issues for the LISS, including low dissolved
oxygen levels (hypoxia), pathogen contamination in
swimming waters and shellfish-harvesting areas,
declining populations of living resources, degradation of
coastal habitats, contamination of bottom sediments by
toxics, and increasing volumes of floatable trash and
debris.
Environmental Concerns
Environmental concerns in Long Island Sound
include hypoxia, toxic substances, and land-use changes.
Low levels of dissolved oxygen have caused significant
adverse ecological effects in the bottom-water habitats
of Long Island Sound and affected the area's living
resources (LISS, 1994). Since 1987, the areal extent and
temporal duration of hypoxia in the Sound have exhib-
ited improving trends, due in part to nitrogen-reduction
efforts, such as sewage treatment plant (STP) upgrades.
Toxic substances, including metals and organic chemi-
cals, enter the Sound from manufacturing sources,
stormwater runoff, household cleaning and pest-control
products, and automobile and power plant emissions.
Although releases of many contaminants in the water-
shed have declined since the late 1980s, contaminants
continue to pose a threat to living resources in Long
Island Sound (LISS, 2003c). The loss of wetlands,
forests, farm areas, and other open spaces to increased
population, development, and urban sprawl has
increased pollution and stormwater runoff, altered land
surfaces, decreased natural areas, and restricted access to
the Sound (LISS, 1994; LISS, 2003c).
Population Pressures
The population of the 15 NOAA-designated coastal
counties in New York and Connecticut coincident with
the LISS study area increased by only 14% during a
40-year period, from 12.9 million people in 1960 to
14.6 million people in 2000 (Figure 3-49) (U.S. Census
Bureau, 1991; 2001). This rate of population growth
for the LISS study area is roughly half the population
growth rate of 24% for the collective NEP-coincident
coastal counties of the Northeast Coast region. In 2000,
the population density of these 15 coastal counties was
2,170 persons/mi2, more than twice as high as the
population density of 1,055 persons/mi2 for the collec-
tive NEP-coincident coastal counties of the Northeast
Coast region (U.S. Census Bureau, 2001) and second
only to New York/New Jersey Harbor in population
density (3,097 persons/mi2). Population pressures for
this study area are high because the Sound serves the
population of New York City and its surrounding
suburban communities—the largest center for
commerce on the Northeast Coast.
15
= 10
I960
2000
Figure 3-49. Population of NOAA-designated coastal counties
of the LISS study area, 1960-2000 (U.S. Census Bureau, 1991;
2001).
National Estuary Program Coastal Condition Report 109
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Long Island Sound Study
NCA Indices of Estuarine
Condition—Long island Sound
The overall condition of Long Island Sound is rated
poor based on the four NCA indices of estuarine condi-
tion (Figure 3-50). The water quality index for Long
Island Sound is rated fair, and the sediment quality,
benthic, and fish tissue contaminants indices are each
rated poor. Clear gradients in most parameters were
evident in the Sound, with more degraded conditions
noted in the western, more urbanized portion of the
Sound. Figure 3-51 provides a summary of the
percentage of estuarine area rated good, fair, poor, or
missing for each parameter considered. This assessment
is based on data from 86 NCA sites sampled in the
LISS estuarine area in 2000 and 2001.
Overall Condition
Long Island Sound
(1.5)
Water Quality Index (3)
Sediment Quality Index (I)
Benthic Index (I)
Fish Tissue Contaminants
Index (I)
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
Figure 3-50. The
overall condition of
the LISS estuarine
area is poor (U.S.
EPA/NCA).
20 40 60 80 100
Percent NEP Estuarine Area
I Missing
Figure 3-51. Percentage of estuarine area achieving each rating
for all indices and component indicators — Long Island Sound
(U.S. EPA/NCA).
The Nissequogue River
flows north into Long
Island Sound (Eileen
Keenan, NY Sea Grant).
110 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Long Island Sound Study
Water Quality Index
The water quality index for Long Island Sound is
rated fair (Figure 3-52). This index was developed using
data on five component indicators measured by the
NCA: DIN, DIP, chlorophyll a, water clarity, and
dissolved oxygen.
Dissolved Nitrogen and Phosphorus I Long
Island Sound is rated good for DIN concentrations.
Fifty-three percent of the estuarine area was rated good
for DIN concentrations, and 9% of the area was rated
fair. None of the estuarine area was rated poor for DIN,
and NCA data on DIN concentrations were unavailable
for 39% of the LISS estuarine area.
Water Quality Index - Long Island Sound
Site Criteria: Number of component indicators
in poor or fair condition
• Good = No more than I is fair
OFair = I is poor, or 2 or more are fair
• Poor ~ 2 or more are poor
O Missing
Figure 3-52. Water quality index data for Long Island Sound,
2000-2001 (U.S. EPA/NCA).
Long Island Sound is rated fair for DIP concentra-
tions. High to moderate DIP concentrations were
common throughout the Sound, particularly in the
tributaries and offshore waters of Connecticut. DIP
concentrations were rated good in only 16% of the
estuarine area and fair in 69% of the area. Ten percent
of the estuarine area was rated poor for this component
indicator, and NCA data on DIP concentrations were
unavailable for 5% of the LISS estuarine area.
Chlorophyll a I Long Island Sound is rated good
for chlorophyll a concentrations. Relatively large areas
of the Sound had moderately elevated concentrations of
chlorophyll a that were distributed uniformly through-
out the estuarine area. Fifty-six percent of the estuarine
area was rated good for chlorophyll a concentrations,
36% was rated fair, 4% was rated poor, and NCA data
were unavailable for 4% of the LISS estuarine area.
Water Clarity I Water clarity is rated good for
Long Island Sound. Water clarity was rated poor at a
sampling site if light penetration at 1 meter was less
than 10% of surface illumination. No area of the Sound
was rated poor or fair for water clarity; however, NCA
data on water clarity were unavailable for 63% of the
LISS estuarine area.
Dissolved Oxygen Long Island Sound is rated fair
for dissolved oxygen concentrations. A large area of the
Sound had depleted levels of dissolved oxygen in
bottom waters, with 47% of the estuarine area rated fair
for this component indicator and 10% of the area rated
poor. The oxygen-depleted waters were largely restricted
to the western portions of the Sound. NCA data on
dissolved oxygen concentrations were unavailable for
2% of the LISS estuarine area.
National Estuary Program Coastal Condition Report 111
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Long Island Sound Study
Sediment Quality Index
The sediment quality index for Long Island Sound is
rated poor, with 32% of the estuarine area rated poor
and 16% of the area rated fair for sediment quality
condition (Figure 3-53). Ten percent (8 sites) of the
Sound's estuarine area had sediments that were toxic to
amphipods; however, there was little co-occurrence of
toxicity and sediment contamination at the impaired
sites, which were grouped in the western and far eastern
ends of the Sound. A similar distribution was noted for
sites contaminated by moderate and high concentra-
tions of metals and DDT. TOC conditions were not
well characterized for Long Island Sound because data
were unavailable for two-thirds of the LISS estuarine
area.
Sediment Quality Index - Long Island Sound
Sediment Toxicity I Long Island Sound is rated
poor for sediment toxicity, with 10% of the estuarine
area rated poor for this component indicator. NCA data
on sediment toxicity were unavailable for 7% of the
LISS estuarine area.
Sediment Contaminants I Long Island Sound is
rated poor for sediment contaminant concentrations,
with approximately 24% of the estuarine area rated
poor for this component indicator and 18% of the area
rated fair.
Total Organic Carbon I Long Island Sound is
rated good for sediment TOC. Seventeen percent of the
estuarine area was rated good for TOC concentrations,
and 19% was rated fair. Only 1% of the estuarine area
was rated poor for TOC concentrations; however, NCA
data on TOC concentrations were unavailable for 63%
of the LISS estuarine area.
Site Criteria: Number and condition of component indicators
• Good = None are poor, and sediment contaminants is good
OFair = None are poor, and sediment contaminants is fair
• Poor = I or more are poor
O Missing
Figure 3-53. Sediment quality index data for Long Island Sound,
2000-2001 (U.S. EPA/NCA).
112 National Estuary Program Coastal Condition Report
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CHAPTER 3 I NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Long Island
**
Benthic Index
*+•
Fish Tissue Contaminants
Sound Study
Index
Benthic community diversity in Long Island Sound
is rated poor based on the Virginian Province Benthic
Index (Figure 3-54). The east to west gradient that was
noticeable in other parameters is absent in the results
for the benthic index. Rather, the best results are clus-
tered in the western and central portions of the Sound,
and the poorest results are grouped in the nearshore
waters and tributaries in New York and Connecticut.
Consequently, there was a poor correlation between
benthic condition and measures of sediment contami-
nant impairment.
Benthic Index - Long Island Sound
The fish tissue contaminants index for Long Island
Sound is rated poor. Relatively few fish samples (13)
from Long Island Sound were analyzed for contaminant
concentrations; however, roughly a third fell into each
of the good, fair, and poor categories (Figure 3-55).
High levels of PCBs were responsible for nearly all of
the samples rated poor, similar to conditions in other
NEP estuaries of the Northeast Coast region.
Fish Tissue Contaminants Index - Long Island Sound
J_
Site Criteria:
Virginian Province Benthic Index Score
• Good = > 0.0
• Poor = sO.O
O Missing
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
OFair = Falls within Guidance range
• Poor = Exceeds Guidance range
Figure 3-54. Benthic index data for Long Island Sound,
2000-2001 (U.S. EPA/NCA).
Figure 3-55. Fish tissue contaminants index data for Long Island
Sound, 2000-2001 (U.S. EPA/NCA).
I
National Estuary Program Coastal Condition Report 113
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Long Island Sound Study
Tidal Marsh Loss in Long Island
Sound
Throughout the Northeast, tidal marshes are turning
into mudflats, resulting in the loss of important vege-
tated habitats for wading birds, juvenile fish, and inver-
tebrates (LISS, 2004b). Tidal marsh loss—-the loss of
elevation relative to sea level and the conversion of vege-
tated marsh to mudflat— has been observed in Long
Island Sound since the 1980s; however, recent studies
indicate that the magnitude and distribution of these
losses, which primarily occur in the western Sound, are
far greater than previously realized (LISS, 2003b). At a
130-acre site on the Quinnipiac River, for example,
nearly half of the brackish marshes have disappeared
since 1974. The LISS is working to gain an under-
standing of and draw attention to this phenomenon
(LISS, 2004b).
Significant areas of tidal wetland loss within Long
Island Sound and of coastal wetlands elsewhere in New
England have prompted scientists to investigate changes
in these marshes with respect to relative sea-level rise.
In 2001, Dr. Nels Barrett of the NRCS-Connecticut
proposed establishing a long-term program to monitor
the elevation dynamics of tidal marshes using surface
elevation tables (SETs), a technique promoted by Dr.
Don Cahoon of the U.S. Geological Survey (USGS)
Pawtuxent Wildlife Research Center. SETs are tools for
measuring changes in marsh surface elevation and
sedimentation. With funding from the Long Island
Sound Fund— a grant program administered by the
Connecticut Department of Environmental Protection
(CT DEP)— Dr. Barrett partnered with Dr. Cahoon
and Dr. R. Scott Warren of Connecticut College to
establish SET arrays at Barn Island in Stonington, CT.
The nine SET benchmarks were constructed as a first
step toward an envisioned network of SETs throughout
the Sound. To help gather baseline information on
marsh health, a network of 15 SETs is being established
around the Sound. The CT DEP s Office of Long Island
Sound Program, with funding from Connecticut's
Coastal Zone Management Program, has purchased an
additional 20 SET arrays that will be deployed in Con-
necticut marshes in 2005. The LISS has also provided
support for the New York State Department of
Environmental Conservation (NYSDEC), in partner-
ship with the Marine Sciences Research Center at Stony
Brook University, to install and monitor SETs in New
York marshes (Barrett and Warren, 2005; LISS, 2005b).
In June 2003, the LISS and the NYSDEC held a
workshop to share information regarding the possible
causes of tidal marsh loss in the Sound. The participants
highlighted the need to gather baseline information on
the health and spatial distribution of the Sound's
marshes and identified priority research topics. The LISS
is helping to address these recommendations by support-
ing projects to examine coastal wetland trends in the
Sound and to investigate potential causes of the
observed subsidence (LISS, 2004b).
A researcher collects a sediment core at Sherwood Island in
a patch of Spartina alterniflora surrounded by a mudflat (Suzy
Allman).
114 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Long Island Sound Study
I
A researcher takes SET elevation measures at Barn Island (Dr. R. Scott Warren).
The LISS is funding efforts by the CT DEP and
NYSDEC to determine the rates of tidal marsh loss in
the Sound. Through an agreement with the CT DEP,
the FWS is interpreting wetland boundaries from
archival aerial photographs taken between 1974 and
2000 of strategic coves and tidal rivers in the Connect-
icut portion of the western Sound. In New York, the
NYSDEC will acquire aerial infrared photography of
tidal marshes and will examine wetland trends by
comparing these images with aerial photographs taken
in 1930 (LISS, 2005b).
With support from an LISS research grant, Dr.
Daniel Civco of the University of Connecticut and Dr.
Martha Gilmore of Wesleyan University are collabo-
rating on a project to identify and delineate coastal
marshes and to distinguish various types of marsh vege-
tation. In addition, they are developing a cost-effective
way to track changes in the condition of wetlands over
time using remote-sensing satellite imagery coupled
with in situ radiometry and other field data collection.
These data sets and protocols can help provide coastal
resource managers, municipal officials, and researchers
with baseline information for current land management
and long-term monitoring of habitat changes (LISS,
2004b).
One hypothesis formulated at the tidal wetlands-loss
workshop was that excessive loading of nutrients, such
as nitrogen and phosphorus, plays a role in causing
marsh loss. In 2004, the LISS awarded a research grant
to Dr. Shimon Anisfeld of Yale University to investigate
the possible role of nutrients in contributing to marsh
drowning. Dr. Anisfeld s research focuses on whether
high levels of nitrogen, while increasing above-ground
plant production, might actually decrease the growth of
below-ground material, such as roots. Dr. Anisfeld is
also testing a theory that, as nutrients increase in the
marsh peat, bacteria increase and consume more organic
matter. Dr. Anisfeld is assessing site conditions and
factors, including nutrient levels, at three Connecticut
marshes: a degraded marsh at Sherwood Island State
Park in Westport, a stable marsh at Hoadley Creek in
Guilford, and a restored marsh at Jarvis Creek in
Branford (LISS, 2004b).
These efforts to monitor trends in the Long Island
Sound's coastal habitats and investigate potential causes
of tidal marsh loss are critical to understanding the
changes occurring in the Sound's marshes. The partner-
ships fostered by the LISS provide a unique opportunity
for the States of Connecticut and New York, local
researchers, and federal agencies to work together to
develop strategies to minimize tidal marsh loss and
protect coastal habitats.
For more information, visit http://www.
longislandsoundstudy.net.
National Estuary Program Coastal Condition Report 115
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Long Island Sound Study
Long Islland Sound Study
Indicators of Estuarine Condition
The LISS uses more than 40 specific environmental
measures to assess the ecological condition of Long
Island Sound (LISS, 2003c). These indicators are
primarily associated with water and sediment quality,
habitat restoration and protection, and fish and wildlife
concerns.
Water and Sediment Quality
The following indicators have been formalized as
measures used by the CT DEP and NYSDEC to
evaluate water and sediment quality in the Long Island
Sound estuarine area:
• Hypoxia (areal extent and duration of hypoxic
zones, with dissolved oxygen levels less than 3
mg/L)
• Nitrogen concentrations in several constituent
forms in tributaries and from both point and non-
point sources
• Total phosphorus concentrations in tributaries
• Chlorophyll a concentrations
• Number of beach closure days (New York and
Connecticut)
• Total fecal coliform counts in tributaries.
Hypoxia is most severe and prevalent in the western
portion of Long Island Sound (NYSDEC, 2006). Since
1991, the CT DEP has conducted a comprehensive
water quality monitoring program in the Sound that
allows the LISS to track how hypoxia varies from year
to year. Between October and May, water quality
450
Maximum Area and Duration of Hypoxia
Hypoxia is defined as less than 3.0 mg/L
Area of Hypoxia D Duration of Hypoxia
1987 1989 1991 1993 1995 1997 1999 2001
Year
Figure 3-56. Hypoxia in Long Island Sound appears to have
generally improved since 1987 (data obtained from CT DEP).
samples are collected once a month from 17 sites. Bi-
weekly hypoxia surveys start in mid-June and end in
September, with up to 36 sites being sampled in each
survey (LISS, 2004b). The Interstate Environmental
Commission (IEC) conducts additional monitoring of
the western Sound for dissolved oxygen levels during
the summer months. The area and duration of hypoxic
occurences in the Sound have fluctuated from year to
year, but appear to have improved since the late 1980s
(NYSDEC, 2006) (Figure 3-56).
Trends in nitrogen concentrations in tributaries to
the Sound have varied between 1971 and 1998. In
general, total nitrogen increased from 1975 to 1988 and
began to decline thereafter (Trench and Vecchia, 2002).
In the Connecticut River, which discharges 70% of
fresh water to the Sound, downward trends in total
nitrogen since 1988 are most likely the result of
improved nitrogen removal at municipal WWTPs, but
could also relate to changes in land use (i.e., agricultural
to residential or forest) (Mullaney, 2004). Reductions in
nitrogen concentrations in the Connecticut River are
likely not related to atmospheric sources because wet
deposition of nitrogen oxides in precipitation has
remained relatively unchanged since the 1980s (Driscoll
et al., 2001). Figure 3-57 shows a decreasing trend in
overall nitrogen loading to the Sound between 1991
and 2001. In general, Sound-wide nitrogen loads from
point sources have also decreased (LISS, 2003a)t For
example, improvements to STPs in New York and
Connecticut reduced the amount of nitrogen entering
the Sound by 28% between 1994 and 2003 (LISS,
2003b).
80,000
70,000
60,000
50,000
40,000
30,000
20,000
10,000
0
• Coastal Point Source
• Coastal Non-point Source
D Riverine Nitrogen
1991 1992 1993 1994 1995 19961997 1998 199920002001
Year
ce: USGS and CT DEP
Figure 3-57. Trends in nitrogen loading to Long Island Sound
(data obtained from USGS and CT DEP).
116 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Long Island Sound Sludy
Total phosphorus concentrations are measured in
the tributaries of Long Island Sound to assess the
effect of total loading on overall nutrient balance and
eutrophication. Phosphorus inputs are having far less
impact than nitrogen inputs from point source and
non-point sources in this system. Total phosphorus
levels showed a declining trend in Long Island Sound
tributaries between the years 1981 and 1988, most
likely due to improvements at municipal STPs and the
declining use of phosphate-based detergents (Trench
and Korzendorfer, 1997).
Chlorophyll a levels are monitored closely to
evaluate nutrient over-enrichment and to observe the
effects of point and non-point source loadings of
nitrogen to the Sound. In recent years, chlorophyll a
measures have demonstrated erratic results, but high
concentrations have coincided with large algal bloom
events. These events have been detrimental to the
growth of eelgrass and other SAV and have led to
conditions of hypoxia in near-bottom waters. In 2003,
chlorophyll a levels in western Long Island Sound
were recorded as high as 25 ug/L, with average levels
around 15 ug/L. Both peak and average chlorophyll a
levels were higher between 2001 and 2003 than they
were between 1998 and 2000 (LISS, 2003a).
One of the key indicators for pathogen contamina-
tion in Long Island Sound is the number of beach
closure days associated with bacteria levels in water.
New York, Connecticut, and EPA coordinate to test
waters at 240 swimming beaches to determine
whether water is safe from disease-causing pathogens.
Sewage pump station overflows accounted for some
beach closures, whereas all other closures were caused
by rain or high bacteria levels. Beach closures during
the past 10 years do not indicate any trend in
pathogen contamination in Long Island Sound
(Figure 3-58).
Total fecal coliform counts are also measured in
Long Island Sound tributaries to help evaluate
pathogen contamination from a variety of sources.
Results of monitoring for fecal coliform have been
highly variable in the past few years.
500
450
400
350
300
250
200
ISO
100
50
0
D CT Pathogen Closures
D NY Pathogen Closures
•*!)
1993 1994 1995 1996 1997 1998 1999 2000 2001 2002
Year
Figure 3-58. Trends in beach closures in Long Island Sound
(1993-2002) (data obtained from CT DEP and NYSDEC).
Habitat Quality
The following two measures are used as indicators to
determine the success or failure of habitat restoration
and protection efforts implemented by state agencies
and EPA in Long Island Sound:
• Acres of coastal habitat restored
• Number of river miles restored for anadromous
(migratory) fish passage (LISS, 2005a).
In 1998, Connecticut, New York, and EPA created
the LISS Habitat Restoration Initiative (HRI) and
adopted goals to restore 2,000 acres of the Sound's
coastal habitat by the year 2008. The majority of
restoration projects in Long Island Sound have targeted
tidal wetlands that were degraded by human develop-
ment or tidal restrictions. Between 1998 and 2003,
almost 500 acres of coastal habitat were restored
through the HRI (LISS, 2003c).
The HRI also uses the number of river miles restored
for anadromous (migratory) fish passage as a major
indicator for the success of habitat restoration. In 1998,
the LISS adopted a goal of restoring 100 miles of
migratory river corridors for anadromous fish by 2008.
As of 2003, 52 miles of stream had been restored for
fish migration, and as a result, species such as striped
bass, blueback herring, and American shad are now
swimming into formerly inaccessible streams (LISS,
2003c; LISS, 2004a). Rebuilding riverine migratory
corridors creates huge benefits for both recreational and
commercial fisheries in this region.
National Estuary Program Coastal Condition Report 117
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Long Island Sound Study
Living Resources
Living resource indicators tracked by the LISS
include finfish and shellfish abundance in Long Island
Sound. In the late 1980s and early 1990s, several
marine fish stocks were declining in the Sound, and as a
result, management actions to limit exploitation and
rebuild stocks were instituted. Scup and striped bass
have responded well to management efforts, and popu-
lations of these species are rebounding; however, species
that favor cold water temperatures, such as winter
flounder, continue to experience declines. Traditionally,
the most economically important shellfish harvested in
the Sound have been oysters and lobsters. The
harvesting of Long Island Sound oysters has declined
significantly since the peak year of 1992 due to two
deadly parasitic diseases, MSX and Dermo. The Sound's
lobster harvests, which had developed into a $40
million a year industry by 1997, have also dropped
dramatically as the result of a variety of infections and
diseases (LISS, 2003c). The poor health of the Sound's
lobsters and oysters has affected the Sound's marine
economy, recreational fishers, and the ecosystem.
Bird populations around the Sound are threatened
by habitat loss and by human and predator intrusion
into nesting areas. The LISS bird population indicators
focus on osprey, least terns, and piping plovers. As a
result of efforts to build nesting platforms and to
protect nests, the number of osprey and piping plover
nesting adults is increasing around the Sound (LISS,
2003c); however, the number of nesting least tern adults
has declined since the 1980s (LISS, 2003a).
Environmental Stressors
More than 8 million people live in the Long Island
Sound watershed, and more than 20 million live within
about an hour's drive of the Sound. Approximately 60%
of total nitrogen inputs to the Sound come from STPs,
and stormwater runoff carries contaminants from roads,
parking lots, and construction sites to the Sound (LISS,
2003c).
The primary sources of bacterial pathogens in the
Sound's waters are CSOs, malfunctioning STPs, illegal
connections to storm sewers, malfunctioning septic
systems, and discharges from marine vessels. Pathogen
contamination has impacted the commercial economy
of the region and has led to closings at many Long
Island Sound beaches and shellfish-harvesting areas
(LISS, 2003a). In New York alone, more than 48,000
acres of shellfish beds were completely closed or
restricted from harvest in 1990 due to pathogen conta-
mination (U.S. EPA, 2006c).
Progress continues to be made in reducing bacterial
pathogens in Long Island Sound. In 2002, 134 marine
vessel pump-out stations were servicing the Sound
(compared to just 43 in 1995), and new stations
continue to be built (LISS, 2003a). Fecal coliform
counts in Long Island Sound tributaries displayed a
recognizable downward trend over time between 1981
and 1988, possibly due to better agricultural practices
and improvements at municipal STPs (Trench and
Korzendorfer, 1997).
Current Projects,
Accomplishments, and Future
Goals
Some of the current projects and recent accomplish-
ments of the LISS are summarized below:
• The total point-source nitrogen load to the Sound
continued a 14-year declining trend through
2003. The total 2003 load from New York and
Connecticut point sources is estimated at 159,969
Ibs/day, a decrease of more than 50,500 Ibs/day
from the 1990s baseline (LISS, 2003a).
• As of December 2003, 30 municipal STPs in
Connecticut have completed upgrades, including
nitrogen removal, at a cost of more than $340
million (LISS, 2004a).
• Of the nine LISS-funded research projects
awarded in 2000 and 2002, five have been
completed and four are ongoing. Completed
projects include studies of the causes and extent of
lobster morbidity and mortality; isotope tracers of
nitrates in the Sound to help distinguish sources
of pollution; metal contaminant concentrations in
Long Island Sound sediments over time; bottom
water and sediments at critical sites in Long Island
Sound; and the effects of trace metals, organic
carbon, and inorganic nutrients in surface waters
118 National Estuary Program Coastal Condition Report
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i
CHAPTER 3 • NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Long Island Sound Study
on phytoplankton growth. Projects that are
ongoing include studies of phytoplankton
dynamics to determine shifts in primary produc-
tivity, water column oxygen production, and
consumption; new approaches for assessing muta-
genic risk of contaminants in Long Island Sound;
and the status and productivity of salt marsh
breeding sparrows.
Future goals outlined in the LISS CCMP include the
following:
• Low dissolved oxygen concentrations - Reduce
nitrogen from STPs and other point sources;
reduce nitrogen loads from non-point sources;
continue the management of hypoxia; fund
implementation of hypoxia management plans;
and monitor and assess hypoxic conditions in the
Sound.
• Pathogens - Control pathogen contamination to
Long Island Sound from CSOs, non-point
sources, STPs, vessel discharges, and individual
on-site systems/discharges; provide public educa-
tion regarding causes of contamination; and
improve monitoring and assessment methods.
• Toxic substances - Control and prevent toxic
contamination from all sources; address sediment
contamination; improve human health risk
management; monitor and assess toxic contami-
nants; and conduct research to investigate toxic
contamination.
• Floatable debris — Control floatable debris from
CSOs and storm sewers and increase floatable
debris cleanup efforts.
• Habitats - Restore and enhance aquatic and
terrestrial habitats; protect and acquire habitat;
develop inventories and management strategies for
aquatic and terrestrial habitats; manage endan-
gered and threatened species, harvested species,
and exotic and nuisance species; educate the
public; develop databases; conduct Sound-wide
and site-specific research and monitoring; and
conduct living resources and habitat research.
Conclusion
The overall condition of Long Island Sound is rated
poor based on the four NCA indices of estuarine condi-
tion. Based on LISS findings, the most significant envi-
ronmental priorities in Long Island Sound are low
dissolved oxygen levels in bottom waters (hypoxia);
pathogen contamination in swimming waters and shell-
fish-harvesting areas; declines in finfish and commercial
shellfish populations; loss of coastal habitat; and
increases in floatable debris. Since 1991, there has been
a reduction in overall nitrogen loadings to the Sound, as
well as in inputs from point sources. Upgrades to
municipal STPs have had a major impact on reducing
nitrogen discharges from coastal and tributary sources.
Construction of pump-out stations has helped to reduce
discharges of vessel sewage and the levels of pathogens
in near-coastal areas of Long Island Sound. Protection
of oyster beds and the lobster population is still an
extremely critical priority for the economic viability of
the fishing industry in Long Island Sound.
National Estuary Program Coastal Condition Report 119
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Peconic Estuary Program
Peconic Estuary Program
Gardiners
Shelter Island
Island v
Long Island Sound
Ffeconic Estuary Program
www.peconicestuary.org
i_
Background
The Peconic Estuary encompasses a series of
connected bays between the north and south forks of
eastern Long Island, NY. The Estuary's watershed spans
more than 125,000 acres of land and 158,000 acres of
surface water and features more than 100 distinct
harbors, embayments, and tributaries (PEP, 2001; Balla
et al., 2005). The Estuary provides important habitat
and spawning and nursery grounds for a wide variety of
marine organisms. The most notable species in the
Estuary include shellfish, such as bay scallops and hard
clams, and finfish, such as bay anchovy, Atlantic silver-
side, scup, summer flounder (also called fluke), winter
authampton
' Great Peconic Bay
Gardners Bay
Little Peconic Bay
Flanders Bay
Atlantic Ocean
NEP Study Area
flounder, windowpane flounder, weakfish, and black-
fish. Eelgrass meadows are found in the eastern portion
of the Estuary and provide food, shelter, and nursery
grounds to many forms of marine life, including
shrimp, bay scallops, crabs, and fish (Balla et al., 2005;
SCDHS, 2006). The eelgrass beds also stabilize the
Estuary bottom and are an important component of the
nutrient cycle of this ecosystem.
The Peconic Estuary was declared an Estuary of
National Significance in 1992, and the Peconic Estuary
Program (PEP) is sponsored by EPA, the NYSDEC,
and the Suffolk County Department of Health Services
(SCDHS) (SCDHS, 2006). The PEP Management
120 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Peconic Estuary Program
Conference, established in 1993, is composed of
numerous stakeholders, including citizens, businesses,
non-profit groups, and local, state, and federal govern-
mental agencies (PEP, 2006). Approved by EPA in
November 2001, the Peconic Estuary Program Compre-
hensive Conservation and Management Plan (PEP, 2001)
promotes a holistic approach to restoring and protecting
the Estuary and its watershed.
Environmental Concerns
Land-use changes, SAV coverage, and phytoplankton
and dinoflagellate blooms are some of the environ-
mental concerns for the Peconic Estuary. The region's
population growth and accompanying development
pose substantial threats to the Estuary's water quality,
nutrient balance, and habitat. Urbanization of the
watershed continues, with approximately 600 acres per
year converted from agriculture and vacant land to
developed uses, mostly residential homes. The estimated
8,700 acres of eelgrass found throughout the Estuary in
the 1930s (a conservative estimate) has dwindled to
1,550 acres of eelgrass today (119 beds). Blooms of the
phytoplankton brown tide, Aureococcus anophagefferens,
decimated the commercially significant fishery for
Peconic Estuary scallops, particularly during the 1980s.
Although brown tide blooms have not occurred since
1997, those species most affected (e.g., bay scallops and
eelgrass) have not rebounded (Balla et al., 2005; PEP,
2006). In addition, blooms of the dinoflagellate
Cochlodinium polykrikoides are of recent concern (Nuzzi,
2005). Other priority management issues are nutrient
pollution, habitat and living resources, critical lands
protection, pathogens, and toxic contaminants (PEP,
2001).
Population Pressures
The population of the NOAA-designated coastal
county (Suffolk) coincident with the PEP study area
increased by 113% during a 40-year period, from 0.67
million people in 1960 to almost 1.42 million people in
2000 (Figure 3-59) (U.S. Census Bureau, 1991; 2001).
This rate of population growth for the PEP study area is
almost five times the population growth rate of 24% for
the collective NEP-coincident coastal counties of the
Northeast Coast region. A majority of this population
growth has taken place in the western portion of Suffolk
o
a
o
a.
2000
Figure 3-59. Population of NOAA-designated coastal county of
the PEP study area, 1960-2000 (U.S. Census Bureau, 1991; 2001).
County, outside of the Peconic watershed. In 2000, the
population density of this NEP-coincident coastal
county (1,558 persons/mi2) was the third-highest
density calculated for any of the Northeast Coast NEPs
and was about 50% higher than the population density
of 1,055 persons/mi2 for the collective NEP-coincident
coastal counties of the Northeast Coast region (U.S.
Census Bureau, 2001). Population pressures for this
NEP study area are mounting, particularly for second
homes and during the summer months, because the
Peconic Estuary serves as a major center for recreational
activities for the large urban population of New York
City and Long Island.
NCA Indices of Estuarine
Condition—Peconic Estuary
The overall condition of the Peconic Estuary is rated
good based on three of the four NCA indices of estu-
arine condition (Figure 3-60). The water quality and
fish tissue contaminants indices are both rated good,
Overall Condition
Peconic Estuary
(4.33)
Fair
Water Quality Index (5)
Sediment Quality Index
(missing)
Benthic Index (3)
Fish Tissue Contaminants
Index (S)
Figure 3-60. The
overall condition of
the PEP estuarine area
is good (U.S.
EPA/NCA).
National Estuary Program Coastal Condition Report 121
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Peconic Estuary Program
and the benthic index is rated fair. No data were avail-
able to calculate a sediment quality index for the
Peconic Estuary. Figure 3-61 provides a summary of the
percentage of estuarine area rated good, fair, poor, or
missing for each parameter considered. This assessment
is based on data from 30 NCA sites sampled in the PEP
estuarine area in 2000, 2001, and 2002. Please refer to
Tables 1-24, 1-25, and 1-26 (Chapter 1) for a summary
of the criteria used to develop the rating for each index
and component indicator.
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80
Percent NEP Estuarine Area
Missing
Figure 3-61. Percentage of estuarine area achieving each rating
for all indices and component indicators — Peconic Estuary
(U.S. EPA/NCA).
Water Quality Index
The water quality index for the Peconic Estuary is
rated good; however, water quality data were unavailable
for a third of the estuarine area (Figure 3-62). The water
quality index was developed using NCA data on five
component indicators: DIN, DIP, chlorophyll a, water
clarity, and dissolved oxygen. DIN concentrations were
uniformly low in the estuarine area, and moderate DIP
concentrations were evident in most of the Estuary
where data were available. Water clarity was satisfactory
everywhere in the Estuary, and there was only one
incidence of moderate oxygen concentrations. In all
respects, water quality condition in the Peconic Estuary
is similar to that observed in eastern Long Island Sound.
Dissolved Nitrogen and Phosphorus I The
Peconic Estuary is rated good for DIN concentrations,
with 67% of the estuarine area rated good for DIN
concentrations and none of the area rated poor. NCA
Water Quality Index - Peconic Estuary
Site Criteria: Number of component indicators
in poor or fair condition
• Good = No more than I is fair
O Fair = I is poor, or 2 or more are fair
• Poor = 2 or more are poor
O Missing
Figure 3-62. Water quality index data for the: Peconic Estuary,
200CV2002 (U.S. EPA/NCA).
122 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Peconic Estuary Program
data on DIN concentrations were unavailable for 33%
of the PEP estuarine area.
The Peconic Estuary is rated fair for DIP concentra-
tions, with 14% of the estuarine area rated good for
DIP concentrations and 53% of the area rated fair.
None of the PEP estuarine area was rated poor for DIP
concentrations, although NCA data on this component
indicator were unavailable for 33% of the area. A more
important measure for the evaluation of eutrophic
condition for the Peconic Estuary may be the overall
nitrogen load to the system.
Chlorophyll a \ The Peconic Estuary is rated good
for chlorophyll a concentrations. Forty-eight percent of
the estuarine area was rated good, 19% was rated fair,
and none of the area was rated poor for chlorophyll a
concentrations; however, NCA data on this component
indicator were unavailable for 33% of the PEP estuarine
area.
Water Clarity I Water clarity in the Peconic
Estuary is rated good, with 100% of the estuarine area
rated good for this component indicator. Water clarity
was rated poor at a sampling site if light penetration at
1 meter was less than 10% of surface illumination.
Dissolved Oxygen I The Peconic Estuary is rated
good for dissolved oxygen concentrations, with 99% of
the estuarine area rated good for dissolved oxygen
concentrations and 1% of the area rated fair. None of
the estuarine area was rated poor for this component
indicator; however, the PEP has identified numerous
areas of the Estuary that experience periods of low
dissolved oxygen levels, particularly during the summer
months.
Sediment Quality Index
The NCA survey did not collect sediment quality
data for the Peconic Estuary for any of the sediment
component indicators in 2000—2002; therefore, a sedi-
ment quality index was not developed for this report.
Sediment Toxicity I The NCA 2000-2002 surveys
did not collect sediment toxicity data for the Peconic
Estuary; therefore, sediment toxicity in the Estuary has
not been rated for this report.
Sediment Contaminants I The NCA 2000-2002
surveys did not collect sediment contaminants data for
the Peconic Estuary; therefore, sediment contaminant
concentrations in the Estuary have not been rated for
this report.
Total Organic Carbon I The NCA 2000-2002
surveys did not collect sediment TOC data for the
Peconic Estuary; therefore, sediment TOC has not been
rated for this report.
An SCDHS sanitarian uses a Secchi disk to measure water clarity
(Shana Miller).
National Estuary Program Coastal Condition Report 123
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Peconic Estuary Program
Benthic Index
The Peconic Estuary has one of the best measures of
benthic community diversity in the Northeast Coast
region, with 86% of the estuarine area rated good by
the Virginian Province Benthic Index (Figure 3-63);
however, the benthic index for the Peconic Estuary is
rated fair overall because 14% of the estuarine area was
rated poor for benthic condition.
Benthic Index - Peconic Estuary
Site Criteria:
Virginian Province Benthic Index Score
• Good = > 0.0
• Poor = s 0.0
O Missing
Good
86%
Figure 3-63. Benthic index data for the Peconic Estuary,
2000-2002 (U.S. EPA/NCA).
Fish Tissue Contaminants Index
The fish tissue contaminants index is rated good for
the Peconic Estuary. Only three fish samples from the
Peconic Estuary were analyzed for fish tissue contami-
nant concentrations, with two samples rated good and
one sample rated fair (Figure 3-64). More data are
needed to make an adequate assessment of fish tissue
contaminant levels for the Estuary. Unfortunately, rela-
tively few fish were analyzed in neighboring Long Island
Sound waters, so it is difficult to determine an accurate
assessment of fish tissue contaminant levels in this
portion of the Northeast Coast region. EPA, in cooper-
ation with the PEP, has completed a significant study of
toxic contamination in shellfish and finfish tissue;
however, the results of this study are not yet available.
Fish Tissue Contaminants Index - Peconic Estuary
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
OFair = Falls within Guidance range
• Poor = Exceeds Guidance range
Figure 3-64. Fish tissue contaminants index data for the
Peconic Estuary, 2000-2002 (U.S. EPA/NCA).
124 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Peconic Estuary Program
Peconic Estuary Program
Indicators of Estuarine Condition
Compared to other estuaries nationwide, the Peconic
Estuary is considered a relatively healthy system (PEP,
2001). For example, more than a third of the Peconic
watershed is protected open space, protecting natural
habitats, groundwater-recharge areas, and surface water
quality. On the other hand, the Peconic Estuary shows
signs of environmental stress, particularly in the more
densely developed areas and tidal creeks. According to
the PEP, low dissolved oxygen conditions occur in
approximately 3% of the Estuary; numerous pesticides
have been detected in groundwater and surface waters;
and some local fisheries, most notably bay scallops and
winter flounder, no longer support commercial harvests
(Ballaetal., 2005).
The PEP developed a list of 18 formal indicators and
published a comprehensive environmental status report
for the Peconic Estuary in March 2005 (Balla et al.,
2005). All the PEP's environmental indicators are listed
in the report, and a subset is discussed below.
Water and Sediment Quality
The following indicator measures are used to eval-
uate environmental changes and stressors affecting water
and sediment quality in the Peconic Estuary:
• Number of bathing beach closures
• Acreage of shellfish bed closures
• Onset and duration of brown tide events
• Dissolved oxygen levels
• Total nitrogen levels
• Water clarity
• Pesticides in ground and surface waters.
The number of bathing beach and shellfish bed
closures are used as indicators of excess pathogens in
estuarine waters. From 1980 through 2004, there were a
total of 43 beach closure days at four different bathing
beaches within the Peconic Estuary; however, these were
mostly precautionary closures. As of January 2004,
3,419 acres were closed and 1,803 acres were seasonally
open to shellfishing (Balla et al., 2005) (Figure 3-65),
although almost 96% of the Peconic Estuary was avail-
able for shellfish harvesting at some point in 2004.
Year-Round & Seasonal
Shellfish Bed Closures
t -. *
J- i "" • Permanent Closures
i. , \'?X """ Seasonal Closures
Figure 3-65. Permanent and seasonal shellfish closures in
Peconic Bay on January 1, 2004 (PEP).
Some shellfish beds, such as those around Plum Island,
were closed in 2004 due to administrative reasons rather
than because of poor water quality (PEP, 2006).
Stormwater runoff is the largest non-point source
contributor of pathogens to the Peconic Estuary. Other
contributions may come from wildlife, failing septic
systems, improperly treated effluent from WWTPs, and
illegally discharged wastes from boats (Balla et al.,
2005).
Another measurable impairment of Peconic Estuary
water quality is the occurrence of the harmful algal
bloom (HAB) dubbed "brown tide," and it is unknown
whether onset, duration, and cessation of these blooms
are naturally occurring or related to human impacts on
the watershed. Brown tide blooms persisted in high
concentrations for extended periods in all or part of the
Estuary from 1985 through 1988, 1990 through 1992,
1995, and 1997. Brown tides have not bloomed in high
concentrations since 1997, but this issue continues to
be an important management topic, particularly when
efforts are mounted to restore shellfisheries and eelgrass
meadows (Balla et al., 2005; PEP, 2006).
One of the most significant water quality concerns
for the Peconic Estuary has been excess nitrogen
loading, especially in the western portion of the Estuary.
There seemed to be an overall decrease in total nitrogen
in the Estuary's surface waters from 1994 to 2005;
however, the specific cause (e.g., decreased loading,
increased uptake in the food web, or a combination of
other mechanisms) is not known. Nitrogen inputs to
National Estuary Program Coastal Condition Report 125
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Peconic Estuary Program
the Estuary originate from excessive agricultural and
residential fertilizer use, on-site disposal systems, atmos-
pheric deposition, nutrient-enriched bottom sediments,
STPs, and stormwater runoff. Most of the nitrogen
enters the Estuary from the atmosphere (rainfall) and
groundwater, although STPs are an important factor in
select localized areas (Balla et al., 2005).
The relationship between excessive nitrogen loading
and low dissolved oxygen levels in estuaries is well
documented. The Peconic Estuary has excellent water
quality with regard to dissolved oxygen levels, with less
than 3% of the estuarine area periodically failing to
meet New York's dissolved oxygen standard of 5 mg/L.
However, the PEP strives to maintain or improve both
dissolved oxygen and total nitrogen levels in the west-
ernmost portions of the Estuary (Balla et al., 2005).
Monitoring of point sources, upgrades to sewage
systems, and fertilizer-reduction programs are all impor-
tant actions that could be used to control nitrogen
loads, particularly given the fact that development and
population increases are likely.
Continuous monitoring equipment has been
deployed throughout the main stem of the Peconic
Estuary. These devices download information every
fifteen minutes and are set one meter off the Estuary
bottom. Figure 3-66 depicts the dissolved oxygen
concentrations experienced on July 15, 2004 (a typical
summer day). The tidal Peconic River station, the most
landward monitoring site of the three locations, experi-
enced dissolved oxygen levels that were well below the
New York State dissolved oxygen standard of 5 mg/L.
Of the three sites, these waters have the least amount of
ocean flushing and are most affected by land use and
STP effluent discharges (Balla et al., 2005). Great
Peconic Bay, the most seaward of the monitoring sites,
did not experience any dissolved oxygen problems on
July 15, 2004, most likely due to the mixing of the
Bay's waters with more oxygenated waters from the
seaward boundary (Balla et al., 2005; Personal commu-
nication, Bavaro, 2006). Flanders Bay, a station located
between the tidal Peconic River and Great Peconic Bay,
showed diurnal depressions in dissolved oxygen levels
(Balla et al., 2005).
--a.'
Great Peconic DO Standard
Figure 3-66. Dissolved oxygen concentrations at the three
continuous monitoring locations on July 15, 2004 (Balla et al., 2005).
Habitat Quality
The indicators used by the PEP to evaluate habitat
changes over time include the following:
• Extent of eelgrass beds (acres)
• Extent of tidal wetlands (acres)
• Area of habitat restoration (acres).
The extent of eelgrass beds in the Peconic Estuary
continues to decline, with an areal decrease of at least
82% since the 1930s. Despite generally good water
quality, eelgrass beds, measured at 1,550 acres in 2005,
are not expanding. The most extensive Peconic wetlands
losses occurred prior to 1972. The approximately 5,700
acres of estuarine wetlands in Peconic Estuary are
constantly threatened by the degradation of surround-
ing buffer areas and the invasive common reed
Phragmites austmlis. The wide variety of habitat-restora-
tion efforts undertaken in the Estuary have included the
replanting of eelgrass, restoration of intertidal marsh,
control of common reed growth, and construction of
fish passages. Most of these projects have been small,
ranging in size from one-tenth of an acre to several
acres, but there have been several open-marsh water
management and grassland projects of about 50 acres in
scope (Balla et al., 2005).
126 National Estuary Program Coastal Condition Report
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CHAPTER 3 ' NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Peconic Estuary Program
Living Resources
The PEP uses the following key indicator measures
to study the overall health of the living resources in the
Peconic Estuary system:
• Bay scallop commercial landings
• Winter flounder population abundance
• Piping plover nests and nesting productivity
• Osprey nests and nesting productivity
• Toxic substances in sediments, biota, and ground-
water.
Peconic Estuary scallop landings are now a fraction
of what was once a nationally significant fishery. In the
1970s and mid-1980s, the harvest of bay scallops
ranged from 100,000 to 700,000 pounds of meat. Since
1996, commercial landings ranged from zero to just
under 6,000 pounds. Although brown tides have had a
large effect on the overall population of scallops, habitat
loss, changes in predator-prey relationships, and over-
harvesting also play a role. Winter flounder are consid-
ered an overfished species and have declined throughout
the northeastern United States. In the Peconic Estuary,
the average catch/tow from 1987 to 1995 was 15.6 for
winter flounder, whereas the mean winter flounder/tow
was 0.4 and 1.4 in 2002 and 2003, respectively (Balla et
al., 2005).
A variety of shorebirds are found nesting, feeding,
and breeding along the shores of the Peconic Estuary
and its islands. Some of these shorebirds are federally
listed as threatened or endangered or are rare in New
York, such as the piping plover, least tern, roseate tern,
and common tern. The Peconic Estuary is also home to
more than half of the ospreys on Long Island; the popu-
lation of this species has burgeoned since the banning of
DDT in 1972. Piping plover breeding pairs on Long
Island have generally increased in numbers since the
mid-1980s, when the total population was slightly more
than 100 pairs. By 2002, the number of Long Island
piping plover breeding pairs rose to 369, of which 57
were found in the PEP study area (Balla et al., 2005).
Environmental Stressors
The following indicators are used to assess the
impact of human activities on the Peconic Estuary:
• Extent of shoreline hardening
• Extent of impervious surfaces
• Extent of land protection.
The largest threat to beaches and other shoreline
habitat is shoreline hardening. Use of bulkheads,
rip-rap, jetties, groins, and other hardened structures
has been widely permitted to stabilize shoreline in front
of waterfront property throughout the Estuary. These
structures have replaced beaches with uplands, increased
shoreline erosion, and altered sediment accretion
patterns that may lead to loss of wetlands and beaches.
More than 6% of the Peconic Estuary shoreline has
hardened surfaces (Balla et al., 2005). Data on imper-
vious surfaces has been collected, and analysis of these
data is underway. Using GIS capabilities, the PEP has
finalized its Critical Lands Protection Plan (PEP, 2004)
to evaluate land available for development and to
identify priorities for protection across the Estuary.
Scientists collect sediment samples in a tidal creek on the North
Fork of Long Island to test for toxic contamination (Rick Balla).
National Estuary Program Coastal Condition Report 127
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Peconic Estuary Program
Critical Lands Protection in the
Peconic Estuary Watershed
Increasing development in the Peconic Estuary
watershed continues to result in the loss and fragmen-
tation of open space and natural habitats, degraded
groundwater quality, and declines in local plant and
wildlife populations. As of 2001, almost half of the
nearly 114,000 acres of land in the watershed's 5 eastern
towns was developed, with more than 30% protected
and more than 20% still available for development.
More than 2,500 parcels of the developed area,
comprising 3,500 acres, were developed between 1998
and 2001 (PEP, 2004).
The PEP's Critical Lands Protection Plan (PEP, 2004)
identified and prioritized for protection the land avail-
able for development in the Peconic watershed. Using
environmental criteria and GIS, each parcel was evalu-
ated through the lens of habitat and water quality
protection. The strategy and resulting plan were not
meant to be the sole reference for land protection in the
region, but rather a tool for state and local agencies that
make land acquisition decisions based, in part, on
estuarine considerations (PEP, 2004). Almost 70% of
the 25,271 acres of remaining land available for devel-
opment in the Peconic watershed have been designated
as "Critical Lands Protection Strategy (CLPS) high-
priority parcels" (Gringalunas et al., 2004).
The towns, county, state, and private land.trusts have
been instrumental in acquiring open space in the
Peconic Estuary watershed. As of 2005, the most widely
used land protection tool is full-fee acquisition from
willing sellers. Although the Community Preservation
Fund (CPF; 2% real estate transfer tax) is the most
successful land protection program on Long Island,
raising more than $245 million through January 2005,
it does not sufficiently keep up with the rate of develop-
ment and loss of critical landscapes. An estimated
$ 1.375 billion would be needed to protect all of the
vacant parcels in die Peconic watershed (approximately
17,000 acres) that meet at least one of the plan's envi-
ronmental criteria (see map). Future CPF revenues
could purchase less than 10% of diese parcels. Given
these findings, it is apparent that current land acquisi-
tion funding, including the additional funding from
county, state, and federal sources, is not sufficient to
keep pace with the current and anticipated rates of
development.
Large amounts of land can be protected without
having to expend large sums of money. Alternative
protection tools include clearing restrictions, clustering
requirements, rezoning, overlay districts, easements,
purchase of development rights, and overall better
land-use practices. It is estimated that the implementa-
tion of clearing restrictions would protect an additional
Non-market Benefits Associated with Open Space Acquisition in Riverhead, NY,
Using a 3% Discount Rate (Gringalunas et al., 2004)
Non-market Benefit
On-site recreational use for bird watching and wildlife viewing
Off-site water quality impacts on recreational swimming
Localized amenity values to adjacent property owners
Cost per Acre
$209,362
$5,216
$18,300
128 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Peconic Estuary Program
3,183 acres in the five East End Towns and that
acquiring an equivalent amount of land would cost
approximately $355 million. If these same lands were
developed with both clearing restrictions and clustering
requirements, a total of 3,491 acres would be protected,
and the estimated cost for acquiring an equivalent
amount of land would be $382 million (PEP, 2004).
As part of a case study conducted in 2004, the costs
and benefits of protecting 220 acres of open space in
Riverhead, NY, through outright acquisition in perpe-
tuity were examined. The cost of acquiring die open
space was estimated to range from $22 million to $38
million. These costs were compared to estimated
PEP watershed
boundary
^*b3 Community
Preservation
Fund (CPF)
Parcels
Protected land
I I Developed and
agricultural land
Bordering town
economic impact of three non-market benefits (see
table). The estimated impact of these benefits ranged
from $20.5 million to $51.4 million, depending on the
discount rate selected. Although only three benefits
were analyzed, the mid-point of the range of estimated
benefit impact exceeds the mid-point of die estimated
costs, thereby strengthening the argument for continued
land protection (Gringalunas et al., 2004).
Much of the Peconic watershed will be built-out in
the next decade. The PEP's efforts to highlight land-
protection goals, funding gaps, and protection tools are
critical in guiding the watershed s final landscape.
Vacant land Developed, subdividable land
Meets one criterion* Meets one criterion*
Meets two criteria* Meets two criteria*
Meets three criteria* •• Meets three criteria*
%i&t Meets four criteria* •• Meets four criteria*
* Only parcels which fit into one or more of the following categories
are shown: Adjacent to protected, Aggregates >IO acres, 3 hits
including 1000 feet, 10 acres or greater.
rf
\.
\
Map of prioritization of environmental criteria for Shelter Island (PEP).
National Estuary Program Coastal Condition Report 1 29
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Peconic Estuary Program
Current Projects,
Accomplishments, and Future
Goals
Some of the major environmental accomplishments
of the PEP include the following:
• Restoration projects - Between 1993 and 2005,
more than 120 priority demonstration and imple-
mentation projects were funded using federal
and state funds totaling more than $20.2 million.
Projects include upgrades to STPs; restoration
of wetlands, eelgrass beds, and fish passages;
construction of artificial wetlands; and mitigation
of stormwater runoff (Personal communication,
Bavaro, 2006).
• Nitrogen total maximum daily load (TMDL) -
A nitrogen TMDL for waters in the western
Estuary will be submitted to EPA in 2006.
Nitrogen loadings to these waters need to be
reduced to alleviate dissolved oxygen impairments.
• STP upgrades - In 2001, the Riverhead and Sag
Harbor STP upgraded to tertiary treatment with
ultraviolet light disinfection.
• Agricultural nitrogen reduction - The PEP was
responsible for bringing the region's agricultural
community and other stakeholders together for
the first time to develop a strategy to lower
nutrient and pesticide inputs to the environment.
• Promotion of best management practices
(BMPs) — The PEP promotes projects, such as the
Stop Throwing Out Pollutants (STOP) Program,
integrated pest management, and stormwater
mitigation at marinas, golf courses, and other
facilities, to reduce levels of toxics in the water-
shed.
• Benthic mapping — Underwater land maps are
being created for the Peconic Estuary to docu-
ment bathymetry and distribution of natural
resources, identify potential sites for commercial
aquaculture operations, assess biodiversity, and
clarify Essential Fish Habitat designations.
• Habitat restoration plan - The PEP identified
the need for 72 restoration projects encompassing
836 acres, with an estimated cost of more than
$42 million (PEP, 2002).
• Vessel Waste No-Discharge Zone - In 2002, the
entire Peconic Estuary was designated a Vessel
Waste No-Discharge Zone, whereby the direct
discharge of treated and untreated wastes from
marine toilets is prohibited. In addition, the PEP
aids municipalities in acquiring additional vessel
waste pump-out boats.
Conclusion
Compared to other NEP estuaries, the Peconic
Estuary is a relatively healthy system. For example, more
than a third of the Peconic Estuary watershed is
protected open space, preserving natural habitats,
groundwater-recharge areas, and surface water quality.
On the other hand, the Peconic Estuary shows signs of
environmental stress, particularly in the more densely
developed areas and in the tidal creeks. Monitoring data
from Suffolk County show that water quality across the
Peconic F.stuary is in relatively good condition. This
finding is consistent with EPA's overall condition rating
of good based on three of the indices used by the NCA.
The PEP feels that more scientific inquiry and moni-
toring of the Peconic Estuary and its watershed is
needed to accurately understand the causes and effects
of pollutants, and that additional funding is critical to
develop indicators, monitor them over time, and report
to the public about Estuary conditions.
Bay scallops were once a nationally significant fishery in Peconic
Estuary (Shana Miller).
130 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New York/New Jersey Harbor Estuary Program
New York/New Jersey Harbor Estuary Program
New York - New Jersey
Harbor Estuary Program
www.harborestuary.org
Background
The core area of the New York/New Jersey Harbor
extends from the tidal waters of the Hudson-Raritan
Estuary to Sandy Hook, NJ, and Rockaway Point, NY,
at the mouth of the Harbor. This core area includes
the Hudson River, Upper Bay, Lower Bay, Arthur Kill,
Kill Van Kull, and Raritan Bay. The NEP study area
also includes the East and Harlem rivers and Jamaica
Bay in New York, and the Hackensack, Passaic, Raritan,
Shrewsbury, Navesink, and Rahway rivers and Newark
and Sandy Hook bays in New Jersey. The actual
drainage basin or watershed of the Harbor encompasses
Jamaica Bay
Upper New Yort. Bay
Newark Bay
Lower New York Bay
Sandy Hook Bay
Atlantic Ocean
about 16,300 mi", including much of eastern New York,
northern New Jersey, and small parts of western
Connecticut, Massachusetts, and Vermont. The quality of
the estuary's water is affected not only by activities occur-
ring directly in the Harbor and New York Bight (the
ocean area that extends approximately 100 miles beyond
Harbor waters), but also by industry, agriculture, and
other individual practices throughout this larger water-
shed (NY/NJ HEP, 2006).
The New York/New Jersey Harbor Estuary Program
(also known as the HEP) was designated an Estuary of
National Significance in 1988 by EPA, in response to a
National Estuary Program Coastal Condition Report 131
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New York/New Jersey Harbor Estuary Program
request by the two states' Governors. The HEP was
convened as an interstate partnership of federal, state,
and local governments; scientists; civic and environ-
mental advocates; the fishing community; business
leaders; and educators. In 1987, Congress also required
the preparation of a restoration plan for the New York
Bight; however, because the Harbor and New York
Bight are inextticably linked within the larger
ecosystem, these two plans were later joined (NY/NJ
HEP, 1996; 2006).
Environmental Concerns
Some of the primary environmental concerns in the
New York/New Jersey Harbor system include toxic
contamination, pathogens, and wetland loss. Levels of
mercury are still above the ERM values for sediments in
all basins of the estuary, and levels of contaminants in
fish have resulted in the issuance of health advisories
against fish consumption. In 1988, large improvements
made at STPs helped end the dischatge of roughly
210 million gallons of untreated sewage per day from
Manhattan and Brooklyn and reduced fecal coliform
levels in the estuary. CSOs still contribute raw sewage to
the Harbor's waterways when it rains, and some shell-
fish beds have remained closed for decades. Compared
to historic acreage levels, about 80% of the estuary's
tidal wetlands and most of the 224,000 acres of the
urban core's freshwater wetlands are gone. Despite these
losses, Clean Water Act regulations have helped reduce
wetland losses substantially in the past 10 to 15 years
(Steinberg, 2004).
Population Pressures
The population of the 21 NOAA-designated coastal
counties coincident with the HEP study area increased
by 13% during a 40-year period, from 15 million
people in 1960 to almost 16.9 million people in 2000
(Figure 3-67) (U.S. Census Bureau, 1991; 2001). This
rate of population growth for the HEP study area is
about half the population growth rate of 24% for the
collective NEP-coincident coastal counties of the
Northeast Coast region. In 2000, the population density
of these 21 NEP-coincident coastal counties (3,097
persons/mi2) was the highest density calculated for any
of the Northeast NEP study areas and was three times
a
o
a.
2000
Figure 3-67. Population of NOAA-designated coastal counties
of the HEP study area, 1960-2000 (U.S. Census Bureau, 199 I;
2001).
higher than the population density of 1,055 persons/
mi2 for the collective NEP-coincident coastal counties
of the Northeast Coast region (U.S. Census Bureau,
2001). Population pressures for the HEP study area are
extremely high because this estuary serves the major
metropolitan area of New York City—one of the largest
port facilities on the East Coast and a center for inter-
national commerce and banking.
NCA Indices of Estuarine
Condition—New York/
New Jersey Harbor
The overall condition of the New York/New Jersey
Harbor is rated poor based on the four indices of
estuarine condition used by the NCA (Figure 3-68).
All four indices—the water quality index, sediment
quality index, benthic index, and fish tissue contami-
nants index—are also rated poor for the New York/
Overall Condition
New York/New Jersey Harbor
(1.0)
Fair
Water Quality Index (I)
Sediment Quality Index (I)
Benthic Index (I)
Fish Tissue Contaminants
Index (I)
Figure 3-68. The
overall condition of
the HEP estuarine
area is poor (U.S.
EPA/NCA).
132 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New York/New jersey Harbor Estuary Program
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Estuarine Area
| [""] Missing
Figure 3-69. Percentage of NEP estuanne area achieving each
rating for all indices and component indicators — New York/New
jersey Harbor (U.S. EPA/NCA),
New Jersey Harbor. Figure 3-69 provides a summary of
the percentage of estuarine area rated good, fair, poor,
or missing for each parameter considered. This assess-
ment is based on data from 32 NCA sites sampled in
the HEP estuarine area in 2000 and 2001. Please refer
to Tables 1-24, 1-25, and 1-26 (Chapter 1) for a
summary of the criteria used to develop the rating for
each index and component indicator.
Water Quality Index
The water quality index for the New York/New
Jersey Harbor is rated poor. This index was developed
using NCA data on five component indicators: DIN,
DIP, chlorophyll a, water clarity, and dissolved oxygen.
None of the estuarine area was rated good for water
quality, and 38% of the area was rated fair or poor
(Figure 3-70). Water quality data were unavailable for
62% of the HEP estuarine area; therefore, this water
quality index rating is only tentative. The available data
show a wide occurrence of elevated concentrations of
DIN and DIP and relatively few sites where chloro-
phyll a levels were elevated. Water clarity was largely
satisfactory in the Harbor, with 11 % of the estuarine
area in fair or poor condition for this component indi-
cator. This finding is a departure from the tendency for
Northeast Coast NEP estuaries to have relatively clear
water conditions, and the first indication of the
degraded clarity that is usually found in estuaries in the
southern part of the Northeast Coast region. Dissolved
oxygen concentrations were satisfactory in 62% of the
HEP estuarine area.
Dissolved Nitrogen and Phosphorus \ The
New York/New Jersey Harbor is rated fair for DIN
concentrations. Four percent of the estuarine area was
rated good for DIN concentrations, 12% of the area
was rated fair, and 21 % of the area was rated poor.
NCA data on DIN concentrations were unavailable for
Water Quality Index - New York/New Jersey Harbor
Site Criteria: Number of component
indicators in poor or fair condition
• Good= No more than I is fair
OFair = I is poor, or 2 or
more are fair
• Poor - 2 or more are poor
O Missing
Figure 3-70. Water quality index data for New York/
New Jersey Harbor, 2000-2001 (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 133
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New York/New Jersey Harbor Estuary Program
63% of the HEP estuarine area. The New York/New
Jersey Harbor is rated poor for DIP concentrations,
with 4% of the estuarine area rated good for this
component indicator and 33% of the area rated poor.
NCA data on DIP concentrations were unavailable for
63% of the HEP estuarine area.
Chlorophyll a \ The New York/New Jersey Harbor
is rated good for chlorophyll a concentrations, with
28% of the estuarine area rated good for this compo-
nent indicator, 4% of the area rated fair, and 4% of the
area rated poor. NCA data for chlorophyll a concen-
trations were unavailable for 64% of the HEP estuarine
area.
Water Clarity \ Water clarity in the New York/
New Jersey Harbor is rated good. Water clarity was
rated poor at a sampling site if light penetration at
1 meter was less than 10% of surface illumination.
Eighty-six percent of the estuarine area was rated good
for water clarity, 8% was rated fair, and only 3% was
rated poor. NCA data on water clarity were unavailable
for 3% of the HEP estuarine area.
Dissolved Oxygen I The New York/New Jersey
Harbor is rated good for dissolved oxygen concentra-
tions, with 62% of the estuarine area rated good for this
component indicator and none of the area rated poor.
NCA data on dissolved oxygen concentrations were
unavailable for 21% of the HEP estuarine area.
Sediment Quality Index
The sediment quality index for the New York/New
Jersey Harbor is rated poor, with 65% of the estuarine
area rated poor for sediment quality condition (Figure
3-71). This index was developed using NCA data on
three component indicators: sediment toxicity, sediment
contaminants, and sediment TOC. Three survey sites
(accounting for 25% of the HEP estuarine area) showed
toxicity toward amphipods; metals and PCBs were most
often responsible for contamination at impaired sites;
and about a third of the estuarine area had elevated
TOC levels in sediment.
Sediment Quality Index - New York/New Jersey
Harbor
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
OFair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Figure 3-71. Sediment quality index data for New York/
New Jersey Harbor 2000-2001 (U.S. EPA/NCA).
Sediment Toxicity I The New York/New Jersey
Harbor is rated poor for sediment toxicity, with 25%
of the estuarine area rated poor for this component
indicator. NCA data on sediment toxiciry were unavail-
able for 1% of the HEP estuarine area.
Sediment Contaminants \ The New York/New
Jersey Harbor is rated poor for sediment contaminant
concentrations, with more than half (57%) of the
estuarine area rated poor for this component indicator
and an additional 13% of the area rated fair.
Total Organic Carbon \ The New York/New
Jersey Harbor is rated good for sediment TOC, with
55% of the estuarine area rated good for this compo-
nent indicator, 29% of the area rated fair, and only 5%
of the area rated poor. NCA data on sediment TOC
were unavailable for 11 % of the HEP estuarine area.
134 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New York/New Jersey Harbor Estuary Program
&
Benthic Index
-~
Fish Tissue Contaminants Index
Based on NCA monitoring data, the benthic index
for the New York/New Jersey Harbor is rated poor. A
third of the Harbor's estaurine area had degraded
benthic communities, whereas 58% of the area exhib-
ited healthy benthic communities, as judged by the
Virginian Province Benthic Index (Figure 3-72).
Benthic Index - New York/New Jersey Harbor
Site Criteria:
Virginian Province Benthic Index Score
• Good= > 0.0
• Poor = s 0.0
O Missing
Good
58%
Figure 3-72. Benthic index data for New York/New Jersey
Harbor, 2000-2001 (U.S. EPA/NCA).
The fish tissue contaminants index for the New
York/New Jersey Harbor is rated poor. Relatively few
fish from the Harbor (14 fish samples) were analyzed
for fish tissue contaminant concentrations (Figure
3-73). All of the fish analyzed either fell within the
range of EPA Advisory Guidance values (29%) or
exceeded EPA Advisory Guidance values (71%) for
fish consumption, most commonly for PCBs and,
occasionally, for DDT and mercury.
Fish Tissue Contaminants Index - New York/
New Jersey Harbor
Site Criteria: EPA Guidance concentration
• Good - Below Guidance range
OFair = Falls within Guidance range
• Poor = Exceeds Guidance range
Figure 3-73. Fish tissue contaminants index data for New York/
New Jersey Harbon 2000-2001 (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 135
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New York/New Jersey Harbor Estuary Program
New York/New Jersey Harbor-
wide Water Quality Survey
The HEP reports that it has collaborated with
numerous federal, state, and municipal agencies to
initiate a long-term water quality monitoring program
that covers all of the waters of the New York/New Jersey
Harbor. New York City has monitored die New York
side of the Harbor for nearly 100 years, but the HEP
has recognized that a previous lack of monitoring data
for the New Jersey waters of the Harbor is a significant
concern.
To address this issue, the HEP formed an ad hoc
monitoring group in 2002 to assess existing water
quality monitoring efforts in the Harbor and to make
recommendations to fill data gaps. This group included
representatives from the New Jersey Harbor Discharges
Group (NJHDG), New Jersey Department of Environ-
mental Protection (NJDEP), New York City Depart-
ment of Environmental Protection (NYCDEP),
NYSDEC, National Park Service (NFS), IEC, EPA,
and the New Jersey Sea Grant.
Although the collective monitoring group made
recommendations about what needed to be done to fill
data gaps, the NJHDG made the long-term commit-
ment to the New Jersey data-collection program. The
NJHDG is convinced that a robust water quality data-
base is needed to allow the member agencies to make
informed decisions about future needs and to allow
the group to be confident that regulatory decisions are
made based on high-quality environmental measure-
ments.
The water quality surveys now conducted by the
NJHDG and the NYCDEP are entirely complementary,
and staff from all the participating agencies continue to
collaborate on common issues. Parameters measured
include dissolved oxygen, total suspended solids, fecal
coliform bacteria, nitrogen, phosphorus, and salinity.
Efforts are also underway to investigate adding real-time
data collection to the monitoring effort.
Through these combined efforts, the data from the
more than 60 stations in the HEP estuarine area can
now be used to represent the water quality of the entire
Harbor and will form the basis for documenting
changes in water quality over time. Additional informa-
tion on these programs is available from the HEP at
www.harborestuary.org.
Passaic Valley Sewerage Commissioners (PVSC) vessel collecting
water quality data as part of the Harbor-wide survey (PVSC).
136 National Estuary Program Coastal Condition Report
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CHAPTER 3 ! NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New York/New jersey Harbor Estuary Program
New York/New Jersey Harbor
Estuary Program Indicators of
Estuarine Condition
Water and Sediment Quality
Table 3-1 presents trends in the main indicators used
by the HEP. The NYCDEP collects water samples every
two weeks at a series of stations around the Harbor to
measure dissolved oxygen in surface and bottom waters
to evaluate changes in water quality in the estuary.
Historically, dissolved oxygen levels were routinely
below 1.5 rng/L in summer months; however, since the
1970s, dissolved oxygen levels have been above the
minimum EPA guideline of 23 mg/L at most sites,
with mean Harbor-wide dissolved oxygen concentra-
tions fluctuating between 5 and 7 mg/L in the surface
and bottom waters of the HEP study area. When
dissolved oxygen concentrations are above 4.8 mg/L, an
area is considered to achieve objectives for the protec-
tion of marine life. Overall, dissolved oxygen levels in
Table 3-1. Trends in Water Quality Indicators
Measured by the HEP (Steinberg et al., 2004)
Toxic Contamination
Contaminant levels
Contaminant loadings
Sediment toxicity
Contaminants in fish tissue
Pathogens
Acres of shellfish beds open
Disease linked to
contaminated shellfish
Levels of coliform bacteria
Beach closures
Floatable Debris
Floatable debris
Improving trend
Improving trend
No trend
Improving trend
Improving trend
Improving trend
Improving trend
No trend
No trend
Nutrients and Organic Enrichment
Nutrient levels and loadings
Dissolved oxygen
Chlorophyll a
Transparency
Harmful algal blooms
Mixed trend
Improving trend
No trend
No trend
Improving trend
the Harbor improved considerably between 1990 and
2000 (Steinberg et al., 2004). The HEP's target is to
increase water quality for the area so that dissolved
oxygen levels never drop below 4.8 mg/L (30 mi2
currently achieve this target) (NY/NJ HEP, 2004).
Figure 3-74 illustrates changes in dissolved oxygen
concentrations in the Harbor from 1946 to 2001.
DIN and total nitrogen levels are monitored to eval-
uate water quality changes in the New York/New Jersey
Harbor. For both nitrogen and phosphorus, loadings
have decreased from most sources except STPs (nutrient
loads were higher in 1994-1995 than they were in the
same subbasins in 1988-1989). Although nutrient
levels have fluctuated over time, they are not considered
"limiting" elements for phytoplankton growth in this
estuarine system. Total nitrogen levels in the mid-1990s
were primarily driven by atmospheric sources, STPs,
and tributary loadings. Ammonia and nitrate-nitrite
concentrations were fairly stable between 1985 and
2000, averaging between 0.2 and 0.5 ug/L in the Inner
Harbor, Lower New York Harbor, and Raritan Bay
subbasins, with only slightly higher levels and fluctua-
tions of ammonia nitrogen in Jamaica Bay (Steinberg
et al., 2004).
Chlorophyll a is used as an index of phytoplankton
biomass in this system by the NYCDEP and the
NJDEP. Excessive phytoplankton conditions are defined
based on the abundance and extent of HABs. A HAB
index is used to quantify the severity and extent of
blooms (5 rating levels) in the Harbor and to charac-
terize the severity of the impact. These monitoring
Q
£ 2
0
Surface Dissolved Oxygen
• Bottom Dissolved Oxygen
*••••* -
•-•V-
1946 1951 1956 1961 1966 1971 1976 1981 1986 1991 1996 2001
Year
Figure 3-74. Trends in dissolved oxygen levels in surface and
bottom waters of the New York/New Jersey Harbor (Steinberg
et al., 2004).
National Estuary Program Coastal Condition Report 137
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New York/New jersey Harbor Estuary Program
agencies correlate water quality and a host of other envi-
ronmental variables (e.g., temperature, salinity) with
chlorophyll a levels in the estuary's waters (NY/NJ HEP,
2006). Since 2000, chlorophyll a levels have been
highest in Jamaica Bay, with some levels measured at
more than 50 ug/L (Steinberg et al., 2004). HABs are
monitored closely, but are not a formal indicator of
water quality in the Harbor. The NYCDEP, NJDEP,
IEC, and NFS are all involved in recording HABs in
the estuary (NY/NJ HEP, 2006). Most blooms in this
system discolor the water and reduce water clarity, with
only rare cases of blooms occurring that are severe
enough to cause food poisoning in humans. Outbreaks
of brown tides have not been observed in New
York/New Jersey Harbor (HRF, 2002).
The number of beach closures is another primary
indicator of water quality in the HEP study area. New
York beaches are monitored by the state's county health
departments. The New York City Department of
Health and Mental Hygiene (NCY DOHMH) Sanitary
Code requires that if there is a potential risk to human
health, then bathing beaches should not be open for
public use. The NYC DOHMH monitors public and
private beaches once a week in Richmond, Kings,
Queens, and Bronx counties; county health depart-
ments decide on the frequency of monitoring. All of the
coastal counties in New York regularly test for total
coliform, fecal coliform, and Enterococci bacteria and
monitor ocean and bay beaches. New Jersey has one of
the most comprehensive beach monitoring programs in
the country, and some sampling stations are currently
monitored for both fecal coliform and Enterococci
bacteria. New Jersey not only monitors the recreational
bathing beaches, but also samples environmental moni-
toring stations that are not bathing beaches. There were
beach closures in the core area of the New York portion
of the Harbor in 1988 and 1989 and in the core area of
the New Jersey portion the between 1988 and 1991.
In the New York portion of the core area, no beach
closures occurred between 1990 and 1993. In the
New Jersey portion, there were no beach closures due
to high bacteria between 1992 and 1993 and no
precautionary closures between 1989 and 1993 (Yuhas,
2002a). Figure 3-75 illustrates trends in beach closures
over time in the New Jersey portion of the Harbor area.
Concentrations of toxics in New York/New Jersey
Harbor sediments and fish tissue are the primary
indicators used to evaluate water and sediment quality.
An objective of the HEP is to complete characterization
of sediment loadings by 2005 and to ensure that suit-
able reduction targets are achieved by 2009, including a
specific goal to reduce sediment hot spots to the point
that the levels of toxics in newly deposited sediments do
not inhibit a thriving healthy ecosystem or threaten
oyster reef habitats. The HEP has also set a guideline
that all dredged materials from the estuary will have
beneficial uses. By 2009, the HEP hopes to increase the
areal extent of Harbor surface sediments below the
20
_o
u
18-
16-
14-
12
10-
8
6
4
2
CI Total number of precautionary closures
• Total number of high bacteria closures
JL
Li
1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002
Year
Figure 3-75. Number of beach closures by year at New Jersey beaches located in New York/
New Jersey Harbor (Yuhas, 2002a).
138 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New York/New Jersey Harbor Estuary Program
ERM values from the 1993-1994 baseline of 50% to
target levels set in 2005 (NY/NJ HEP, 2004). Striped
bass are a very popular catch for recreational anglers,
and PCB tissue levels in striped bass are an indicator
used by the HEP. The HEP has set a target that total
PCBs levels in striped bass and other fish shall not
exceed the FDA guideline of 2 ppm to protect human
health (NY/NJ HEP, 2004). PCB levels recorded in
the past have led to closure of the commercial fishery
and issuance of fish consumption advisories for striped
bass (Steinberg et al., 2004).
Habitat Quality
The acres of wetlands lost or acquired is used to
evaluate environmental changes to natural habitat
conditions and to track the health of estuary habitat in
the New York/New Jersey Harbor. Trends in acreage of
various habitat types are monitored over time using
aerial photography and GIS technology. Approximately
20,000 acres of tidal wetlands now remain in the
Harbor core area of both states (Steinberg et al., 2004).
One of the specific targets for habitat improvement is
to acquire 2,700 acres of land above the 2001 baseline
level by 2009 (NY/NJ HEP, 2004). It is difficult to
evaluate the overall function and health of different
habitats, other than to study changes in the population
sizes of the organisms these habitats support.
About 80% of the tidal wetlands and underwater
lands in the Harbor area (300,000 acres) have been
altered or destroyed over time, primarily due to filling,
dredging, and other human activities. In 1990, an oil
spill at Arthur Kill destroyed about 200 acres of salt
marsh. New Jersey lost about 2.5% of its wetland
acreage statewide between 1984 and 1995. Coastal
wetland losses in Jamaica Bay (NY) and Arthur Kill
(NJ) have been quite evident, and Little Neck Bay and
coastal areas in the southeast Bronx have also suffered
substantial losses. Loss of marsh grass islands in
Jamaica Bay are some of the most alarming changes
reported by the NYCDEP. If losses in this area
continue at the present rate, all islands in this subbasin
of New York/New Jersey Harbor will be gone by 2024.
Habitat loss, dredging, and filling in the Hackensack
Meadowlands has affected local populations of osprey,
crabs, and juvenile fish, as well as the overall hydrology
of this area. About 25% of tidal estuaries in the Hack-
ensack Meadowlands disappeared between 1969 and
Table 3-2. Trends in Habitat Quality and Wildlife
Indicators Measured by the HEP (Steinberg et al.,
2004)
Changes in Habitat Acreage
(overall)
Wetland acreage
Changes in Newark Bay
Wetlands in Jamaica Bay
Habitat in the Hackensack
Meadowlands
Abundance of Wading Birds
Abundance of Fish and
Crustaceans (overall)
Striped bass
American shad
Winter flounder
Summer flounder
White perch
American eel
Forage fish
Blue crab
Benthic Community Health
Sediment loading
Improving trend
Improving trend
Improving trend
Deteriorating trend
Improving trend
Deteriorating
trend
Mixed trend
No trend
Deteriorating trend
No trend
No trend
Deteriorating trend
Deteriorating trend
No trend
No trend
Improving trend
Improving trend
1995. In contrast, Newark Bay has exhibited minimal
losses in wetland acres during the past 10 years (Stein-
berg et al., 2004). Table 3-2 shows some of the key
trends in habitat loss and species changes over time in
the New York/New Jersey Harbor estuarine system.
Living Resources
One of the most remarkable characteristics of the
New York/New Jersey Harbor is the diverse range of
living resources that populate the estuary's waters and
coastal wetlands. The HEP, along with the NYSDEC,
NJDEP, and other local agencies, is heavily involved in
monitoring and assessing the abundance and health of
wading birds, fisheries, shellfish populations, and other
wildlife. The HEP is currently establishing a list of key
plant and animal species that are representative of the
biodiversity of the Harbor, and the program is working
to set targets for these populations (NY/NJ HEP, 2004).
The HEP study area is home to a variety of finfish
and shellfish species, including striped bass, bluefish,
freshwater sunfish, sturgeon, shad, winter and summer
National Estuary Program Coastal Condition Report 139
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New York/New Jersey Harbor Estuary Program
flounder, white perch, American eel, and a variety of
forage fish. In total, more than 100 species live in the
Harbor for some or all of their life cycle, and many are
commercially important fish stocks. Generally, an index
of abundance is used to evaluate population sizes over
time. Overfishing, habitat destruction, and contamina-
tion by toxics are the major concerns that affect both
fish and blue crab populations in the Harbor.
Many environmental groups and locals in the HEP
study area consider the striped bass to be one of the
enduring symbols of this system. The striped bass
population has remained fairly constant during the past
two decades, but abundance of other species such as
white perch, American eel, and American shad has been
declining. Catches of striped bass in Jamaica Bay have
been better than in other subbasins of this estuary, but
the reasons for this are not clear. The catch per unit
effort (CPUE) of American shad has generally declined
since the mid-1980s, and other species, such as the
alewife and blueback herring, have exhibited similar
declines over this same period. Relative abundance and
catch of winter flounder has been a concern in some
areas, but catch levels have stabilized in Jamaica Bay and
Haverstraw Bay since the early 1990s. The abundance
of white perch has been declining since the 1980s,
which is likely due to water quality conditions in the
Harbor because this ecologically important species
spends the entire year in this estuary. Three important
forage fish monitored in the HEP estuarine area—bay
anchovy, Atlantic silverside, and killifish—are also likely
affected by changes in salinity, temperature, river flow,
and other factors in the Harbor. Blue crabs are harvested
in both the New York and New Jersey waters of this
estuary, but total landings are much lower than in the
Chesapeake Bay system. The benthic community of the
New York/New Jersey Harbor is considered impacted,
or of degraded quality, as determined by using species
index measures and toxicity tests to assess the health of
benthic habitats (Steinberg et al., 2004).
Shellfish bed closures and shellfish landings are also
monitored in the HEP study area. Shellfish beds are
classified using the guidelines of the National Shellfish
Sanitation Program. The direct harvesting of shellfish is
only permitted in portions of the Navesink and Shrews-
bury rivers between November and April. Although
direct shellfish harvesting is prohibited in all other
portions of the study area, several shellifish beds are
designated as "special restricted." In these waters, shell-
fishers may harvest shellfish and transport them either
to a purification plant in a process known as depuration
harvesting, or to clean waters approved for shellfishing
in a process known as relay harvesting. After purification
at the depuration plant or in the clean waters, the shell-
fish are sent to market. In New York, hard clams are
relay harvested in areas of the Great Kills Harbor and
Raritan Bay between April and October, and more than
77,000 bushels of hard clams were produced in 2001.
These shellfish beds were closed to relay harvest in 2002
due to an outbreak of the shellfish parasite QPX. A
limited portion of the beds was reopened for relay
harvest in 2005, and approximately 17,600 bushels of
hard clams were produced that year (IEC, 2006;
Personal communication, Hoffman, 2006). In New
Jersey, both relay harvest and depuration programs are
active year-round in parts of Raritan Bay, Sandy Hook
Bay, Navesink River, and Shrewsburg River. In 2002,
5,425 acres of shellfish beds in the New Jersey portion
of Raritan Bay were upgraded from "prohibited" to
"special restricted" (Yuhas, 2002b). More than
38.8 million clams were collected through these
harvesting programs from Raritan and Sandy Hook bays
in 2004 (Personal communication, Celestino, 2006).
Double-breasted cormorant populations have increased in the
New York/New Jersey Harbor (Lee Karney, FWS).
140 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
New York/New Jersey Harbor Estuary Program
Although there were virtually no wading birds in this
estuary in the 1960s, populations of herons, egrets,
ibises, and other birds can be seen in New York/New
Jersey Harbor today. The abundance of herring gulls
declined substantially between 1995 and 2001 (Stein-
berg et al., 2004). Double-breasted cormorants have
increased in population numbers, expanding their
nesting area on a number of Harbor islands (Bernick et
al., 2005). Populations of black-crowned night heron,
yellow-crowned night heron, glossy ibis, snowy egret,
and great egret all showed significant population
declines between 1997 and 2001; however, the resur-
gence of ospreys is a good indicator that some areas of
the Harbor are cleaner and healthier than in the past
(Steinberg et al., 2004).
Environmental Stressors
Floatable trash is another major indicator of water
and near-coastal conditions in the HEP study area. The
NJDEP's Clean Shores Program, which utilizes prison
labor, collected 2,563 tons of floatables and wood in
2000. These efforts addressed about 115 miles of shore-
line statewide, with the greatest efforts in the New York/
New Jersey Harbor area (Yuhas, 2002a). The HEP has
set a goal to decrease floatables discharged from CSOs
in New York/New Jersey Harbor to an average of
679 cubic yards of trash by 2009 (NY/NJ HEP, 2004).
In 1988, the Short-term Action Plan for Addressing
Floatable Debris in the New York Bight (U.S. EPA, 1989)
was developed by federal and state entities, and the
USAGE captured 543 tons of material that year, 90%
of which was wood. For 2000, the estimated total
captured was 5,399 tons of floatable debris. All float-
ables are transported out-of-state for disposal, and wood
is transported to out-of-state recycling facilities. Daily
helicopter surveillance fly-overs of the New York/New
Jersey Harbor area, the south shore of Long Island, and
the New Jersey coastline are conducted by state and
federal agencies. The NYCDEP deploys a skimmer boat
for daily floatables collection, commissioned via funding
from an EPA Marine CSO Construction Grant. During
2000, 320 tons (81% wood) were collected by this
vessel. In addition, area volunteer groups and organiza-
tions conduct beach and underwater debris cleanups
during the spring and fall seasons (Yuhas, 2002a).
Current Projects,
Accomplishments, and Future
Goals
Some of the major environmental accomplishments
of the HEP include the following:
• The successful restoration of habitat in the Arthur
Kill area of the New York/New Jersey Harbor
following the Exxon Byway oil spill in 1990.
• The Rahway River Association's restoration
project (1996-2002) resulted in the creation of a
new park in Rahway, NJ, the demolition of
11 unoccupied homes, and the restoration of
4 acres of urban land area (Barnes, 2002).
• Vast improvements in the study area's water
quality due to the construction of and upgrades to
publicly owned treatment works (POTWs)
(Steinberg et al., 2004).
Conclusion
The overall condition of New York/New Jersey
Harbor is rated poor based on the four indices of estu-
arine condition used by the NCA. The HEP has found
that, although some measures of estuarine health in the
study area have demonstrated improvements over time
(including increases in dissolved oxygen levels and
reductions in nutrient loadings), other trends, such as
ongoing fish consumption advisories and declines in
some fish and wading bird populations, have not been
as positive. The inadequate availability of data is still a
significant barrier to properly interpreting indicators in
this estuary system. Some indicators that were once
used are no longer monitored, and some data gaps and
inconsistencies exist among available spatial and
temporal monitoring data for this estuary. Comprehen-
sive monitoring of water quality on the New York side
of the Harbor has produced data for nearly 100 years.
The NJDEP has an excellent system for reporting
closures and beach conditions over time; however, the
collection of comprehensive water quality data on the
New Jersey side of the Harbor has occurred only
recently. Citizens, regulators, and scientists must
continue to work together to realize the HEP's vision to
maintain a healthy and productive Harbor ecosystem
with full beneficial uses.
National Estuary Program Coastal Condition Report 141
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barnegat Bay National Estuary Program
Barnegat Bay National Estuary Program
www.bbep.org
Background
Barnegat Bay in New Jersey covers more than 42
miles of shoreline, from Point Pleasant Canal to Little
Egg Harbor Inlet, and stretches over all of Ocean and
parts of Monmouth counties (BBNEP, 2005a). Habitats
found within the Barnegat Bay watershed vary from
coastal dunes and marshes (much of these areas have
been heavily developed) to the New Jersey pine
barrens—a distinctive pine forest characterized by sandy
soils and fire-adapted plant species, such as pitch pine,
and protected from extensive development. Barnegat
Bay is protected from the open ocean by a system of
barrier island dunes. The Bay itself is very shallow, with
a relatively small amount of fresh water flowing from
tributaries and a limited connection to the ocean.
Groundwater is the source of most of the freshwater
input to the estuary (BBNEP, 2003), with additional
freshwater input coming from several major tributary
rivers, including the Metedeconk and Toms rivers, as
well as the Cedar and Oyster creeks.
EPA designated Barnegat Bay an Estuary of National
Significance on July 10, 1995 (BBNEP, 2002). Although
long recognized for its great aesthetic, economic, and
recreational value, the Bay is now affected by an array of
human impacts that potentially threaten its ecological
142 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barnegat Bay National Estuary Program
integrity. More than 500,000 people live within the
660-mi2 area of the Barnegat Bay watershed, and the
area's population more than doubles during the summer
season. In the last half-century, the Barnegat Bay area
has undergone dramatic development due to increasing
population growth, with land uses changing from prin-
cipally undeveloped and agricultural land to residential
development (BBNEP, 2002). To help protect and
preserve the ecological integrity of this estuary, the
Barnegat Bay National Estuary Program (BBNEP) has
instituted public participation efforts with citizens and
other watershed stakeholders who live, work, and
recreate in the Bay area.
Environmental Concerns
During the 1990s, the municipalities surrounding
Barnegat Bay reported population growth that exceeded
20% per year on average (BBNEP, 2002). The devel-
opment that accompanied this increased population
growth has resulted in significant land-use changes.
Boat traffic in Barnegat Bay has also grown, raising
concerns about general use conflicts and impacts on the
Bay's water quality. Since its inception in 1995, the
BBNEP has focused on several of the area's environ-
mental concerns, including the following:
• Non-point source pollution and water quality
degradation
• Habitat loss and alteration
• Human activities and competing uses
• Water supply protection.
Population Pressures
The population of the 3 NOAA-designated coastal
counties (Burlington, Monmouth, and Ocean) coinci-
dent with the BBNEP study area increased by 132%
during a 40-year period, from 0.67 million people in
1960 to almost 1.55 million people in 2000 (Figure
3-76) (U.S. Census Bureau, 1991; 2001). This rate of
population growth for the BBNEP study area is more
than five times the population growth rate of 24% for
the collective NEP-coincident coastal counties of the
Northeast Coast region. In 2000, the population
density of the BBNEP's 3 coastal counties was 807
persons/mi2, slightly lower than the population density
of 1,055 persons/mi2 for the collective NEP-coincident
I960
2000
Figure 3-76. Population of NOAA-designated coastal counties
of the BBNEP study area, 1960-2000 (U.S. Census Bureau, 199 I;
2001).
coastal counties of the Northeast Coast region (U.S.
Census Bureau, 2001).
NCA Indices of Estuarine
Condition—Barnegat Bay
The overall condition of Barnegat Bay is rated fair
based on the four indices of estuarine condition used by
the NCA (Figure 3-77). The water quality and sedi-
ment quality indices for Barnegat Bay are rated good to
fair, and the benthic and fish tissue contaminants
indices are rated fair. Figure 3-78 provides a summary
of the percentage of estuarine area rated good, fair, poor,
or missing for each parameter considered. This assess-
ment is based on data from 30 NCA sites sampled in
the BBNEP estuarine area in 2000 and 2001. Please
refer to Tables 1-24, 1-25, and 1-26 (Chapter 1) for a
summary of the criteria used to develop the rating for
each index and component indicator.
Overall Condition
Barnegat Bay (3.5)
Water Quality Index (4)
Sediment Quality Index (4)
Benthic Index (3)
Fish Tissue Contaminants
Index (3)
Figure 3-77. The
overall condition of
the BBNEP estuarine
area is fair (U.S.
EPA/NCA).
National Estuary Program Coastal Condition Report 143
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barnegat Bay National Estuary Program
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Estuarine Area
Missing
Figure 3-78. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Barnegat Bay
(U.S. EPA/NCA).
Water Quality Index
The water quality index for Barnegat Bay is rated
good to fair. This index was developed using NCA data
on five component indicators: DIN, DIP, chlorophyll a,
water clarity, and dissolved oxygen (Figure 3-79).
Elevated DIN and DIP concentrations measured in
Barnegat Bay covered one of the smallest extents of all
Northeast NEP estuaries, and chlorophyll a concentra-
tions were moderately high in about a third of the Bay.
Water clarity was fair or poor in 40% of the Bay, in
accordance with the observation that water in the
southern estuaries of the Northeast Coast region is
noticeably less clear than in estuaries farther north. All
Barnegat Bay stations reported satisfactory dissolved
oxygen levels.
Dissolved Nitrogen and Phosphorus I Barnegat
Bay is rated good for DIN concentrations, with 73% of
the estuarine area rated good for this component indi-
cator, 19% of the area rated fair, and none of area rated
poor. NCA data on DIN concentrations were unavail-
able for 8% of the BBNEP estuarine area.
Barnegat Bay is also rated good for DIP concentra-
tions, with 62% of the area rated good, 30% of the area
rated fair, and none of the estuarine area rated poor.
NCA data on DIP concentrations were unavailable for
8% of the BBNEP estuarine area.
Chlorophyll a Barnegat Bay is rated good for
chlorophyll a concentrations. Fifty percent of the estu-
arine area was rated good for this component indicator,
32% of the area was rated fair, and 2% of the area was
rated poor. NCA data on chlorophyll a. concentrations
were unavailable for 16% of the BBNEP estuarine area.
Water Quality Index - Barnegat Bay
Site Criteria: Number of component
indicators in poor or fair condition
9 Good = No more than I is fair
OFair = I is poor, or 2 or more are fair
• Poor = 2 or more are poor
O Missing
Figure 3-79. Water quality index data for Barnegat Bay,
2000-2001 (U.S. EPA/NCA).
144 National Estuary Program Coastal Condition Report
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CHAPTER 3 ! NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barnegat Bay National Estuary Progran
Water Clarity I The water clarity rating for
Barnegat Bay is poor. Water clarity was rated poor at a
sampling site if light penetration at 1 meter was less
than 10% of surface illumination. Twenty-seven percent
of the estuarine area was rated poor for this component
indicator, 49% of the area was rated good, and 13% of
the area was rated fair. NCA data on water clarity were
unavailable for 11% of the BBNEP estuarine area.
Dissolved Oxygen Barnegat Bay is rated good for
dissolved oxygen concentrations, with 100% of the
estuarine area rated good for this component indicator.
Sediment Quality Index
The sediment quality index for Barnegat Bay is rated
good to fair. Fourteen percent of the estuarine area was
classified as having fair or poor sediment quality,
primarily in the Bay's tributaries (Figure 3-80). Toxic
sediments were detected at only one site in Barnegat
Sediment Quality Index - Barnegat Bay
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
OFair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Missing Poor
5% 6% Fair
Figure 3-80. Sediment quality index data for Barnegat Bay,
2000-2001 (U.S. EPA/NCA).
Bay, and relatively little sediment contamination was
noted (fair or poor in 12% of the Bays estuarine area),
a finding typical of the southernmost estuaries of the
Northeast Coast region. TOC levels were elevated in
about a quarter of the Bay's estuarine area.
Sediment Toxicity Barnegat Bay is rated good for
sediment toxicity, with only 1 % of the estuarine area
rated poor for this component indicator. NCA data on
sediment toxicity were unavailable for 5% of the
BBNEP estuarine area.
Sediment Contaminants I Barnegat Bay is rated
good for sediment contaminant concentrations. Only
4% of the estuarine area was rated poor for this compo-
nent indicator, and an additional 8% of the area was
rated fair.
Iota/ Organic Carbon i Barnegat Bay is rated
good for sediment TOC. Seventy-one -percent of the
estuarine area was rated good for TOC concentrations,
and 21% of the area was rated fair. Only 3% of the
estuarine area was rated poor for this component
indicator, and NCA data on TOC concentrations were
unavailable for 5% of the BBNEP estuarine area.
Headwaters of the Toms River (BBNEP).
National Estuary Program Coastal Condition Report 145
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barnegat Bay National Estuary Program
Benthic Index
Fish Tissue Contaminants Index
Benthic condition in Barnegat Bay is rated fair, as
evaluated by the Virginian Province Benthic Index.
Four sites (13%) in Barnegat Bay merited a poor rating
for benthic condition; two of these sites also reported
sediment contamination (Figure 3-81).
Benthic Index - Barnegat Bay
Thirteen fish samples were analyzed for chemical
contaminants in Barnegat Bay, and 31% of samples
were found to have elevated concentrations of mercury,
the pesticide dieldrin, or PCBs (Figure 3-82); therefore,
the fish tissue contaminants index for Barnegat Bay is
rated fair.
Fish Tissue Contaminants Index - Barnegat Bay
Site Criteria:
Virginian Province Benthic Index Score
• Good= > 0.0
• Poor = <; 0.0
O Missing
Site Criteria: EPA Guidance concentration
• Good= Below Guidance range
O Fair = Falls within Guidance range
• Poor = Exceeds Guidance range
Figure 3-81. Benthic index data for Barnegat Bay, 2000-2001
(U.S. EPA/NCA).
Figure 3-82. Fish tissue contaminants index data for Barnegat
Bay, 2000-2001 (U.S. EPA/NCA).
146 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barnegal Bay National Estuary Progran
Barnegat Bay National Estuary
Program Indicators of Estuarine
Condition
The BBNEP uses several primary indicators to eval-
uate environmental conditions and stressors in the Bay's
estuarine area, including land-use changes; SAV distribu-
tion, abundance, and health; signature species; shellfish
beds; and HABs. The BBNEP's indicators were selected
based on their public acceptability, availability of historic
data, and relevance to the goals set forth in the program's
Comprehensive Conservation and Management Plan
(BBNEP, 2002). Several additional indicators are used
by the NJDEP, Rutgers University Institute of Marine
Science, and USGS in the overall monitoring of this
estuarine system (BBNEP, 2003). Based on all of these
indicators, several waterbodies in the BBNEP estaurine
area have been identified as impaired (Table 3-3).
More than 20 secondary indicators are also used
internally by the BBNEP to help evaluate environmental
changes in the Bay; however, most of these secondary
indicators are considered less appropriate than the
primary indicators for conveying environmental
concerns to the public. A variety of secondary indicators
are used for evaluating living resources; environmental
stressors; and water, sediment, and habitat quality in the
study area. For example, some of the secondary indica-
tors used for water quality include dissolved oxygen,
nutrient levels, salinity, turbidity, water temperature,
pH, and saltwater intrusion. The program also uses
measured levels of toxic contaminants in sediments to
assess sediment quality in the Bay (BBNEP, 2003).
Data gaps exist for many of these indicators regarding
both spatial and temporal information (BBNEP, 2003).
Secondary indicators for evaluating water quality,
habitat, or living resources in the Bay have been
approved for use by any of the BBNEP's state partners
or other local agencies involved in managing the estuary
system.
Table 3-3. Waterbodies Assessed as Impaired Based on the Indicators Used by the BBNEP and Partners
(BBNEP, 2003)
Waterbody
Name
Metedeconk
River Estuary
Reach # / Pollution/Impact:
Location Water Quality Violation
Fecal coliform
Pollutant/
Biological
Impact
Use
Impairment
Shellfish
consumption
Lake
Carasaljo
Lakewood,
Ocean County
Mercury in
fish tissue
Fish
consumption
Pohatcong/ Ocean County Elevated bacteria, phosphorus, Heavy Boating and
Tukerton Lake sedimentation macrophyte fishing
Current source: Non-point sources, growth
including suspended solids from
surrounding urban areas and bacteria and
phosphorus from surrounding septic systems
Manahawkin
Lake
Elevated bacteria, phosphorus
Current source: Resident goose and
gull populations.
Former source: Surrounding septic
systems, most of which have been
eliminated through sewering
Localized heavy
macrophyte
growth
Primary contact:
Recreation
Some boating and
fishing impairment
Toms River
Estuary
02040301 -018-022 Fecal coliform
Shellfish
consumption
Toms River
02040301-018-080/
nrToms River
pH, fecal coliform
Primary contact:
Aquatic life support
Barnegat Bay
Portion adjacent
to Toms River
Fecal coliform
Shellfish
consumption
National Estuary Program Coastal Condition Report 147
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barnegat Bay National Estuary Program
SAV Distribution, Abundance,
and Health in Barnegat Bay
SAV, such as seagrass, is a key indicator of the envi-
ronmental health of the Barnegat Bay-Little Egg Harbor
Estuary. Seagrass beds are important in maintaining the
energy flow and nutrients cycling of the estuary and
serve as part of the estuarine food chain. For these
reasons, seagrasses rank among the most sensitive indi-
cators of long-term water quality and can be used as a
sentinel of coastal ecosystem health (Dennison et al.,
1993). Seagrass beds provide a critical structural compo-
nent in an otherwise barren sandy bottom, serving as
essential habitat for a host of organisms, including
mollusks, crabs, worms, fish, and waterfowl.
In recent years, seagrasses have suffered due to
declining water quality; physical damage from dredging
and resulting sedimentation; and the occurrence of
brown tides, benthic algal infestations, boat scarring,
and disease. To remain healthy, seagrasses are dependent
on comparatively clear waters. As Barnegat Bay waters
become more turbid due to HABs and suspended sedi-
ment, the light levels needed to sustain photosynthesis
and seagrass productivity decrease. Nutrient enrichment
of the Bay's waters, whether from runoff, atmospheric
deposition, or boat wastes, promotes HABs and infesta-
tions of some types of algae that coat the seagrass blades
and threaten the longevity of the seagrass beds.
During the past 30 years, significant declines in SAV
have occurred in New Jersey estuaries (Lathrop and
Bognar, 2001), resulting in the reduction of essential
fish habitat and the potential loss of important
commercial and recreational species. In addition,
nutrient enrichment has caused blooms of phyto-
plankton and benthic macroalgae. Dinoflagellate and
brown-tide blooms can reduce light availability;
adversely affect SAV such as eelgrass (Zostera marina)
(Dennison et al., 1989); and cause negative impacts on
other living resources (Bricelj and Lonsdale, 1997).
Brown-tide blooms are now a recurring phenomenon in
the coastal bays of New Jersey, New York, and Maryland.
In response to shading stress, it appears that eelgrass may
also be susceptible to infection by "wasting disease"
(Labyrinthula zosterae) (Bologna and Gastrich, unpub-
lished data). This disease, which decimated eelgrass beds
worldwide during the 1930s (den Hartog, 1987), may
signal a significant decline in water quality. Aside from
the impacts of wasting disease on eelgrass, large-scale
losses of SAV habitat can occur due to the additional
physiological stress associated with HABs.
Status and Trends
Investigators led by Dr. Richard G. Lathrop at the
Grant F. Walton Center for Remote Sensing and Spatial
Analysis (CRSSA) at Rutgers University and the Jacques
Cousteau NERR are monitoring SAV beds in the
Barnegat Bay-Little Egg Harbor Estuary. During 2003,
these researchers conducted an extensive SAV mapping
project to better understand the present status of the
estuary's seagrass habitats. This project was conducted
using advanced digital images shot from an aircraft-
mounted camera flown along the entire length of the
estuary. Color imagery was used in the spring (May 4
and 5, 2003), before Bay waters became too turbid,
thereby enabling the researchers to visualize the Bay
bottom and determine the location and extent of the
seagrass beds. The aerial imaging was complemented by
boat-based surveys in the Bay to determine species type
(e.g., eelgrass, widgeon grass [Ruppia maritima]), percent
coverage, blade height, and sediment type. Using these
advanced computer-aided interpretation techniques,
researchers were able to map precisely the location, areal
extent, and percent coverage of the seagrass beds in great
detail. The resulting maps documented 12,804 acres of
seagrass beds in the Barnegat Bay-Little Egg Harbor
Estuary (see map) (Lathrop, 2004).
SAV distribution in the Barnegat Bay-Little Egg
Harbor Estuary appears to have remained reasonably
stable when compared with the maps of the period from
1990—2000. This stability is a positive outcome consid-
ering the continued development of the watershed, as
well as the severe brown-tide occurrences that were
148 National Estuary Program Coastal Condition Report
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CHAPTER 3 ' NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barnegat Boy National Estuary Program
prevalent in the Bay during
2001 and 2002. However, the
condition of the indicator
appears to have changed substan-
tially from previous years. Since
1968, for example, periodic
mapping surveys in the Barnegat
Bay-Little Egg Harbor Estuary
indicated significant shifts in
seagrass distribution. In partic-
ular, earlier surveys showed
evidence of a decline in the
seagrass extent between the late
1970s and the mid-1990s,
especially in the northern areas
of the Bay. Boat-based surveys
conducted between 1996 and
1999 mapped 15,025 acres of
seagrass. A decline of approxi-
mately 2,220 acres, or 15% of
seagrass beds, appears to have
occurred between the late 1990s
and 2003 maps. Rather than
representing a significant decline
in seagrass, the difference in
acreage is most likely due to a
change in mapping techniques
and the timing of the aerial
imagery acquisition (Lathrop,
2004).
SA V in Barnegat Bay -
Little Egg Harbor - Great Bay,,
Bottom Classification
•I Dense (80-100%)
• Moderate (40 - 80 %)
Bi Sparse (10 -40%)
Hi Macro Algae
I I Shallow Sand/Mud Flats
E53 Deep Water/Channels
New
Jersey
10
Kilometers
Source: Grant F. MMhm Center for
Sensing C Spatial Analysis, 2003
SAV coverage in Barnegat Bay and Little Egg Harbor (Grant F. Walton CRSSA).
National Estuary Program Coastal Condition Report 149
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barnegot Bay National Estuary Program
Water and Sediment Quality
The following four primary indicators help the
BBNEP measure water and sediment quality in
Barnegat Bay:
• Number (and duration) of bathing beach closures
• Acres of shellfish beds open/closed
• Presence of HABs (e.g., acres of coverage)
• Freshwater inputs to the Bay (e.g., changes in
stream flow, water allocation).
The number and duration of beach closures in the
BBNEP study area is an indicator of water quality and
is measured to help determine if bathing areas are safe
for public use. The NJDEP helps report on levels of
fecal coliform bacteria recorded in water samples and
evaluates swimming conditions in the waters of Barne-
gat Bay. New Jersey's surface water quality standards in
for recreational contact with estuarine waters specify
that fecal coliform levels should be below a mean of
50/100 mL within 1,500 feet of the shoreline. From
1988 to 1998, 834 beach closings were registered in
the estuary as a result of elevated fecal coliform counts
in water samples (BBNEP, 2002), Fecal coliform
bacteria data collected by the USGS/NJDEP water
quality network have shown an improvement in the
Toms River area between 1988 and 1992 (BBNEP,
2001).
The number of acres of shellfish beds that are open
or closed for harvesting is also a good indicator of
pathogen levels in the Bay. Bacterial standards for
shellfish harvesting are set by the Interstate Shellfish
Sanitation Conference. New Jersey uses fecal coliform
measures to determine the areas of Barnegat Bay that
are safe for shellfishing and the areas that are of poten-
tial risk to public health. The general trend in the
BBNEP study area during the past 30 years has been
toward fewer restrictions on shellfish harvesting. The
largest areas of shellfish-harvesting restriction occur in
the tributaries of Barnegat Bay, from Toms River
northward, and along the barrier island in the same
portion of the Bay. The harvesting of shellfish from all
man-made lagoons and marinas is also prohibited
(BBNEP, 2001).
The presence and growth of HABs is another
indicator of water quality in the BBNEP system.
Brown tides caused by a toxic dinoflagellate
(Aureococcus anaphagefferens) have had severe effects on
eelgrass beds, and the damage associated with these
blooms has occurred with increasing frequency. Brown
tides may also reduce local fishing, swimming, and
boating activities in the estuary. HABs are monitored
for frequency of occurrence, area/extent, and intensity,
and the abundance and species composition of HABs
provides information about changing water quality
conditions (BBNEP, 2003). Educational information
about the effects of these blooms has been made avail-
able to the public through local newspapers and
outreach materials from the Rutgers University Cooper-
ative Extension.
Freshwater inputs to Barnegat Bay are monitored
closely as another primary indicator of water quality
and environmental stress. The New Jersey Statewide
Water Supply Master Plan (NJDEP, 1996) identifies the
Barnegat Bay watershed as an area that will experience a
significant water supply deficit by the year 2040.
Despite this prediction, withdrawal of potable water for
this area is almost completely consumptive because
most wastewater is discharged to the ocean. These
actions result in saltwater intrusion and reduced stream
flow. Modifications to the Barnegat Bay landscape also
change the natural hydrology by reducing recharge and
increasing runoff. Monitoring surface water discharge is
the most cost-effective means to monitor freshwater
inputs (BBNEP, 2003). The USGS measures short- and
long-term changes in base flow and water consumption
in the northern part of the Bay, but continuous gauging
is not available in the southern part of this system.
Osprey nest at Island Beach State Park, Seaside Park, Nj (BBNEP).
1 50 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Bornegat Bay National Estuary Program
Habitat Quality
The following two measures are primary indicators
used by BBNEP to evaluate habitat loss and/or changes
in quality of land in the watershed:
• SAV distribution and abundance (acres)
• Land-use change (acres).
Land-use change in the Barnegat Bay watershed is a
major indicator used to evaluate environmental changes
to this ecosystem. The developed area of the Bay water-
shed increased from 18% in 1972 to 28% in 1995
(BBNEP, 2002). With more than 70% of the Barnegat
Bay shoreline already developed, the remaining undevel-
oped shoreline areas are especially valuable as open
space (BBNEP, 2003).
The BBNEP monitors shoreline habitats, island
nesting habitats, and other sensitive areas as secondary
indicators of habitat quality (BBNEP, 2003). Salt
marshes are one of these sensitive habitats. Roughly
90% percent of Barnegat Bay's salt marshes are
protected by some form of public conservation owner-
ship (e.g., national wildlife refuge, state game manage-
ment area, state/local park, or private conservation
trust) (BBNEP, 2001). A variety of shorebirds and colo-
nial nesting birds, such as common terns (Sterna
hirundo), black skimmers (Rhynchops niger), and
Forster's terns (Sterna forsteri), nest almost exclusively on
salt marsh or dredge spoil islands for protection from
mammalian predators. Sixty-one Barnegat Bay islands
have been ranked for their importance as nesting
habitat for common terns, black skimmers, and
Forster's terns, based on data collected from the mid-
1970s to the present (BBNEP, 2003). Other critical
wildlife habitat areas that should receive special consid-
eration are coastal dune scrub/shrub and large areas of
cultivation/grassland. Dune grass and shrub vegetation
serve a useful role in stabilizing dunes and protecting
beaches against wind and wave erosion. Extensive
remnants of these habitats exist at Island Beach State
Park and at the Holgate section of Forsythe National
Wildlife Refuge. The dune scrub/shrub and woodland
communities of the barrier islands fronting Barnegat
Bay have largely been destroyed or substantially altered
(BBNEP, 2002).
Living Resources
The BBNEP uses several signature species as primary
indicators of the living resources in the Bay. These
species include the following:
• Hard clams
• Colonial nesting waterbirds
• Osprey.
The hard clam (Mercenaria mercenaria) is an impor-
tant commercial and recreational fishery species that
lives in the fine-grained sediments and SAV beds of the
Bay. Hard clams are a good indicator of estuarine health
because they are long-lived and have a wide distribution
throughout the Bay (BBNEP, 2003). Hard clam popu-
lations have decreased over time (BBNEP, 2002), with
the amount of hard clams harvested in Barnegat Bay
falling from about 820,000 pounds to approximately
65,000 pounds between 1989 and 1997 (BBNEP,
2001).
Barnegat Bay provides nesting habitat for 20 species
of colonial waterbirds, including 10 species of long-
legged wading birds, 6 species of terns, 3 species of
gulls, black skimmers, and piping plover. These birds
are good indicators of the living resources in the Bay
because they have high sensitivities to chemical contam-
inants, human disturbance, the availability of resources,
and the overall quality of the available habitat. Since
1985, the NJDEP has conducted ground and aerial
surveys to assess the abundance of these birds. These
surveys have indicated that some species have experi-
enced population decreases due to habitat loss, human
disturbance, and predation (BBNEP, 2003).
The NJDEP conducts an annual census of the
osprey population in the Bay to record the number of
nesting pairs and fledglings success (BBNEP, 2003).
Statewide, the number of ospreys increased between
1975 and 1998, from 50 to more than 250 nests.
Although specific data for Barnegat Bay are unavailable,
the Bay has historically been an important nesting area
for this species. Osprey populations in the region are
limited by available nesting habitat, predation, exposure
to toxics, and human disturbance (BBNEP, 2001).
National Estuary Program Coastal Condition Report 151
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barnegot Bay National Estuary Program
The BBNEP also uses several secondary indicators
to assess living resources, including the abundance of
shellfish and finfish, the composition and abundance of
benthic communities, and the presence of rare plant
and animal populations (BBNEP, 2003).
Environmental Stressors
Several of the BBNEP s secondary indicators can be
used to evaluate the impact of human activities in the
estuary. These indicators include the following:
• Amount and type of floatable debris
• Number of registered boats.
For example, boating is a popular activity in the
study area. A variety of different watercraft support
182 marinas in the Barnegat Bay watershed (BBNEP,
2002). Between 1979 and 1988, the estimated number
of boats in the Bay increased from 30,000 to 53,200
(BBNEP, 2001).
Current Projects,
Accomplishments, and Future
Goals
Some of the recent environmental success stories
achieved in the Barnegat Bay system include the
following:
• On June 6, 2003, EPA announced the establish-
ment of a No-Discharge Zone in Barnegat Bay.
This designation prohibits boats from releasing
treated or untreated sewage into the Bay. Roughly
75 marinas in Ocean County maintain land-
based pump-out stations to further reduce illegal
discharges of sewage (Ocean County Department
of Planning, 2006).
• In 2004, the BBNEP, in partnership with the
Jacques Cousteau NERR, implemented a multi-
tiered public education approach aligned with the
NJDEP s Phase II Municipal Stormwater Permit-
ting Program. A steering committee of interested
county, academic, and local educational organiza-
tions was formed to provide outreach and assis-
tance to the 37 municipalities within the Bay's
watershed on new Phase II Stormwater regula-
tions. Examples of the committee's services
include workshops, technical assistance, public
outreach assistance, and Stormwater resources.
In addition, the BBNEP developed and imple-
mented six Phase II Municipal Stormwater
Roundtables in 2005 to help the municipalities
achieve compliance with the new state regulations.
The Ocean County Department of Planning also
supplied matching funds to assist: municipalities
with the development of their EPA-required
Stormwater Pollution Prevention Plans.
The BBNEP and the Ocean County Department
of Planning funded the purchase of dune grass for
a restoration project on Island Beach State Park,
where the BBNEP contributed more than 15,000
plants (Lynch, 2003).
Between October 2003 and September 2005,
more than 3,200 acres of habitat in the Bay's
watershed were preserved by state, county, and
municipal agencies (BBNEP, 200 5b).
The BBNEP and its partner, the Rutgers
University Institute of Marine and Coastal
Science, have recently completed a demographic
investigation of SAV in Barnegat Bay. This investi-
gation included an assessment of the potential
impacts of benthic macroalgae and brown tides.
The BBNEP has also partnered with Montclair
State University to assess the effects of harmful
macroalgal blooms on the Bay's SAV.
The BBNEP, in partnership with Rutgers Univer-
sity, USGS, and the NJDEP, has established two
Mobile pump-out stations, such as the boat shown here, help
reduce sewage discharges to Barnegat Bay (BBNEP).
1 52 National Estuary Program Coastal Condition Report
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CHAPTER 3 i NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barnegat Bay National Estuary Program
water quality monitoring stations and data loggers
in the Bay to record and deliver real-time data to
an NJDEP Web site. These data loggers monitor
some of the BBNEP's secondary indicators, such as
turbidity, salinity, and dissolved oxygen (NJDEP,
2006). The BBNEP and other partner agencies
plan to deploy several more data loggers at addi-
tional sites in the near future.
The Ocean County Soil Conservation District
is working in the Barnegat Bay watershed to
increase groundwater recharge in developed areas
by establishing Rain Garden Basins and repairing
poorly constructed retention basins. In addition,
the District is working to establish outdoor class-
rooms and rain gardens at schools throughout the
watershed. Four outdoor classrooms were estab-
lished in 2005, and the District has a goal to
establish 50 classrooms in Ocean County by the
year 2009 (BBNEP, 2005c).
The Rutgers Cooperative Research and Extension
of Ocean County has partnered with the BBNEP
and Ocean County to educate citizens about the
Bay, its watersheds, and human impacts on the
estuary by using hard clams and oysters as living
representatives of the Bay's ecosystem. The group
is also working with volunteers to seed and grow
hard clams in the Bay.
Conclusion
The overall condition of Barnegat Bay is rated fair
based on the four indices of estuarine condition used by
the NCA survey. Non-point source pollution/water
quality degradation, habitat loss and alteration, human
activities and competing uses, and water supply protec-
tion remain the most critical environmental concerns in
Barnegat Bay. The apparent decline in SAV beds is a
cause for concern and warrants further investigation.
Some causes of habitat loss/fragmentation and the
decline of fish and wildlife species in the BBNEP study
area are not well understood. Similarly, although there is
a clear indication that human development has led to
declining water quality (associated with non-point
source pollution), quantifying this impact on water
quality and aquatic habitats in the estuary is more diffi-
cult. More research is warranted on the relationship
between habitat loss and alteration in the estuary water-
shed and the impacts on nesting birds and other wildlife
in the ecosystem.
I
Barnegat Lighthouse, Long Beach Island, NJ (BBNEP).
National Estuary Program Coastal Condition Report 1 53
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CHAPTER 3 NORTHEAST-COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Partnership for the Delaware Estuary
Partnership for the Delaware Estuary
DELAWARE
ESTUARY
www.delawareestuary.org
Background
The Delaware Estuary stretches from the falls at
Trenton, NJ, and Morrisville, PA, south to the mouth
of the Delaware Bay between Cape May, NJ, and Cape
Henlopen, DE. In addition to its remarkable natural
habitats, the Delaware Estuary has one of the world's
highest concentrations of heavy industry and maintains
the world's largest freshwater port, which is also
regarded as a strategic military port (DRBC, 2005;
PDE, 2005). The port is home to the second-largest
Atlantic Ocean
Cape May
Cape Henlopen
refming-petrochemical center in the United States,
providing 70% of gasoline and heating oil for the entire
East Coast (Martin et al., 1996). The NEP study area for
the Estuary covers roughly 6,747 mi2 of land that drains
into 134 miles of the Delaware River and Bay. The study
area is part of the larger Delaware River Basin, which is
13,539 mi2 and drains parts of Pennsylvania (50.3%),
New Jersey (23.3%), New York (18.5%), and Delaware
(7.9%) (PDE, 2002b).
1 54 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Partnership for the Delaware Estuary
Primary freshwater inflows to the Delaware Estuary
are from the Delaware and Schuylkill rivers (Sutton et
al., 1996). The water budget for the basin includes
numerous human uses, including public water supply,
power generation, and other industrial needs. For
example, the Delaware River Basin provides a source of
drinking water for more than 15 million people (2000
estimate), and New York City uses up to 800 million
gallons per day from the upper Delaware River for its
drinking water (Martin et al., 1996; DRBC, 2005).
More than 200 migrant and resident finfish and
shellfish species use the Delaware Estuary for feeding,
spawning, or nursery grounds. These species include
sharks, skates, blue crab, striped bass, shad, sturgeon,
American eel, blueback herring, Atlantic menhaden,
alewife, bluefish, weakfish, and flounder. Oysters and
blue crabs represent important shellfish resources in this
system. The Estuary is also home to the largest popula-
tion of horseshoe crabs in the world and is an impor-
tant link in the migratory path of a wide variety of
shorebirds and waterfowl (Dove and Nyman, 1995).
Natural habitats in this watershed include tidal salt
marshes, tidal freshwater marshes, intertidal mudflats,
oyster reefs, beaches, inland wetlands, and upland
meadows and forests. Of particular note are the exten-
sive tidal wetlands that fringe much of the margin of
the Estuary. Historically, the Estuary's wetland habitats
provided critical habitat for many of the region's threat-
ened and endangered species. Today, these habitats are
still believed to play a fundamental role in sustaining
the ecology and helping to maintain water quality for
the overall estuarine system (Kreeger et al., 2006).
The Partnership for the Delaware Estuary (PDE)
oversees the NEP for the Delaware Estuary. The PDE
was established in 1996 and is currently implementing
its CCMP, The Delaware Estuary—Discover its Secrets:
A Management Plan for the Delaware Estuary (Delaware
Estuary Program, 1996). The PDE is the only tri-state
NEP, and its principal partners include the States of
Delaware and New Jersey; the Commonwealth of
Pennsylvania; the Delaware River Basin Commission
(DRBC); and the City of Philadelphia. Various key
federal, state, and local agencies; non-profit organiza-
tions; the private sector; and citizens' groups also
continue to play a critical role. Through the collective
efforts and coordinated authorities of its participants,
the PDE continues to strive for success in its role to
implement the CCMP and address new and emerging
issues that impact the Estuary. The role of the PDE is to
act as a coordinator, information clearinghouse, facili-
tator, leader in providing a regional watershed focus,
setter of environmental indicators and goals, and
provider of incentives throughout the Delaware Estuary
region to encourage actions toward the implementation
of the CCMP.
Environmental Concerns
Changes in land use, the area's legacy of pollution,
and declines in living resources are some of the top
environmental concerns in the Delaware Estuary.
Between 1970 and 1990, developed land within the
watershed increased by 19.6%, and forecasts indicate
that the amount of developed land in the region will
increase by 36%, or roughly 275,000 acres, between
1990 and 2020 (PDE, 2002b). Residential and
commercial development pressures impact the total
acreage of natural lands, parklands, and farmlands in
the watershed, reducing the amount of ecologically
important wetland habitats, open areas for public
recreation, and economically valuable farmland in the
region. Such changes in land use have customarily been
associated with increased stormwater runoff, which
carries higher concentrations of nutrients, toxics, and
heavy metals to the Estuary. The greater Philadelphia
region was a former center for the Industrial Revolution
in the New World and contains a legacy of pollution
lasting more than 300 years. Much of the contaminant
load in this area's present-day stormwater runoff can be
attributed to the activities of past industry (Sharp,
2005). ATMDL process is currently underway to
address the legacy of PCB contamination in the tidal
river and Estuary, and mercury levels in fish tissue
necessitate consumption advisories for many edible
estuarine and freshwater fish species (Santoro, 2004;
U.S. EPA, 2005a). In addition, the area's populations of
finfish and shellfish decreased throughout the early
1900s due to overfishing, habitat loss, and water quality
declines (Martin et al., 1996).
I
National Estuary Program Coastal Condition Report 155
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Partnership for the Delaware Estuary
Population Pressures
The population of the 24 NCAA-designated coastal
counties in Delaware, Maryland, New Jersey, and
Pennsylvania coincident with the PDE study area
increased by 35% during a 40-year period, from
7 million people in 1960 to almost 9.4 million people
in 2000 (Figure 3-83) (U.S. Census Bureau, 1991;
2001). This rate of population growth for the PDE
study area is slightly higher than the population growth
rate of 24% for the collective NEP-coincident coastal
counties of the Northeast Coast region. In 2000, the
population density of the Delaware Estuary's 24 coastal
counties was 772 persons/mi2, about 27% lower than
the population density of 1,055 persons/mi2 for the
collective NEP-coincident coastal counties of the
Northeast Coast region (U.S. Census Bureau, 2001).
Population pressures for this study area are likely high
because the Estuary serves a major metropolitan area
that is a center for industry, commerce, and commercial
and recreational fishing.
10
E 6
o 4
•a
O. 2
I960
2000
Figure 3-83. Population of NOAA-designated coastal counties of
the PDE study area, 1960-2000 (U.S. Census Bureau, 199 I; 2001).
The following sections of this report discuss two different
approaches for characterizing estuarine condition. The
Delaware Estuary is a complex system with many features
that are distinctly different from other large estuaries.
Ideally, a comprehensive assessment of conditions would
consider as much physical, chemical, biological, and
ecological information as possible, including data collected
by both national and regional programs.
Approach I -The NCA provides unbiased, quality-
assured data that can be used to make consistent "snap-
shot" comparisons among the nation's estuaries. These
comparisons are expressed in terms of the percent of
estuarine area in good, fair, or poor condition.
Approach 2 - Each individual NEP collects site-specific
estuarine data in support of local problem-solving efforts.
These data are difficult to compare among NEPs, within
regions, or nationally because the sampling and evaluation
procedures used by the NEPs are often unique to their
individual estuaries; however, these evaluations are impor-
tant because NEP-collected data can evaluate spatial and
temporal changes in estuarine condition on a more in-
depth scale than can be achieved by the NCA snapshot
approach. As an example of the importance of considering
information from both approaches, the water quality
condition rating for the Delaware Estuary differs between
the two approaches because it reflects different sampling
metrics, approaches, and interpretations. Whereas the
NCA survey places emphasis on nutrient conditions to
understand eutrophication problems, regional NEP
programs in the Delaware Estuary have found that
eutrophication outcomes linked to high nutrient levels
are not as problematic as other water quality stressors.
NCA Indices of Estuarine
Condition—Delaware Estuary
The overall condition of the Delaware Estuary is rated
poor based on the four indices of estuarine condition
used by the NCA (Figure 3-84). The sediment quality
index for the Delaware Estuary is rated good to fair, and
the water quality, benthic, and fish tissue contaminants
indices are each rated poor. Figure 3-85 provides a
summary of the percentage of estuarine area rated good,
fair, poor, or missing for each parameter considered. This
assessment is based on data from 74 NCA stations
sampled in the PDE estuarine area in 2000 and 2001.
Please refer to Tables 1-24, 1-25, and 1-26 (Chapter 1)
for a summary of the criteria used to develop the rating
for each index and component indicator.
1 56 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Partnership for the Delaware Estuary
Overall Condition
Delaware Estuary
1.75)
Water Quality Index (I)
Sediment Quality Index (4)
Benthic Index (I)
Fish Tissue Contaminants
Index (I)
Figure 3-84. The
overall condition of
the PDE estuarine
area is poor (U.S.
EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80
Percent NEP Estuarine Area
100
Missing
Figure 3-85. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Delaware
Estuary (U.S. EPA/NCA).
Water Quality Index
The water quality index for the Delaware Estuary is
rated poor. This index was developed using NCA data
on five component indicators: DIN, DIP, chlorophyll a,
water clarity, and dissolved oxygen. Sixty-seven percent
of the estuarine area was rated fair for water quality,
27% of the area was rated poor, and less than 1 % of
the area was rated good. NCA data on water quality
were unavailable for 6% of the PDE estuarine area
(Figure 3-86). In general, the Delaware Estuary received
better ratings for the component indicators of the water
quality index than its rating for the index. The Estuary
is rated good for dissolved oxygen; fair for DIP, chloro-
phyll a, and water clarity; and poor for DIN.
Water Quality Index - Delaware Estuary
I
Site Criteria:
Number of component indicators
in poor or fair condition
• Good = No more than I is fair
OFair = I is poor, or 2 or
more are fair
• Poor = 2 or more are poor
O Missing
Figure 3-86. Water quality index data for the Delaware Estuary,
2000-2001 (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 1 57
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Partnership for the Delaware Estuary
EPA has interpreted these ratings to indicate that the
Delaware Estuary is a highly productive and relatively
well-mixed system. The NCA data show that the Dela-
ware Estuary has high nitrogen loadings and elevated
levels of chlorophyll a relative to other NEP estuaries of
the Northeast Coast. These elevated chlorophyll a levels
indicate that an abundance of phytoplankton is present
in the PDE estuarine waters. During the NCA evalua-
tion period, all of the measured dissolved oxygen
concentrations were greater than 2 mg/L, and 89% of
the estuarine area was rated good for this component
indicator. This finding may indicate that the well-mixed
nature of the Estuary is decoupling, at least at times, the
typical linkages between increased DIN, DIP, and
chlorophyll a concentrations and the occurrence of
hypoxic conditions; however, in 2000 and 2001, the
NCA collected most of the dissolved oxygen data during
the early fall (October). As a result, the degree to which
this decoupling may be occurring is uncertain because of
the minimal amount of dissolved oxygen data collected
during the summer season (July 1 though September
30), which represents a more critical time period for
water quality. The PDE has collected dissolved oxygen
data during the summer (see Figure 3-90), and these
findings are discussed later in this profile.
Dissolved Nitrogen and Phosphorus I The
Delaware Estuary is rated poor for DIN concentrations.
Nine percent of the estuarine area was rated good for
DIN concentrations, 49% of the area was rated fair,
and 37% of the area was rated poor. NCA data on DIN
concentrations were unavailable for 5% of the PDE
estuarine area.
The Delaware Estuary is rated fair for DIP concentra-
tions. Thirteen percent of the estuarine area was rated
good for DIP concentrations, 61% of the area was rated
fair, and 20% of the area was rated poor. NCA data on
DIP concentrations were unavailable for 6% of the PDE
estuarine area.
Chlorophyll a I The Delaware Estuary is rated fair
for chlorophyll a concentrations. Twenty percent of the
estuarine area was rated good for this component indi-
cator, 63% of the area was rated fair, and 12% of the
area was rated poor. NCA data on chlorophyll a concen-
trations were unavailable for 5% of the PDE estuarine
area.
Water Clarity \ The water clarity rating for the
Delaware Estuary is fair. Diminished water clarity is
common in mid-Atlantic estuaries; therefore, the refer-
ence levels used to characterize water clarity were
different for the more naturally turbid Delaware
Estuary. Greater turbidity was required in the Delaware
Estuary to merit a fair or poor rating than in neigh-
boring estuaries. Water clarity was rated poor at a
sampling site in if light penetration at 1 meter was less
than 5% of surface illumination. Twenty-one percent of
the estuarine area was rated poor for this component
indicator, 71% of the area was rated good, and 8% of
the area was rated fair.
Dissolved Oxygen I The Delaware Estuary is rated
good for dissolved oxygen concentrations. Dissolved
oxygen concentrations were rated good in 89% of the
estuarine area and fair in 1 % of the area. There were no
areas where dissolved oxygen concentrations were rated
poor. NCA data on dissolved oxygen concentrations
were unavailable for 10% of the PDE estuarine area.
Sediment Quality Index
Based on the NCA data, the sediment quality index
for the Delaware Estuary is rated good to fair. This
index was developed using NCA data on three compo-
nent indicators: sediment toxicity, sediment contami-
nants, and sediment TOC. Sixty-five percent of the
estuarine area was rated good for sediment quality, 18%
was rated fair, and 6% was rated poor; NCA data on
sediment quality were unavailable for 11 % of the PDE
estuarine area (Figure 3-87). Of the component indica-
tors, sediment contaminant and sediment TOC concen-
trations in Delaware Estuary were rated good, but
sediment toxicity was rated poor.
Sediment Toxicity I Based on NCA data, the
Delaware Estuary is rated poor for sediment toxicity
because 5% of the area was rated poor for this compo-
nent indicator. It should be noted that this measure-
ment of sediment toxicity is very close to a rating of
good (less than 5% of the area rated poor) and that
NCA data on sediment toxicity data were unavailable
for 12% of the PDE estuarine area.
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Sediment Quality Index - Delaware Estuary
Site Criteria: Number and condition of
component indicators
9 Good = None are poor, and sediment
contaminants is good
O Fair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Good
Figure 3-87. Sediment quality index data for the Delaware
Estuary, 2000-2001 (U.S. EPA/NCA).
Sediment Contaminants \ The Delaware Estuary
is rated good for sediment contaminant concentrations.
Only 1 % of the estuarine area was rated poor for this
component indicator, and 18% of the area was rated
fair. The highest levels of sediment contaminants were
measured in the vicinity of Philadelphia and the
Maurice River.
Total Organic Carbon I The Delaware Estuary is
rated good for sediment TOC. Sixty-seven percent of
the estuarine area was rated good for this component
indicator, and 19% of the area was rated fair. No
portions of the Delaware Estuary were rated poor for
this component indicator; however, NCA data were
unavailable for 14% of the PDE estuarine area.
Benthic Index
The benthic condition rating for the Delaware
Estuary is poor, as evaluated by the Virginian Province
Benthic Index. The benthic index was rated good for
34% of the area and poor for 29% of the area. NCA
data on benthic condition were unavailable for a
significant portion (37%) of the PDE estuarine area
(Figure 3-88).
Benthic Index - Delaware Estuary
I
Site Criteria:
Virginian Province Benthic
Index Score
»Good = > 0.0
• Poor = ^ 0.0
O Missing
Figure 3-88. Benthic index data for the Delaware Estuary,
2000-2001 (U.S. EPA/NCA).
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Partnership for the Delaware Estuary
Fish Tissue Contaminants Index - Delaware Estuary
Fish Tissue Contaminants Index
The fish tissue contaminants index for the Delaware
Estuary is rated poor (Figure 3-89). Thirty percent of
fish tissues sampled were rated good for contaminant
concentrations, and 8% were rated fair. Sixty-two
percent of fish tissues sampled were rated poor for
contaminant concentrations, with unsatisfactory
concentrations of PCBs, DDT, PAHs, or the pesticide
dieldrin exhibited in fish tissues.
Partnership for the Delaware
Estuary Indicators of Estuarine
Condition
The PDE interpreted both the NEP's long-term
monitoring data and the data collected by the NCA
survey to form an integrated assessment of conditions in
the Delaware Estuary. This analysis demonstrates the
importance of considering information from both
approaches because the water quality condition rating
differs between the two data sets, reflecting different
sampling metrics, approaches, and interpretations.
Whereas the NCA survey places emphasis on nutrient
conditions to understand eutrophication problems,
regional NEP programs in the Delaware Estuary have
found that the problems associated with eutrophication
are dwarfed by problems from other water quality
stressors. Based on the combined findings of the
national and regional programs, and considering condi-
tion metrics in addition to water quality, the PDE rates
the overall condition of the Delaware Estuary as fair
(Personal communication, Kreeger, 2006).
The PDE has developed an initial suite of land and
water indicators for water quality, habitat, and living
resources, which are being used to assess progress in
meeting program objectives to establish quantitative
goals and to direct restoration efforts. Environmental
conditions in the Estuary are currently monitored by
numerous programs, as shown in Table 3-4. The PDE,
EPA, DRBC, and a number of other partners are
currently in the process of developing a conceptual
framework that links science with management activi-
ties and integrates indicators, goals, restoration strate-
gies, and monitoring efforts (Kreeger et al., 2006). The
status of some of the PDE's indicators is discussed in
this section. Additional information about the PDE's
Site Criteria:
EPA Guidance concentration
• Good = Below Guidance range
OFair = Falls within Guidance range
• Poor = Exceeds Guidance range
Good
Figure 3-89. Fish tissue contaminants index data for the
Delaware Estuary, 2000-2001 (U.S. EPA/NCA).
indicators and the Estuary's monitoring programs can
be found at http://www.delawareestuary.org and
http://www.state.nj. us/drbc.
Water and Sediment Quality
Water quality sampling is a collaborative effort
between EPA and the state and regional partners
managing the Delaware Estuary. Each year, water
samples are routinely collected 12 times during the
period from March to October. The following measures
are key indicators used for evaluating water quality in
the Delaware Estuary:
• Nutrients
• Dissolved oxygen
• Chlorophyll a
• Turbidity
• Toxics
• Bacteria.
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Table 3-4. Examples of Monitoring Programs in the
Tidal Delaware Estuary (Santoro, 2004)
Program
Purpose
Estuary boat run
TMDLs
Automated dissolved
oxygen and specific
conductance
monitoring
Groundwater and
surface water flow
monitoring
Sediment surveys
Ambient toxicity
surveys
Fish tissue analysis
Assess compliance with water
quality standards for conven-
tional pollutants, metals, and
volatile organics; develop and
calibrate water quality models
for conventional and toxic
pollutants
Collect, analyze, and assess air,
ambient water, sediment, and
tributary samples for contami-
nants of concern forTMDL
efforts
Assess compliance with water
quality standards; provide data
to upgrade standards to fishable/
swimmable levels; track salt
fronts; and regulate reservoir
releases
Provide data for regulating
river flows and groundwater
usage
Provide data on sediment
concentrations of toxic pollut-
ants for water quality models
Assess compliance with chronic
whole-effluent water quality
standards
Assess impairment of fish
consumption use by bioaccumu-
lative pollutants
The levels of most nutrients in the Delaware Estuary
have generally been increasing since the early 1900s.
Phosphorus levels are an exception and have changed
little since the 1980s. The portion of the Delaware
River between Burlington, NJ, and Wilmington, DE,
has the highest nitrogen concentrations of any major
estuary in the United States. Between 1998 and 2003,
nutrient loadings to the Estuary continued to be
elevated. Nutrient levels of nitrate-nitrogen, nitrite,
ammonia nitrogen, total phosphorus, and orthophos-
phate are monitored in the Estuary, and in general, were
higher in channel stations than in other portions of the
Delaware Estuary (Santoro, 2004).
Since the late 1970s, dissolved oxygen levels have
shown substantial improvements in the Camden-Phila-
delphia stretch of the Delaware Estuary. Historically,
dissolved oxygen levels in the waters around this heavily
industrialized area were significantly lower than in other
reaches of the Delaware River, and seasonal declines in
dissolved oxygen levels were dramatic. Figure 3-90
shows this drop in dissolved oxygen levels between river
miles 75 and 95 in 1967 and 1980 (Santoro, 2004).
The resulting hypoxic area discouraged or blocked the
passage of many fish during their natural migration and
resulted in population declines for certain fish species,
such as the striped bass. Pollution-control measures and
protective management have helped dissolved oxygen in
estuarine waters rebound to acceptable levels (PDE,
2002b).
Chlorophyll a and turbidity are also monitored in
the Delaware Estuary. Chlorophyll a is used as an indi-
cator of algal biomass to assess the growth of the phyto-
plankton community in the Estuary. Mean chlorophyll
a concentrations in the Delaware Estuary are similar to
those measured in Chesapeake Bay, where eutrophica-
tion has been a major concern. Despite these levels of
chlorophyll a, the Delaware Estuary has not yet
experienced the negative signs typically associated with
eutrophication (e.g., fish kills, algal blooms, and water
discoloration) (Santoro, 2004). Several possible explana-
tions for this lack of eutrophication exist, including the
complex interrelationships between nutrient concentra-
tions, turbidity, light penetration, and the degree of
hydrodynamic mixing and flushing that occur in
different areas of the Estuary. For example, high levels
of turbidity and flushing typically observed near Reedy
Island, DE, may be a natural feature of the system that
could interfere with biological processes (Kreeger et al.,
2006).
7-
6-
S -
4 -
3 -
2-
I -
0
Saturation
-1967
1980
2003
10
30
50
70 90
River Mile
110
130
Figure 3-90. Annual dissolved oxygen levels for 1967, 1980, and
2003 along the main channel of the Delaware River from Trenton,
Nj,to the mouth of the Delaware Bay (Santoro, 2004).
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
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Toxic substances exist in the water and sediments of
the Delaware Estuary, and contaminant issues are
currently considered a top water quality concern for the
PDE (Kreeger et al., 2006). High PCB concentrations
are routinely measured in ambient water samples
collected from the Philadelphia-Camden reach of the
river during periods of low flow. When samples were
obtained during periods of high river flow, PCB levels
were lower and more evenly distributed throughout the
Estuary (Santoro, 2004). The 1997 Mid-Atlantic
Integrated Assessment (MAJA) study analyzed Delaware
Estuary sediments for metals, PCBs, pesticides, and
other organic contaminants. Metals, pesticides, PCBs,
and organic contaminants were most frequently
detected above their ERLs in sediments collected along
the main stem of the Delaware River between Trenton,
NJ, and the C&D Canal (just south of Wilmington,
DE) (Santoro, 2000).
Habitat Quality
A diverse array of habitat types predominate the
Delaware Estuary system, including tidal salt marshes,
tidal freshwater marshes, non-tidal wetlands, mudflats,
oyster reefs, open bays, upland meadows, forests, and
beaches. Although seagrasses and SAV exist in the Dela-
ware Estuary, they have not historically been reported as
an abundant habitat type. As a result, SAV is not
regarded as a key measure of estuarine condition (as it is
in Chesapeake Bay). Instead, key habitat indicators
identified by the PDE incorporate information about
land-use changes, losses and gains of different wetland
types, acreage of buffer habitats adjacent to tidal
wetlands, miles of riparian buffers, changes in area of
headwater streams and critical habitats, number of fish
blockages removed in streams, and spawning areas for
shad.
For example, between 21 % to 24% of the Estuary's
natural wetland habitats have been lost over time (PDE,
2002b). Freshwater tidal marshes have been dispropor-
tionately lost compared to salt marshes within the tidal
portion of the Estuary (Kreeger et al., 2006), and
invasive species, such as Phragmites (common reed),
Hydrilla, and purple loosestrife, have out-competed
many native plants and altered the quality and breadth
of the Estuary's natural habitats (Kreeger et al., 2006).
Efforts to remove fish blockages and dams are underway
in many areas of the Delaware Estuary watershed,
including the Schuylkill River.
Shell-planting operations help revitalize oyster populations in Delaware Estuary (PDE).
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Living Resources
Changes in the population dynamics and health of
key fish, shellfish, and bird species provide good indica-
tions of the overall health of the living resources in the
Delaware Estuary. Some of these key indicator species
include the horseshoe crab, Eastern oyster, American
shad, shortnose sturgeon, striped bass, bald eagle, and
red knot (Dove and Nyman, 1995; Kreeger et al.,
2006).
Like other mid-Atlantic estuaries, the Delaware
Estuary is home to the Eastern oyster (Crassostrea
virginica). Oysters are valued for several important
reasons. Similar to mussels, clams, and other bivalves,
oysters help filter the surrounding water, enhance
habitat for fish and wildlife, and act as a sentinel
bioindicator of water quality and habitat conditions
(Kreeger et al., 2006). Their importance as bioindicators
follows the lessons learned from the International
Mussel Watch Program; like mussels, suspension-
feeding oysters bioaccumulate many contaminants more
effectively than other types of consumers, and their
sessile lifestyle is conducive to site-specific analyses.
Recent estimates of oyster abundance in the Delaware
Estuary suggest that the average population density of
adults is declining, and especially worrisome is a precip-
itous drop in average spat (juvenile oyster) recruitment
that could result in a point-of-no-return abundance
for the overall population (Santoro, 2004; Powell,
2005). Figure 3-91 shows the long-term trends in oyster
populations in the Delaware Estuary. Despite declines,
oysters remain one of the most important commercial
shellfish in the Delaware Estuary; however, the popula-
tion has been victimized by the parasite Dermo since
1990. Researchers are working to develop a disease-
resistant oyster and to better manage the Eastern oyster
market (PDE, 2002b).
At one time, the population of American shad (Alosa
sapidissima) in the Delaware River supported the largest
shad fishery of any river on the Atlantic Coast. In the
1920s, this population declined due to water quality
degradation, overfishing, and habitat destruction, such
as damming of tributaries, entrainment and impinge-
ment at water intakes, and dredge-and-fill activities. As
water quality improved in the 1970s, the American
shad population in the Delaware Estuary began to
increase (Brown, 2005). In recent years, population
estimates have fluctuated greatly, but remain well below
the species' pre-1900 abundance (PDE, 2001; Santoro,
2004). Researchers believe that the fluctuations
observed between 1999 and 2003 were the result of
natural variations in population (Santoro, 2004). The
environmental stresses experienced by shad are impor-
tant because they are shared by other anadromous
(migratory) and semi-anadromous species, such as
herring, striped bass, and sturgeon (Kreeger et al.,
2006).
1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
Year
Figure 3-91. Fluctuations in oyster abundance in the Delaware Estuary (Santoro, 2004).
National Estuary Program Coastal Condition Report 1 63
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Partnership for the Delaware Estuary
Horseshoe Crabs, Shorebirds,
and People: The Many Facets of
Delaware Estuary's Population
Ecology
The Delaware Estuary is home to the worlds largest
population of horseshoe crabs (Limulus polyphemus).
Horseshoe crabs are not true crabs, but are actually
closer to spiders and scorpions. Their external appear-
ance has remained relatively unchanged during the past
360 million years. Each spring, adult horseshoe crabs
journey from die depths of the ocean to Delaware
Estuary beaches to spawn. Once spawning is complete,
the crabs return to the Estuary, and their eggs are left
buried in the sand to develop and hatch. At the same
time that the horseshoe crabs begin to lay their eggs,
shorebirds are traveling northward from South America
en route to their breeding grounds in the Arctic (PDE,
2002a). The Delaware Estuary is the largest stop-over
for shorebirds in the Atlantic Flyway, and an estimated
425,000 to 1,000,000 migratory shorebirds converge on
the Estuary to feed before continuing their migrations
(PDE, 2002b). Buried eggs migrate to the surface
through wave action and repeated "digging" by the
crabs. Eggs on or near the surface are an easily accessible
source of food for many shorebirds, including red
knots, dulins, ruddy turnstones, sanderlings, and semi-
palmated sandpipers. Each bird can eat thousands of
eggs per day; for example, a sanderling that weighs
50 grams can eat one horseshoe crab egg every five
seconds for 14 hours a day. These eggs provide the
energy that shorebirds need for their flight to the Arctic
(PDE, 2002b).
Over time, the number of horseshoe crabs in the
Estuary has declined, and the current status of the crab
population is the subject of considerable debate and
regulatory attention in the region (Santoro, 2004;
Kreeger et al., 2006). The decrease in the horseshoe
crab population has corresponded with a decrease in the
abundance of several species of shorebirds. For example,
the red knot population, which depends on horseshoe
crab eggs for the energy needed to complete migration,
has shown significant declines in abundance and weight
gain rates. Studies indicate that these declines are linked
with decreases in the horseshoe crab population and die
number of eggs available for foraging (Stiles and
Mizrahi, 2005). The interrelationship of the shorebirds
and horseshoe crabs can also be negatively affected by
habitat loss, a loss of coastal wetlands due to increased
development or erosion, a rise in sea level, and climate
changes (PDE, 2002a).
Shorebirds feast on horseshoe crab eggs before migrating to
their breeding grounds (PDE).
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Partnership for the Delaware Estuary
Many government agencies, fishermen, scientists,
researchers, and local community groups are working to
protect the shorebirds and horseshoe crabs in the
Delaware Estuary region. This work has included the
following:
• The Atlantic States Marine Fisheries Commission
enacted horseshoe crab harvesting control
measures for fishermen in Delaware, New Jersey,
Maryland, and Virginia.
• The U.S. Department of Commerce designated a
1,500 mi2 horseshoe crab preserve in federal
waters to protect horseshoe crabs. This preserve
extends 30 miles into the Atlantic Ocean, from
Peck's Beach, NJ, to Ocean City, MD. This area
was chosen as a preserve because it has the largest
horseshoe crab population on the East Coast.
• The Ecological Research & Development Group
(ERDG), which is a non-profit organization, and
the Virginia Institute of Marine Studies (VIMS)
conducted a study focused on devising alternative
>l . — -•
~f »
Horseshoe crabs journey to the beaches of Delaware Estuary
to spawn (PDE).
bait bags for fishermen. This study discovered that
by using these alternative bait bags, commercial
fishermen would need to use less bait, thus
successfully reducing the number of horseshoe
crabs being harvested. The ERDG has since
produced and distributed more than 6,000 bait
bags to fisherman in Maryland, Delaware, and
New Jersey.
• Teams of researchers from both Delaware and
New Jersey have been monitoring specific species
of birds for weight gain, gender, molt, wing
length, and bill length while the birds are in the
Delaware Estuary. This monitoring of a subset of
species allows for a better picture of the health of
the population, as well as the determination of
which habitat types are preferred for foraging and
roosting.
• The NJDEP conducted a study to determine
what effects a horseshoe crab egg decline might
have on the survival of red knots. This work
provided a baseline for establishing the viability of
the red knot population. During the coming
years, if a red knot population decline is detected,
scientists will be able to distinguish effects and
provide researchers and conservationists with an
early warning sign (PDE, 2002a).
Additional information about horseshoe crabs and
shorebirds in the Delaware Estuary can be found at
http://www.delawareestuary.org.
I
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Partnership for the Delaware Estuary
Current Projects,
Accomplishments, and Future
Goals
Examples of major water-quality-related accomplish-
ments during the past several years for the PDE and its
key partners in Delaware, New Jersey, and Pennsylvania
are the following:
• In 2005, the PDE, DRBC, and several regional
universities formed an alliance to begin to
modernize indicators used to gauge status and
trends of a comprehensive suite of environmental
metrics related to water quality, living resources,
and habitat.
• In July 2004, recognizing the continuing efforts of
die Schuylkill Action Network, EPA awarded a
$1.15 million grant to the Philadelphia Water
Department and the PDE to improve water
quality in the Schuylkill River watershed (U.S.
EPA, 2004b). EPA announced in May 2003 that
the Christina River Basin had been selected to
receive a $ 1 million grant to preserve and protect
this interstate subbasin of the Estuary (DRBC,
2005).
• The DBRC has implemented a comprehensive
program to reduce PCBs and develop appropriate
water quality criteria. As part of these efforts, the
DBRC established a TMDL for PCBs for the
tidal Delaware River (December 2003) and a rule
to establish pollutant-minimization requirements
for PCB discharges (May 2005). In addition, the
DBRC has also set a goal to reduce PCB loadings
to the Estuary by 50% over the next 5 years
(DRBC, 2005).
• The oyster restoration program for the Delaware
Estuary has set a specific goal for a five-fold
increase in the oyster population by 2015 and has
raised more than $2.7 million over the past 2 years
to support this initiative. A shell-planting program
was initiated in 2005 to help in this revitalization
effort (PDE, 2005).
• The PDE continues to reach out to the smaller
suburban and rural municipalities in the region
to assist with the development of a stormwater
management program for these communities.
By implementing one or more outreach programs
(e.g., Clean Water Partners, storm drain marking,
dog waste collection program), communities are
working to improve water quality throughout the
region.
• In 2003, the National Fish and Wildlife Founda-
tion (NFWF), in collaboration with the PDE,
launched its Delaware Estuary Grants Program. In
its first 2 years, the PDE made more than $1.1
million in public and private funds available to
fund 58 projects. In addition, these projects lever-
aged more than $3.8 million in matching funds.
Highlights of initial projects include support for
stormwater retrofits; stream, wetland, and upland
restorations; and outreach to reduce pollution
associated with watershed marinas and boaters
(NFWF, 2005).
Conclusion
The PDE's comprehensive assessment of the
Delaware Estuary rates the Estuary's overall condition as
fair based on the combined findings from both national
and regional programs and reflecting a mix of the posi-
tive and negative findings and trends for different types
of environmental measures. The Delaware Estuary is a
large and complex system that requires consideration of
its particular ecological features by local and regional
NEP-sponsored programs for a complete assessment.
The system is highly productive, relatively well mixed,
and has high nitrogen loadings and elevated levels of
chlorophyll a relative to the other NEP estuaries in the
Northeast Coast region. Based on the four indices of
estuarine condition used by the NCA, the overall
condition of the Delaware Estuary is rated poor, partly
because of high nutrient and chlorophyll ^ levels.
Despite these levels of chlorophyll a, the Delaware
Estuary has not experienced the negative signs typically
associated with eutrophication (e.g., fish kills, FiABs,
and water discoloration). Although concerned about
high nutrient concentrations and watchful for eutrophi-
cation problems, the PDE feels that toxic substances are
a more pressing concern in the Delaware Estuary
because of the more than 300-year contamination
legacy of the Industrial Revolution and its impact on
the Estuary's condition and resources.
166 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Center for the Inland Bays
Center for the Inland Bays
www.inlandbays.org
Rehoboth Boy Afaifc
Indian River Bay Ocean
Indian River Inlet
Assawoman Canal
Uttte Assowomon Boy
Assawoman Bay
Background
The Delaware Inland Bays are located in south-
eastern Sussex County, DE, and are composed of three
estuaries: Rehoboth Bay, Indian River Bay, and Little
Assawoman Bay, which combine to form the smallest
of the 28 NEP estuarine systems (DNREC, 2000).
Rehoboth Bay is the most northerly of the three bays
and adjoins Indian River Bay, which discharges via
Indian River Inlet into the Atlantic Ocean. Connected
to Indian River Bay via the Assawoman Canal, Little
Assawoman Bay is located further south and discharges
into Assawoman Bay. The source of the majority of the
freshwater input to the Bays is groundwater seepage.
In the Rehoboth and Indian River bays, 80% of the
freshwater inputs originate from groundwater
discharging to the Bays directly or indirectly though the
Bays' tributaries. The major tributaries to the Bays
include Indian River, Pepper Creek, Herring Creek,
Love Creek, and Dirickson Creek (DNREC, 2001).
The Center for the Inland Bays (CIB) was established
as part of the NEP in 1994 under the auspices of the
Inland Bays Watershed Enhancement Act (Title 7, Chapter
76). The mission of the CIB is to promote the wise use
and enhancement of the Inland Bays, their tributaries,
and the Inland Bays' watershed. The Bays have an
average depth ranging from 3 to 8 feet and are poorly
flushed by tidal movement; thus, they are especially
sensitive to environmental changes (DNREC, 2001).
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Center for the Inland Bays
Fluctuations in water temperature, changes in salinity,
and increases in pollutant levels can have dramatic
effects on water quality and on the entire ecosystem of
the Bays.
The Delaware Inland Bays are an important agricul-
tural area and a popular tourist destination. In 2002,
one-third of the watershed was devoted to agricultural
uses (CIB, 2004). Approximately 70 million chickens
are produced annually in the watershed, creating more
than 90 tons of manure (DNREC, 2000; CIB, 2002).
Recreation and tourism are also common in the Inland
Bays and contribute approximately $250 million
annually to the local economy. On summer weekends,
the area's population can increase by more than 200%
(DNREC, 2000). Boating is a popular activity, and it is
estimated that 21,000 boaters use the Bays annually.
The potential for illegal sewage discharge from these
boats has led to the closure of some of the Bays' shell-
fish beds (DNREC, 2001).
Environmental Concerns
Water quality impairment and its effects on the
estuarine ecosystem are a significant concern in the
Delaware Inland Bays. Runoff from CAFOs, leaking or
malfunctioning septic systems, and discharges from
municipal treatment facilities can all lead to increases in
nutrients and releases of fecal coliform bacteria to the
Bays. Almost 70% of the streams entering the Bays are
impaired, both from a water quality and habitat stand-
point. Most of this impairment has occurred due to
stream channelization and ditching to improve
drainage. The ecology of the Bays has changed in the
past 40 years, from a clear water system that supported
seagrass, bay scallops, and a variety of other shellfish,
finfish, and waterfowl to a murky water system that no
longer supports a healthy ecology. Instead, this system
enables HABs, nuisance seaweed blooms, and oxygen-
depletion episodes, while suppressing bay grasses, bay
scallops, and the variety and abundance of other
shellfish, finfish, and waterfowl noted in earlier years
(CIB, 2002).
Population Pressures
The population of the NOAA-designated coastal
county (Sussex) coincident with the CIB study area
increased by 114% during a 40-year period, from 0.07
million people in I960 to almost 0.16 million people in
2000 (Figure 3-92) (U.S. Census Bureau, 1991; 2001).
This rate of population growth for the CIB study area is
almost five times the population growth rate of 24% for
the collective NEP-coincident coastal counties of the
Northeast Coast region. In 2000, the population
density of this one coastal county was 166 persons/mi2,
about six times lower than the density of 1,055
persons/mi2 for the collective NEP-coincident coastal
counties of the Northeast Coast region (U.S. Census
Bureau, 2001). Population pressures for this study area
are high, especially during the summer months, because
this area and its beaches and bays serve as a major
recreational center for the Washington, D.C., and
Philadelphia metropolitan areas.
0.20
o 0.15
O 0.10
"5 0.05
0.00
I960 1970 1980 1990 2000
Year
Figure 3-92. Population of NOAA-designated coastal county
of the CIB study area, 1960-2000 (U.S. Census Bureau, 1991; 2001).
NCA Indices of Estuarine
Condition—Delaware Inland
Bays
The overall condition of the Delaware Inland Bays is
rated fair based on the four indices of estuarine condi-
tion used by the NCA (Figure 3-93). The water quality
index for the Delaware Inland Bays is rated fair, the
sediment quality and benthic indices are rated poor,
168 National Estuary Program Coastal Condition Report
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CHAPTER 3 ! NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Center for the Inland Bays
and the fish tissue contaminants index is rated good.
Figure 3-94 provides a summary of the percentage of
estuarine area rated good, fair, poor, or missing for each
parameter considered. This assessment is based on data
from 30 NCA stations sampled in the CIB estuarine
area in 2000 and 2001. Please refer to Tables 1-24, 1-25,
and 1-26 (Chapter 1) for a summary of the criteria used
to develop the rating for each index and component
indicator.
Overall Condition
Delaware Inland Bays
(2.S)
Water Quality Index (3)
Sediment Quality Index (I)
Benthic Index (I)
Fish Tissue Contaminants
Index (5)
Figure 3-93. The
overall condition of the
CIB estuarine area is
fair (U.S. EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80
Percent NEP Estuarine Area
100
Missing
Figure 3-94. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Delaware Inland
Bays (U.S. EPA/NCA).
Water Quality Index - Delaware Inland Bays
Site Criteria:
Number of component indicators
in poor or fair condition
• Good = No more than I is fair
OFair = I is poor, or 2 or
more are fair
• Poor = 2 or more are poor
O Missing
I
Figure 3-95. Water quality index data for the Delaware Inland
Bays, 2000-2001 (U.S. EPA/NCA).
Water Quality Index
Based on the NCA survey results, the water quality
index for the Delaware Inland Bays is rated fair, with
72% of the estuarine area rated fair for water quality
(Figure 3-95). This index was developed using NCA
data on five component indicators: DIN, DIP,
chlorophyll a, water clarity, and dissolved oxygen.
Elevated concentrations of DIN, DIP, and chlorophyll
a were measured in about 60% of the Bays. Diminished
water clarity was evident in 36% of the Bays—a typical
measurement for the southern estuaries of the Northeast
Coast region. Dissolved oxygen concentrations in
bottom waters were greater than 5 mg/L at all locations
sampled during the study period.
National Estuary Program Coastal Condition Report 169
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Center for the Inland Bays
Dissolved Nitrogen and Phosphorus I The
Delaware Inland Bays are rated fair for DIN concen-
trations, with 40% of the estuarine area rated good,
58% of the area rated fair, and 2% of the area rated
poor. The Delaware Inland Bays are also rated fair for
DIP concentrations, with 37% of the estuarine area
rated good for this component indicator, 61 % of area
rated fair, and 2% of the area rated poor.
Chlorophyll a I The Delaware Inland Bays are
rated fair for chlorophyll a concentrations. Forty-six
percent of the estuarine area was rated good for chloro-
phyll a concentrations, 47% was rated fair, and 6% of
the area was rated poor.
Water Clarity I Water clarity in the Delaware
Inland Bays is rated good. Forty-nine percent of the
estuarine area was rated good for this component indi-
cator, 27% of the area was rated fair, and 9% of the area
was rated poor. NCA data on water clarity were unavail-
able for 15% of the GIB estuarine area.
For the purposes of this report, water clarity in the
Delaware Inland Bays was rated poor at a sampling site if
light penetration at I meter was less than 10% of surface
illumination. These criteria are used for estuaries with
normal turbidity and are applied to most U.S. estuaries. In
some areas of the country, more stringent criteria are
applied to support extensive SAV beds or active SAV
restoration programs. Water clarity in these regions is
rated poor at a sampling site if light penetration at I meter
is less than 20% of surface illumination.
Although the more stringent water clarity criteria were
not applied when rating the Delaware Inland Bays in this
report, SAV restoration efforts are underway in this estu-
arine system; thus, these more stringent criteria could be
applicable to the Bays. If these criteria had been applied,
water clarity in the Bays would have been rated poor, with
36% of the estuarine area rated poor (see table below).
Current
Criteria
More
Stringent
Criteria
Rating
Good
Fair
Poor
Missing
(% area)
49
27
9
IS
(% area)
40
8
36
IS
Dissolved Oxygen I The Delaware Inland Bays
are rated good for dissolved oxygen concentrations,
with 100% of the estuarine area rated good for this
component indicator.
Sediment Quality Index
The sediment quality index for the Delaware Inland
Bays is rated poor (Figure 3-96). Fifteen percent of the
estuarine area was rated poor, and less than 1% of the
area was rated fair. This index was developed using
NCA data on three component indicators: sediment
toxicity, sediment contaminants, and sediment TOC.
Sediments were toxic to amphipods at one NCA site;
however, the extent of sediment contamination was
relatively insignificant (8% rated fair). Moderate and
high concentrations of TOC were measured in 19% of
the Bays, largely in the tributaries.
Sediment Quality Index - Delaware Inland Bays
\
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
O Fair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Good
85%
Figure 3-96. Sediment quality index data for the Delaware
Inlands Bays, 2000-2001 (U.S. EPA/NCA).
1 70 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Center for the Inland Bays
Sediment Toxicity I The Delaware Inland Bays
are rated poor for sediment toxicity, with 7% of the
estuarine area rated poor for this component indicator.
Sediment Contaminants The Delaware Inland
Bays are rated good for sediment contaminant concen-
trations. None of the estuarine area was rated poor for
this component indicator, and 8% of the estuarine area
was rated fair.
Total Organic Carbon I The Delaware Inland
Bays are rated good for sediment TOC. Sixty-nine
percent of the estuarine area was rated good for this
component indicator, and 11 % of the area was rated
fair. Only 8% of the area was rated poor for sediment
TOC, and NCA data on TOC concentrations were
unavailable for 12% of the CIB estuarine area.
Benthic Index - Delaware Inland Bays
Site Criteria:
Virginian Province Benthic
Index Score
• Good = > 0.0
• Poor = sO.O
O Missing
Figure 3-97. Benthic index data for the Delaware Inland Bays,
2000-2001 (U.S. EPA/NCA).
Benthic Index
The benthic condition rating for the Delaware
Inland Bays is poor, as evaluated by the Virginian
Province Benthic Index (Figure 3-97). More than a
third of the estuarine area had index scores that indi-
cated an unsatisfactory degree of benthic diversity, with
most of the sites designated as impaired located in
tributaries of the Bays.
Fish Tissue Contaminants Index
Based on NCA survey results, the fish tissue contam-
inants index for the Delaware Inland Bays is rated good.
Only four fish samples were analyzed for chemical
contaminants (Figure 3-98); however, none contained
chemical contaminant concentrations that exceeded the
EPA Advisory Guidance values for fish consumption.
Fish Tissue Contaminants Index
Delaware Inland Bays
I
Site Criteria:
EPA Guidance concentration
• Good = Below Guidance range
O Fair = Falls within Guidance range
• Pool- = Exceeds Guidance range
Figure 3-98. Fish tissue contaminants index data for the
Delaware Inland Bays, 2000-2001 (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 171
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Center for the Inland Bays
Delaware Inland Bays Tributary
Action Team
Eutrophication due to nutrient over-enrichment is
a priority problem for Delaware's Inland Bays. Overall,
the Inland Bays are highly eutrophic, with an increasing
trend towards nutrient enrichment experienced during
die past 40 years (GIB, 2002). These eutrophic condi-
tions have led to nuisance algal blooms, fish kills, large
variations in dissolved oxygen levels, loss of SAV, and
an increase in HABs or harmful phytoplankton blooms.
Some of these blooms have been composed of organ-
isms, such as Pfiesteria and Chattonella, which are
potentially toxic.
Because of degraded water quality conditions
resulting primarily from eutrophication, the Inland
Bays are identified as impaired waters on Delaware's
1996 303(d) list and require die application of
TMDLs. In December 1998, the Delaware Depart-
ment of Natural Resources and Environmental Control
(DNREC) promulgated TMDLs for the Indian River,
Indian River Bay, and Rehobodi Bay, which called for
non-point source nutrient load reductions as high as
85% for nitrogen and 65% for phosphorus. The
Delaware DNREC also called for the elimination of all
point-source discharges to the Inland Bays (DNREC,
1998).
During the autumn of 1998, the GIB initiated a
Tributary Strategy Program in which local stakeholders
(e.g., industry, agriculture, municipalities, real estate
businesses, golf courses, citizens) from each of the
Inland Bays sub-watersheds (e.g., Rehobodi, Indian
River, and Little Assawoman bays) were organized into
an Inland Bays Tributary Action Team (TAT). The TAT
created a body responsible for providing guidance and
direction to the CIB in its mission to reduce nutrient
contributions and restore habitat in the Delaware
Inland Bays (CIB, 2005).
Since January 1999, the TAT has been involved in
a coordinated effort with the Delaware DNREC to
develop pollution-control strategies to meet the required
TMDLs for nitrogen and phosphorus in the Bays. To
accomplish this goal, a public engagement model,
Public Talk — Real Choices, was developed and applied to
this program by the University of Delaware's Coopera-
tive Extension Agency, which co-facilitated the process
with the university's Sea Grant Marine Advisory Service
(CIB, 2005).
An Inland Bays' resident attempting to remove the nuisance
macroalgae Ulva (sea lettuce) from shoreline property
(James Alderman).
172 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Center for the Inland Bays
The purpose of Public Talk — Real Choices was to
move formulation and creation of a major public policy
decision from a state agency (DNREC) to the public for
deliberation and dialogue. Using deliberative dialogue as
its core, Public Talk went further by engaging the public
in learning about the issues, framing issues for delibera-
tion, weighing the costs and consequences of choices,
coming to public judgment, and making decisions. This
was not a model that engaged a small group to simply
make recommendations to a state agency that would
subsequently "sell" the policies to the public via public
workshops and public hearings (GIB, 2005). Instead,
the TAT published the issue book Saving Our Bays:
Our Challenge - Our Choice (GIB, 2000) and distrib-
uted more than 20,000 copies within the watershed
(University of Delaware, 2000). The TAT also hosted
seven public forums in the watershed to educate resi-
dents and visitors about the choices under consideration
and to receive input concerning the development of
pollution-control strategies for the Bays.
Ultimately, the Inland Bays TAT offered three sets
of pollution-control strategy recommendations to the
Delaware DNREC for review and consideration. Based
on these recommendations, the DNREC has proposed
to promulgate a pollution-control strategy for each of
the Inland Bays (DNREC, 2006). Elements of this
strategy are both voluntary and regulatory in nature and
are designed to reduce nutrient loadings from current
and future land practices. This combination of actions
will lead to the achievement of the TMDLs.
Scientific literature and experts in the pertinent fields
were consulted and assisted the Delaware DNREC in
estimating the nutrient reductions that would be
achieved through promulgation of this pollution-
control strategy. In addition, the strategy reviews the
various costs associated with the recommended actions
and, where appropriate, recommends funding mecha-
nisms and implementation schedules while identifying
responsible parties. Finally, the strategy reviews the
agencies and programs charged with implementing
elements of the strategy.
The success of the Inland Bays TAT has prompted
the organization of other similar teams throughout the
state. In fact, pollution-control strategies are now being
formulated by teams representing the watersheds for the
Murderkill, Broadkill, Appoquinimink, and Nanticoke
rivers.
I
National Estuary Program Coastal Condition Report 1 73
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Center for the Inland Bays
Center for the Inland Bays
Indicators of Estuarine Condition
The Inland Bays Scientific and Technical Advisory
Committee (STAC) is a working group that formed the
Inland Bays Indicators Subcommittee in 2001. This
subcommittee developed a preliminary list of environ-
mental indicators that were selected for several purposes,
including the following:
• Communicating the health of the Delaware
Inland Bays and its rivers to public audiences
• Evaluating progress in the CIB restoration effort
• Monitoring environmental conditions and
responses to restoration efforts
• Providing information needed to establish restora-
tion goals
• Regularly informing and involving the public in
the achievement of restoration goals
• Making detailed information and reference data
for these indicators available upon request so that
others may participate in tracking indicator
progress.
These indicators were characterized by their position
in a hierarchy, ranging from Level 1 indicators, which
are used to measure administrative actions such as
issuing permits, to Level 6 indicators, which are indirect
or direct measures of ecological or human health (Table
3-5). All of the information captured by this continuum
has value for stakeholders and policymakers. Although
the indicators toward the higher end of the continuum
(Levels 4 through 6) portray a clearer, more direct
image of the environmental condition of the Bays,
indicators at the lower levels (Levels 1 through 3) are
needed to establish a link between the actions taken and
the effects observed (CIB, 2002).
Table 3-5. Indicators Recommended by the Scientific
and Technical Advisory Committee (CIB, 2002)
Level I. Actions by EPA/State/Local Regulatory
Agencies
a. Septic tank conversions to central sewer system
b. Acquisition of land for parks and open spaces
c. Establishment of Nutrient Management Programs
Level 2. Responses of the Regulated and
Non-regulated Community
(To be developed later pending specific
data collection)
a. Animal waste conversion projects
I. Pelletized fertilizer
2. Fuel
Level 3. Changes in Discharge/Emission Quantities
a. Removal of direct discharges or reductions in load
to the Delaware Inland Bays
Level 4. Changes in Ambient Conditions
a. Nutrient pollution
I. Nitrogen
2. Phosphorus
3. Chlorophyll a
4. Water clarity
a. Sneaker Index
b. Secchi depth
5. Dissolved oxygen
Level 5. Changes in Uptake and/or Assimilation
a. Shellfish-growing area closures
Level 6. Changes in Health, Ecology, or Other
Effects
a. Bay grasses (SAV)
I. Acres
2. Density
3. Changes
4. Biofouling
b. Shellfish - Hard clam landings
c. Fish - Recreational fishing indicator
d. Habitat restoration efforts - SAV
e. Land-use issues
I. Population growth
2. Deforestation
3. Nutrient loading by various land uses
1 74 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Center for the Inland Bays
Water and Sediment Quality
The CIB uses the measurements of several water
quality parameters (nitrogen, phosphorus, chlorophyll a,
water clarity, and dissolved oxygen) as indicators of the
Bays' pollution levels and as a method for detecting
changes in ambient conditions within the Bays. Figure
3-99 compares the Delaware DNREC's water quality
goal and the mean value measured during the 1990s for
several of these parameters. These data show that all four
waterbodies did not achieve the desired goal for DIP
concentrations during the 1990s and that the ability to
meet other goals varied by waterbody. This analysis indi-
cates that Little Assawoman and Indian River bays are
more eutrophic than Rehoboth Bay (CIB, 2002).
Tht fw* nafact w CM*
v trtkal h*r apt tfcc e*p«*t
kvtl »*d tltt ftml. Ifed fe*.
8.5
451
39l
TN
(mg/L) (mg/L)
TN -Total Nitrogen DIN -Dissolved Inorganic Nitrogen
TP - Total Phosphorus DIP -Dissolved Inorganic Phosphorus
Chlor.-Chlorophyll a Secchi Depth-wafer visibility
DIP Chlor. Secchi
(mg/L) (Mg/L) DePth
(inches)
2.5.
Indian River
1.8
1.75,
.15
TN DIN TP DIP Chlor. Secchi
(mg/L) (mg/L) (mg/L) (mg/L) (Mg/L) DePth
(inches)
43,
39|
TN DIN TP DIP Chlor. Secchi
(mg/L) (mg/L) (mg/L) (mg/L) (Mg/L) DePth
(inches)
Little Assawoman Bay |
15
1.01
.15
TN DIN TP DIP Chlor. Secchi
(mg/L) (mg/L) (mg/L) (mg/L) (Mg/L) Depth
(inches)
Figure 3-99. Water quality parameters as compared to water quality goals for the Delaware Inland Bays for the 1990s (CIB, 2004)
National Estuary Program Coastal Condition Report 1 75
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Center for the Inland Bays
Nutrient loads entering the Delaware Inland Bays
come from non-point, point, and atmospheric sources;
however, the majority of the nutrient loadings to the
Bays are derived from non-point sources. The Delaware
DNREC estimated that almost 4,500 pounds of nitro-
gen and 163 pounds of phosphorus enter the Bays each
day from non-point sources, such as septic systems,
stormwater runoff, and agricultural activities (GIB,
2002). Direct discharges from point sources contribute
less than 4% of the Bays' nitrogen loading (DNREC,
2000). Between 1990 and 2000, direct discharges of
nitrogen increased by 32% to 710 pounds per day.
Point-source releases of phosphorus also increased by
6% to 72 pounds per day (GIB, 2004). Nitrogen
loading to the Bays from atmospheric deposition is
estimated to range up to 25% of the total nitrogen load
(DNREC, 2000).
The Sneaker Index has been collected in the Dela-
ware Inland Bays since 2001. This surrogate measure
for water clarity is calculated every year as the water
depth at which Delaware's current governor can no
longer see a pair of white tennis shoes while standing in
the Bays. This method has proven to be a good way to
raise public awareness about water clarity in the Bays.
Submerged sneaker visibility has ranged from a maxi-
mum of 51 inches in 2001 to a minimum of 39 inches
in 2002. In 2004, the Sneaker Index was 44 inches
(CIB, 2004).
The CIB also measures levels of total coliform
bacteria in the waters of Rehoboth Bay and Indian
River Bay as an indicator of the potential for pathogen-
contaminated shellfish to introduce illness to human
populations. The DNREC uses coliform bacteria
measurements to determine if local shellfish beds are
safe for harvesting (CIB, 2004).
Habitat Quality
SAV is considered a good ecological indicator
because ambient water quality conditions are generally
considered to be good if healthy and reproducing SAV
are abundant. The highest concentration and greatest
diversity of SAV in the Bays is located in the Bay's fresh-
water tributaries (CIB, 2002). In the tidal portions of
the Bays, eelgrass, a widely valued seagrass, is considered
a particularly important indicator of water quality.
Historically, the amount of eelgrass declined as nutrient
loads to the Bays increased, and by the early 1970s,
eelgrass and most of the other SAV species had almost
completely died out in the tidal portions of the Bays
(CIB, 2004). Currently, the majority of the Bays' estu-
arine area will not support eelgrass; however, restoration
efforts have reintroduced eelgrass to the Indian River
Inlet (DNREC, 2000; CIB, 2004). Where water quality
is sufficient to support vigorous plant growth, the
restored eelgrass beds are reproducing (DNREC, 2000).
The CIB uses changes in the region's land use to help
characterize the changing landscape of the Bays. Aerial
photography is used to determine the extent of each
land-use category in the Inland Bays watershed. In 2002,
agriculture, forest, urban, and wetlands were the top four
land-use classes in the watershed (Figure 3-100), and
overall, the watershed is becoming more urbanized.
Between 1992 and 2002, urban lands increased by 8,940
acres, or 34%. During the same time period, forested,
agricultural, and barren land acreage declined (CIB,
2004).
Range Barren
Water 2% 1%
12%
Wetlands
16%
Agriculture
34%
Forest
18%
Figure 3-100. Delaware Inland Bays land use in 2002
(CIB, 2004).
Wetlands are an important type of habitat because
they filter nutrients, trap sediments, control flooding,
and support diverse plant and animal communities.
Since 1780, Delaware has lost an estimated 54% of its
wetlands (DNREC, 2000), and between 1982 and
1992, 92% of the 297 acres of wetlands lost in the
Delaware Inland Bays area were freshwater vegetated
wetlands. Agriculture, residential development, and
pond construction were the primary causes for this loss
(DNREC, 2001). In the Delaware Inland Bays water-
shed, the rate of wetlands loss has decreased in recent
years, with wetlands acreage increasing slightly between
1992 and 2002 (DNREC, 2001; CIB, 2004).
1 76 National Estuary Program Coastal Condition Report
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CHAPTER 3 : NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Center for the Inland Bays
Macroalgae (seaweeds) in the Delaware Inland Bays
provide preferred habitat for blue crabs and a variety of
fish. The monitoring of macroalgae (seaweeds) habitat
in the Bays is important because macroalgae are a
sensitive habitat type. As nutrient levels in the water
increase, macroalgae density increases, which can result
in diminished habitat quality, HABs, low dissolved
oxygen levels, and the mortality of fish and benthic
organisms. For example, thick mats of macroalgae
formed in parts of Indian River Bay in 1998, impacting
more than 8 acres and killing an estimated 100,000
clams. Rehoboth Bay has the greatest amount of
macroalgae of the Delaware Inland Bays (DNREC,
2001).
Living Resources
Hard clams were chosen as a GIB indicator because
they are the most important commercial fishery and
one of the most abundant benthic species in the
Delaware Inland Bays (GIB, 2004). Hard clams began
to colonize extensive areas of Rehoboth and Indian
River bays in the 1940s, and the majority of current
habitat in the Bays is suitable for hard clams (DNREC,
2001). Hard clam landings peaked in the 1950s and
1960s and have been increasing in recent years,
including increases from about 300,000 to more than
3.5 million clams between 1987 and 2003 (DNREC,
2001; GIB, 2004). Overall, the CPUE is stable, and the
increase in clam landings is primarily due to a corre-
sponding increase in the amount of effort expended to
catch the clams. In recent years, a large percentage of
each catch has been composed of clams that are in the
smallest size category, which indicates the presence of
more young clams in the Bays. The CIB suspects that
improved water quality is the likely cause of the
increased number of young clams (CIB, 2002; 2004).
Beach-nesting birds and the tiger beetle are consid-
ered to be good indicators of the ecological integrity of
beach and dune communities in the Bays. The piping
plover, least tern, common tern, black skimmer, and
American oystercatcher are the five beach-nesting bird
species that are tied to the Bays' beach and dune
habitat. In the 1960s, these birds resided in the area in
good numbers, and small numbers of least terns,
common terns, and American oystercatchers continue
to nest in the area, although common tern nesting
efforts are sporadic. Piping plovers nest annually in the
study area; however, the population has declined in
recent years and nest productivity is low, primarily due
to predation. Black skimmers have not nested in the
Delaware Inland Bays since 1990, and the tiger beetle
has only been recorded in Cape Henlopen State Park
(DNREC, 2000; 2001).
Recreational fishing in the Delaware Inland Bays is a
popular pastime, and sea trout, summer flounder,
striped bass, and bluefish are commonly caught in the
Bays. Recreational fishing trips and landings are seen as
good indicators because the success of the recreational
fisherman is linked to the ability of the Bays to support
viable fish populations. Between 1988 and 2002, the
number of fishing trips per year has followed an overall
increasing trend. At the same time, the number of fish
caught per trip has remained relatively constant. This
indicates that the Bays are capable of sustaining the
current level of recreational fishing (CIB, 2004).
Environmental Stressors
The centralization of sewers is used as an indicator of
progress made by government action to decrease non-
point source pollution to the Bays. The watershed's
existing 16,000 septic systems discharge nutrients to the
groundwater, which transports the nutrients to the Bays
and tributaries. It is estimated that almost 1,000 pounds
of nitrogen and up to 40 pounds of phosphorus are
discharged on a daily basis to the Bays from existing
and recently removed septic systems. Since 1993, more
than 13,000 septic systems have been replaced with
centralized public sewer systems (CIB, 2002; 2004)
The CIB uses population growth as a good indicator
of overall environmental stress on the Bays and the
watershed. Between 1990 and 2000, the population of
Sussex County increased by more than 38%. The area
of the county with the greatest population growth was
located along the Atlantic Coast portion of the Dela-
ware Inland Bays watershed, where the population
increased by 59% (U.S. Census Bureau 1991; 2001).
Population growth in this area is expected to continue.
By 2020, the population of Sussex County as a whole
is expected to reach 180,000 people, and much of this
population will be concentrated in the watershed
(CIB, 2004).
National Estuary Program Coastal Condition Report 1 77
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Center for the Inland Bays
Current Projects,
Accomplishments, and Future
Goals
The establishment of the CIB was the culmination
of more than 20 years of active public participation and
investigation into the decline of the Delaware Inland
Bays and remedies for the restoration and preservation
of the watershed. The CIB was designed to accomplish
several specific goals:
• Sponsor and support educational activities,
restoration efforts, and land-acquisition programs
that lead to the present and future preservation
and enhancement of the watershed
• Build, maintain, and foster the partnership among
the general public, private sector, and local, state,
and federal governments; this partnership is essen-
tial for establishing and sustaining the policy,
programs, and political will to preserve and restore
the resources of the watershed
• Serve as a forum where Inland Bays watershed
issues may be analyzed and considered for the
purpose of providing responsible officials and the
public with a basis for making informed decisions
concerning the management of the resources of
the watershed.
Some of the CIB's ongoing projects and major
accomplishments in the Delaware Inland Bays' water-
shed include the following:
• In August of 2004, the CIB began a large-scale
scientific research project to determine the ecolog-
ical health of the area's freshwater wetlands.
• Since 1994, the CIB has awarded more than
$1 million to support research, outreach, and
demonstration projects. These projects have
included evaluating HABs, enhancing the restora-
tion of shellfish stocks, and raising water quality
awareness in middle school students.
• More than 100,000 eastern oysters were raised
during 2003 by volunteer oyster gardeners as part
of the CIB's Shellfish Gardening Project, which
was designed as a pilot program to restore oysters
to the Inland Bays. These oysters were later
planted on a constructed oyster reef in Indian
River Bay. Since 2001, the CIB has planted more
than 1.5 million oysters on this reef (CIB, 2005).
Conclusion
The Delaware Inland Bays combine to form the
smallest of the 28 NEP estuarine systems. These Bays
are shallow and poorly flushed by tidal movement, and
as such, are especially sensitive to environmental
changes. The overall condition of Delaware Inland Bays
is rated fair based on the four indices of estuarine condi-
tion used by the NCA. The CIB has developed a suite
of indicators used to measure a variety of elements—
from administrative actions, such as issuing permits, to
those elements that are indirect or direct measures of
ecological or human health. These indicators should
provide a comprehensive picture of the environmental
and human components of the system over time.
1 78 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Maryland Coastal Bays Program
Maryland Coastal Bays Program
Atlantic Ocean
www.mdcoastalbays.org
Background
The total watershed area of the Maryland Coastal
Bays encompasses 175 mi2 and includes more than
117,000 acres of land, 71,000 acres of water, and
280 miles of shoreline (ANEP, 200 lb>. To the east of
Route 113, the watershed of the Coastal Bays includes
Berlin and Ocean City, MD, as well as parts of Snow
Hill and Pocomoke. The Maryland Coastal Bays make
up one of the richest and most diverse estuaries on the
Eastern Seaboard, with more than 115 species of finfish,
17 species of molluscs, 23 species of crustaceans, 360
species of birds, 44 species of mammals, and countless
foraging/grazing organisms inhabiting these waterbodies
(ANEP, 200Ib; Maryland DNR, 2005a). The
Ch/ncoteogue Boy
C/iincoteague Inlet
NEP Study Area
Maryland Coastal Bays are characterized as coastal
lagoons with fairly uniform depths (< 10 feet) and rela-
tively long water residence times (Wazniak et al., 2004;
Wazniak and Hall, 2005). Circulation within the Bays is
controlled by wind and tides, and flushing time is very
slow across the system because tidal exchange is limited
mainly to small channels separating the barrier islands.
River inputs are fairly low due to the area's flat landscape
and sandy soils, and groundwater is a major pathway for
the introduction of fresh water and nutrients to the
Bays. Salinity in the open Bays is similar to seawater,
although portions of the upstream reaches of rivers and
creeks remain fresh (Wazniak and Hall, 2005).
National Estuary Program Coastal Condition Report 1 79
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Maryland Coastal Bays Progran
The Maryland Coastal Bays Program (MCBP) was
established in 1996 as a partnership between the towns
of Ocean City and Berlin, MD; EPA; the NPS;
Worcester County, MD; and the Maryland Department
of Natural Resources (DNR). The MCBP protects the
land and waters of Assawoman Bay, Isle of Wight Bay,
Sinepuxent Bay, Newport Bay, and Chincoteague Bay.
The Coastal Bays' multi-million dollar tourism
industry is fueled by more than 11 million annual
visitors who flock to the Bays to fish, boat, swim, or
enjoy the atmosphere in their favorite bay-side restau-
rant (MCBP, 2005). Although more that 47,000 people
lived in Worcester County in 2000, populations in the
summer season have exceeded 300,000 people (Thomp-
son and Wagenhals, 2002). Tourism-related activities
generate $700 million in annual employee income in
the Coastal Bays (Polhemus and Greeley, 2001). In
2002, commercial landings of fish and shellfish in
Ocean City comprised 12.1 million pounds, valued at
$8.1 million. In 2003, more than 700,000 people
fished 7 million days in Maryland waters, and currently,
recreational crabbing and fishing in the Bays generates
at least $21 million annually (ANEP, 200 Ib; Wazniak
and Hall, 2005). For more than a century, agriculture,
forestry, fishing, farming, hunting, and tourism have
sustained ways of life built on the land and water
resources in these coastal communities. Worcester
County's forests and 474 farms contribute hundreds of
millions of dollars per year to the local economy and
help provide the open space and natural land essential
to the variety of wildlife species that call this area home
(MCBP, 2005).
Environmental Concerns
A variety of environmental concerns in the Maryland
Coastal Bays require the attention of environmental
managers. The majority of these concerns are directly
related to the area's growth and development. Projec-
tions indicate that there will be more than 60,000 resi-
dents living in the Coastal Bays' watershed by 2010
and more than 72,000 residents by 2020 (Wazniak and
Hall, 2005). Pollution from agricultural and urban
runoff, point-source discharges, septic tank system
loadings, atmospheric deposition, and groundwater flow
are all sources of nutrients in the Bays. With the right
mixture of water quality conditions and nutrient
loading levels, blooms of algae can form and block light
infiltration to SAVs, foul boat propellers, and cause
odor problems for homeowners along the Coastal Bays.
Commercial development, the conversion of natural
shorelines, the cumulative impacts of docks and boat
traffic, and the invasion of exotic species have all
degraded and/or eliminated tidal marsh and wetland
habitats, and roughly 50% of the area's forest and
wetlands have been lost during the past 300 years
(ANEP, 200 Ib). Primary sources of pathogen contami-
nation are runoff from livestock operations, urban areas
with failing septic systems, and wildlife. Analysis of
sediments has revealed higher than normal levels of
DDT, arsenic, chlordane, and nickel, which have accu-
mulated from agricultural sources, stormwater, and
other sources (Wazniak and Hall, 2005). Dredging
activities and boating in the Bays can easily resuspend
contaminated sediments into the water column. Trash
and debris that accumulate on estuary beaches of the
Eastern Shore are a threat to local ecosystems and
reduce the recreational value of popular sites along the
coast. In 2002, approximately 50 volunteers scooped a
ton and a half of garbage from the Bays and shoreline
during a single-day event (MCBP, 2002).
Population Pressures
The population of the NOAA-designated coastal
county (Worcester) coincident with the MCBP
study area increased by 96% during a 40-year period,
from about 0.02 million people in 1960 to almost
0.05 million people in 2000 (Figure 3-101) (U.S.
Census Bureau, 1991; 2001). This rate of population
growth for the MCBP study area is four times the
population growth rate of 24% for the collective NEP-
coincident coastal counties of the Northeast Coast
region. In 2000, the population density of this coastal
county was 98 persons/mi2, about one-tenth the popu-
lation density of 1,055 persons/mi2 for the collective
180 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Maryland Coastal Bays Program
0.05
0.04
£ 0.03
0.02
1
0.0,
0.00
I960 1970 1980 1990 2000
Year
Figure 3-101. Population of NOAA-designated coastal county
of the MCBP study area, 1960-2000 (U.S. Census Bureau, 199 I;
2001).
NEP-coincident coastal counties of the Northeast Coast
region (U.S. Census Bureau, 2001). Population pres-
sures for the MCBP study area are especially high
during the summer months because these beaches and
bays serve as a major recreational center for the nearby
metropolitan areas surrounding Washington, D.C.
NCA Indices of Estuarine
Condition—Maryland Coastal
Bays
The overall condition of the Maryland Coastal Bays
is rated fair based on the four indices of estuarine
condition used by the NCA (Figure 3-102). The water
quality index for the Maryland Coastal Bays is rated
poor, the sediment quality and fish tissue contaminants
indices are rated good, and the benthic index is rated
fair. Figure 3-103 provides a summary of the percentage
of estuarine area rated good, fair, poor, or missing for
each parameter considered. This assessment is based on
data from 47 NCA sites sampled in the MCBP
estuarine area in 2000 and 2001. Please refer to Tables
1-24, 1-25, and 1-26 (Chapter 1) for a summary of the
criteria used to develop the rating for each index and
component indicator.
Overall Condition
Maryland Coastal Bays
(3.5)
Water Quality Index (I)
Sediment Quality Index (5)
Benthic Index (3)
Fish Tissue Contaminants
Index (5)
Figure 3-102. The
overall condition of the
MCBP estuarine area is
fair (U.S. EPA/NCA).
I
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80
Percent NEP Estuarine Area
100
I I I Missing
Figure 3-103. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Maryland Coastal
Bays (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 1 81
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Maryland Coastal Bays Program
Water Quality Index
Based on NCA survey results, the water quality index
for the Maryland Coastal Bays is rated poor (Figure
3-104). This index was developed using NCA data on
five component indicators: DIN, DIP, chlorophyll a,
water clarity, and dissolved oxygen.
Water Quality Index - Maryland Coastal Bays
Site Criteria:
Number of component indicators
in poor or fair condition
• Good = No more than I is fair
O Fair = Ms poor, or 2 or
more are fair
WPoor = 2 or more are poor
O Missing
Missing
Good 7%
4%
Fair
49%
Figure 3-104. Water quality index data for the Maryland
Coastal Bays, 2000-2001 (U.S. EPA/NCA).
Dissolved Nitrogen and Phosphorus \ The
Maryland Coastal Bays are rated poor for DIN concen-
trations, with 55% of the estuarine area rated good for
this component indicator, 1 % of the area rated fair, and
43% of area rated poor. DIP concentrations in the
Maryland Coastal Bays are also rated poor, with 31 %
of the estuarine area rated good, 33% of the area rated
fair, and 35% of the area rated poor.
Chlorophyll a I The Maryland Coastal Bays are
rated fair for chlorophyll a concentrations. Twenty
percent of the estuarine area was rated good for this
component indicator, 67% of the area was rated fair,
and 12% of the area was rated poor.
Water Clarity I The water clarity rating for the
Maryland Coastal Bays is poor. If light penetration at a
depth of 1 meter below the water's surface was less than
10% of the surface illumination, water clarity at the
sampling site was rated poor. Twenty-five percent of the
estuarine area was rated poor for water clarity, 19% of
the area was rated good, and 15% of the area was rated
fair. NCA data on water clarity were unavailable for
41% of the MCBP estuarine area.
Dissolved Oxygen I The Maryland Coastal Bays
are rated good for dissolved oxygen concentrations, with
93% of the estuarine area rated good for this compo-
nent indicator and none of the area rated poor. NCA
data on dissolved oxygen concentrations were unavail-
able for 7% of the MCBP estuarine area.
Replanting marsh grass in an effort to protect and rebuild a beach
(Mary Hollinger. NOAA).
182 National Estuary Program Coastal Condition Report
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CHAPTER 3 : NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Maryland Coastal Bays Program
Sediment Quality Index
The sediment quality index for the Maryland Coastal
Bays is rated good (Figure 3-105). This index was
developed using data on three component indicators:
sediment toxicity, sediment contaminants, and sediment
TOG. No sediments collected from the Bays were toxic
to amphipods, and only three sites in the St. Martins
River had low sediment quality ratings due to moderate
concentrations of sediment contaminants and high
concentrations of TOG.
Sediment Quality Index - Maryland Coastal Bays
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
OFair = None are poor and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Figure 3-105. Sediment quality index data for the Maryland
Coastal Bays, 2000-200 1 (U.S. EPA/NCA).
•Scf/init'i/f !(>\i, 0.0
• Poor = sO.O
O Missing
Figure 3-106. Benthic index data for the Maryland Coastal
Bays, 2000-2001 (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 1 83
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Maryland Coastal Bays Program
Fish Tissue Contaminants Index
The fish tissue contaminants index for the Maryland
Coastal Bays is rated good, with 91 % of fish samples
rated good for contaminant concentrations. Only two
fish samples (9%) analyzed for chemical contaminants
had contaminant concentrations that exceeded the EPA
Advisory Guidance values for fish consumption (Figure
3-107). In both cases, the samples contained elevated
concentrations of PCBs.
Fish Tissue Contaminants Index -
Maryland Coastal Bays
Site Criteria:
EPA Guidance concentration
OGood = Below Guidance range
OFair = Falls within Guidance range
OPoor = Exceeds Guidance range
Figure 3-107. Fish tissue contaminants index data for the
Maryland Coastal Bays, 2000-2001 (U.S. EPA/NCA).
Maryland Coastal Bays Program
Indicators of Estuarine Condition
A variety of indicators are used to assess estuarine
health in the Maryland Coastal Bays. The thresholds for
each indicator were approved by the MCBP's STAC.
Many local, state, and federal agencies participate in
monitoring the Coastal Bays' ecosystem. Monitoring
data are used to characterize water quality, habitat, and
living resource conditions in the Coastal Bays, provid-
ing essential information for management actions. The
STAC has developed a variety of indicators for assessing
water quality, stream health, sediment quality, habitat,
living resources, and harmful algae in the Maryland
Coastal Bays. Table 3-6 presents these indicators, along
with their thresholds and monitoring frequencies. The
status and trends of some of these indicators are
discussed below. Additional information about the
Maryland Coastal Bays environmental indicators is
available at http://www.dnr.state.md.us/coastalbays.
Water and Sediment Quality
The STAC's water quality indicators are monitored
by several agencies, including the Maryland DNR,
the NFS at Assateague Island, and MCBP volunteers.
In addition, the University of Maryland Center for
Environmental Science provides expertise in water
quality mapping. The Maryland DNR also assesses
stream health and monitors stream resources and sedi-
ment quality, whereas the USGS analyzes groundwater
inputs to the estuary (Wazniak et al., 2004).
Four water quality indicators are assessed in the
Maryland Coastal Bays— chlorophyll a, total nitrogen,
total phosphorus, and dissolved oxygen. Overall,
nutrient loading is showing measurable impacts on the
area's ecosystem. Monitoring data collected between
2001 and 2003 demonstrated that the upper tributaries
are severely enriched by nitrogen and that phosphorus
enrichment is more widespread throughout the Coastal
Bays. Although many of these upstream areas had
nutrient concentrations above the MCBP's threshold
levels, chlorophyll a concentrations were generally low
in the open Bays. These results are significant because
chlorophyll a measurements are often used to represent
the amount of algae in the water column.
184 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Maryland Coastal Bays Program
• Table 3-6. Water Quality, Stream Health, and Sediment Quality Indicators.Thresholds, and Monitoring Frequencies H
for the Maryland Coastal Bays (Wazniak et al., 2004; Maryland DNR, 2005b) •
Aquatic
Ecosystem
Monitoring
Water Quality
Stream Health
Sediment Quality
Habitat
Living Resources
Harmful Algae
Indicator
Total nitrogen
Total phosphorus
Chlorophyll a
Dissolved oxygen
Water quality index
Stream nitrate
Stream bottom-dwelling
Animal Index 1
Stream bottom-dwelling
Animal Index 2
Freshwater fish index
Excess organic carbon
Ambient toxicity
Mean Apparent Effects
Threshold
Seagrass
Macroalgae
Wetlands
Fish
Fish kills
Blue crabs
Shellfish (clams, scallops,
oysters)
Bottom-dwelling animals
Phytoplankton
HABs
Threshold
No more than 0.65 mg/L for
seagrass growth
No more than 1 mg/L as set
by STAC
No more than 0.037 mg/L for
seagrass growth
No more than 0.0 1 mg/L as set
by STAC
No more than 1 5 pg/L to prevent
low dissolved oxygen levels
No more than 50 ug/L as set
by STAC
No less than 5 mg/L to prevent
effects on aquatic life
No less than 3 mg/L as set by
STAC
Greater than 0.6
Less than 1 mg/L
Less than or equal to 2.8
Less than or equal to 4
Greater than or equal to 4
Less than or equal to 1 %
Significant difference from uncont-
aminated sediment
None
18,951 acres
None
No net loss
No decreasing trend in forage fish
index
None
None
None
MAIA benthic index value > 3
None
Species-specific thresholds
Monitoring
Frequency
Monthly
Monthly
Monthly, as well as continuous
monitoring and water quality
mapping (the latter two
measure total chlorophyll)
Monthly, as well as continuous
monitoring and water quality
mapping
Calculated by combining values
from all water quality indicators
Variable
Annually
Every 5 years
Every 5 years
Periodically
Annually (2000-2003)
Calculated from sediment
contaminant data (2000-2003)
Annual survey
Not routinely monitored
Not monitored directly
Monthly trawl: April - October
Seine: June and September
As needed
Monthly with fish survey
Clams — Annual survey
Annually (2000-2003)
Monthly -Weekly
As needed, when water quality
indicates algae are at high levels
National Estuary Program Coastal Condition Report 1 85
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Maryland Coastal Bays Program
Applied Monitoring: Incorporating
Stable Isotope Analysis into a
Water Quality Index
Environmental managers for the Maryland Coastal
Bays have set several environmental objectives, includ-
ing reducing sewage/septic inputs to the Bays and main-
taining suitable habitat for seagrass and fisheries. Each
objective can be linked to a water quality indicator.
Managers have set reference values for each indicator to
determine whether or not a particular waterbody is
achieving an individual objective. During a pilot study
in 2004, six water quality indicators (dissolved oxygen,
Secchi depth, chlorophyll a, total phosphorus, total
nitrogen, and isotopic ratios of nitrogen) were used to
develop a water quality index for the Maryland Coastal
Bays and tributaries (Jones et al., 2004). The table
below shows the management objective and reference
value for each water quality indicator.
In June 2004, a field-sampling program was
conducted to measure the 6 indicators at approximately
250 sites in the Maryland Coastal Bays. Secchi depths
were determined, and water samples were analyzed for
dissolved oxygen, chlorophyll a, total phosphorus, and
total nitrogen concentrations. Isotopic ratios of nitrogen
(delta nitrogen-15 values) were also measured. Measur-
ing isotopic ratios of nitrogen is important because
various sources of nitrogen to the Bays often have
distinguishable isotopic ratios. For example, elevated
delta nitrogen-15 (6^N) values are associated with
treated sewage effluent. The figure on the next page
displays the sampling results for 515N in the Maryland
Coastal Bays. Elevated 5^N values were found in the
St. Martin River, Isle of Wight Bay, and the southern
portion of Chincoteague Bay (near the town of
Chincoteague and Wallops Island). These elevated
values indicate that sewage is a major source of
nutrients in these portions of the Bays I Jones et al.,
2004).
The sampling sites were divided into reporting
regions by waterbody, and a water quality index for each
region was calculated by comparing the measured values
for each of the six indicators to the reference values for
each management objective (see table below). The
calculated water quality index is a number between zero
Indicators, Management Objectives, and Reference Values Used in the Calculation of the Water Quality Index
for the Maryland Coastal Bays (Jones et al., 2004)
Indicator
Management Objective
Reference Value
Dissolved oxygen
Maintain suitable fisheries habitat
5mg/L
Secchi depth
Clear water
> I meter
Chlorophyll a
Reduce phytoplankton
ISpg/L
Total phosphorus
Reduce phosphorus
<0.037mg/L(l.2 uM)
Total nitrogen
Reduce nitrogen
< 0.65 mg/L (46 uM)
Total ratio of nitrogen
(delta nitrogen-15)
Reduce sewage/septic inputs
< 14%
186 National Estuary Program Coastal Condition Report
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CHAPTER 3 1 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Maryland Coastal Bays Progran
and one. A score of 0.8 and above
indicates that habitat conditions are
considered good for fish and seagrass
survival, whereas a score of 0.4 or
below indicates unsuitable habitat for
either fish or seagrass. Intermediate
values indicate that the system is vari-
able and that some ecosystem func-
tions (e.g., seagrass beds or fish) may
be expected to be present some of the
time. The table below presents the
water quality indices for several water-
bodies in the Maryland Coastal Bays.
The Isle of Wight Bay received a good
water quality index rating, probably
due to the relatively high flushing rate
with the ocean at the southern end of
the Bays. The areas with die lowest
water quality index values were the
St. Martin River and the western side
of Chincoteague Bay (Newport Bay).
Secchi, total phosphorus, and chloro-
phyll a were the main factors resulting
in the poor overall water quality index
rating for Chincoteague Bay (Jones et
al., 2004).
Delta nitrogen-15
(PPt)
\ Av Sinepuxent
Bay
Assawoman
V' Isle of Wight
Bay
Chincoteague
Bay
Chincoteague
Inlet
Data analysis and map production by F. Pantos 2004
Distribution of isotopic ratios of nitrogen in the Maryland Coastal Bays (Jones et al.,
2004).
|^^B Summary of Water Quality Index Ratings by Region (Jones et al., 2004) ^^^^^^^^^^^^^f
Region
Assawoman Bay
Chincoteague Bay
Isle of Wight Bay
Newport Bay
Sinepuxent Bay
Chincoteague Inlet
St. Martin River
Newport Creek
Sites
18
106
20
31
36
7
II
10
WQI
0.56
0.42
0.69
0.33
0.68
0.62
0.29
0.36
Health
Fair
Fair
Good
Poor
Good
Good
Poor
Poor
National Estuary Program Coastal Condition Report 187
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Maryland Coastal Bays Program
Large algal blooms can limit the amount of light
available to seagrasses or reduce dissolved oxygen levels
in the water. Although shallow lagoons typically do
not stratify, oxygen values in the Coastal Bays were
frequently low in some areas. For example, continuous
monitoring data collected during the summer seasons of
2002 through 2004 show that dissolved oxygen levels in
the tributaries Bishopville Prong and Turville Creek
were low (less than 5 mg/L) approximately 40% to
60% of the time (Table 3-7) (Wazniak and Hall, 2005).
The monitoring data on the four component indica-
tors collected from around the Bays between 2001 and
2003 were compared to the threshold values listed in
Table 3-6, which are known to maintain fisheries and
seagrasses. The results of this comparison were then
used to develop the water quality index for a given
waterbody. This index ranks the Bays from best to worst
as follows: Sinepuxent, Chincoteague, Isle of Wright,
Newport, Assawoman, and St. Martin River (Wazniak
and Hall, 2005).
The health of the streams in the MCBP study area is
also assessed for the water quality index. Streams and
small creeks often serve as the initial receptors for the
nutrients, sediments, and chemicals that are later trans-
ported to the Bays, and fish and benthic communities
are used as indicators of stream health. Most streams in
the watershed are degraded with excess nutrients, and
high stream nitrate levels have been observed in all
segments of the Coastal Bays. These elevated stream
nitrate levels indicate excess inputs from human activi-
ties, which can be transported to the stream via surface
runoff or groundwater flow. Data on fish and benthic
animals indicate that most streams in the Coastal Bays
are degraded; however, long-term trend data indicate
that conditions are improving. Most animals found in
the streams were classified as pollution tolerant. Impacts
to the biota of Coastal Bays streams are likely the result
of physical habitat modification within the watershed
due to the extensive ditching that has increased the
number of creeks and tributaries in the region. Man-
made ditched streams generally have less habitat diver-
sity and lower flows than the minimally altered streams
of the Coastal Plain, which retain a more natural
wetland character. This ditching may also affect nutrient
levels in the region's creeks, tributaries, and bays by
allowing groundwater to enter streams more quickly,
thereby decreasing the filtration that the groundwater
would normally have encountered before entering the
Bays (Wazniak and Hall, 2005).
Excess organic carbon, ambient toxicity, and the
mean Apparent Effects Threshold (AET) are used to
assess sediment quality in the Maryland Coastal Bays.
Excess organic carbon is an important measure of sedi-
ment quality because it can be used as an indicator of
an area's rate of eutrophication and degree of pollution.
High excess carbon levels may be caused by frequent
algal blooms, the deposition of excessive plant debris
(e.g., from an eroding marsh), or human inputs.
Elevated excess carbon may also be significant because
metals and other pollutants tend to attach to organic
carbon, concentrating these contaminants in the sedi-
ment. St. Martin River, Herring Creek, and Newport
Table 3-7. Percent of the Time that Dissolved Oxygen Concentrations Were Below Threshold Levels in Two
Tributary Creeks Based on Continuous Monitoring Data Collected During the Summer Season (2002-2004)
(Wazniak and Hall, 2005)
Site
Dissolved Oxygen
Threshold Level
(mg/L)
2002
2003
2004
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Maryland Coastal Bays Program
Creek have excessively organic-rich sediments, which
may have an impact on benthic communities.
Sediments in the open-water areas of the Bays are not
enriched in organic carbon (Wazniak et al., 2004;
Wazniak and Hall, 2005). In 1999, the Maryland DNR
conducted a pilot study of sediment toxicity in samples
collected from five sites in the Coastal Bays, with
subsequent toxicity studies conducted by the NCA.
Overall, sediments in the study area show little evidence
of toxicity (Wazniak and Hall, 2005).
Mean AET values are an evaluation criterion derived
from a correlation of the weight of evidence from
multiple matched chemical and biological effects data
sets. AET values generally fall between the ERL and
ERM values (Wazniak and Hall, 2005). The AET is
used to assess the combined impact of multiple contam-
inants and is more sensitive to low contaminant
concentrations. The AET results show a higher poten-
tial for chemical contaminants to impact living
resources in the St. Martin River, Assawoman Bay, and
Herring, Turville, and Newport creeks (Figure 3-108).
Higher AET results can also indicate higher levels of
contaminants in the sediment (Wazniak et al., 2004).
Based on the AET and using NCA 2000 contaminant
data, bottom sediments in the southern Maryland
Coastal Bays (Sinepuxent, Newport, and Chincoteague
bays) and the open water areas in Assawoman and Isle
of Wight bays are not impaired by high levels of conta-
minants; concentrations for most metals are generally
within background levels; and most organic contami-
nants are at trace levels or below detection limits.
Higher contaminant levels were restricted to localized
areas in tributaries in the northern bays and in Newport
Creek. These areas were also high in TOC (Wazniak
and Hall, 2005).
Apparent Chemical
Contaminant Effects: 2000
• 0- 0.05 mean AET
• 0.05-0.1 mean AET
O.I-O.I5 mean AET
i 0.15-0.2 mean AET
0.2-0.35 mean AET
O Failed ambient tox
test in 2000
OoMnCfty
Figure 3-108. Map of mean Apparent Effects Threshold
measurements for samples collected in 2000 by the Maryland
Geological Survey (Wazniak et al., 2004).
Assateague Island National Seashore, Maryland (NPS).
National Estuary Program Coastal Condition Report 1 89
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Maryland Cocstal Boys Program
Habitat Quality
The status and trends of seagrass, macroalgae, and
wetlands habitat in the Maryland Coastal Bays have
been assessed. Virginia Institute of Marine Science
(VIMS) conducts an annual aerial survey of seagrass bed
distribution, whereas the Maryland DNR monitors
macroalgae abundance and distribution. In addition,
the Maryland Department of the Environment (MDE)
teams with the Maryland DNR to collect data on
wetlands. Seagrasses have been increasing in the Coastal
Bays and are estimated to cover 67% of the potential
habitat in the Bays. The 2003 acreage of 17,942 acres
represents the second-highest total documented in the
Coastal Bays and an overall 320% increase since annual
data collection began in 1986 (Wazniak et al., in press)
(Figure 3-109). Macroalgae, also known as seaweeds,
are abundant and distributed throughout the Bays
(Wazniak and Hall, 2005). Some macroalgae species are
occurring at harmful levels in some areas, causing such
problems as blocking needed light from SAV, decreasing
oxygen levels, and fouling boat propellers (Wazniak et
al., 2004). Wetlands in the Coastal Bays have decreased
substantially (up to 60%), especially in the northern
Bays (Wazniak and Hall, 2005).
Living Resources
Fish, shellfish, and benthic communities are surveyed
by the Maryland DNR and VERSAR, whereas fish kills
are monitored by the MDE. There are species-specific
thresholds that are used to determine ir an HAB has
occurred. Monitoring is also performed as needed when
routine water quality indicates algae at high levels or a
specific incidence occurs (e.g., fish kill, color complaint).
The Maryland Coastal Bays provide habitat for
140 species of finfish (Wazniak et al., 2004; Wazniak
and Hall, 2005). Although finfish in the Bays are
diverse, the forage fish index has been declining over
time. This index is based on the abundance of the four
most common forage species (e.g., bay anchovy,
menhaden, spot, and Atlantic silverside). The decline in
the forage fish index has been dominated by the
decreasing abundance of spot; however, the populations
of other species assessed by the index have also been
slowly declining. Low dissolved oxygen levels in the
Maryland Coastal Bays have caused two-thirds of fish
kills (where the cause was determined), and sporadic fish
kills due to low oxygen appear to be increasing in
frequency (Wazniak and Hall, 2005).
<
I
20,000-1
18,000-
16,000-
14,000-
12,000-
10,000
8,000-
Assawoman Bay
Isle of Wight Bay
St. Martin's River
Sinepuxent Bay
Newport Bay
Chincoteague Bay
1986 1987 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 199920002001 20022003
Years
Figure 3-109. Seagrass abundance in the Maryland Coastal Bays (Wazniak and Hall, 2005).
190 National Estuary Program Coastal Condition Report
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Maryland Coastal Bays Program
Based on the MAIA benthic index, benthic commu-
nities are generally faring poorly in the creeks and better
in the open Bays (Figure 3-110). Catches of hard clams
have declined during the past three decades, but have
been relatively stable for the past 10 years. Bay scallops
have recently returned to the area and have been found
in most Bay segments, although in low numbers
(Wazniak and Hall, 2005).
Between 2001 and 2003, the highest diversity of
phytoplankton in the Maryland Coastal Bays occurred
during the winter, with varied long-term phytoplankton
trends at individual sampling sites. For example, phyto-
plankton abundance decreased in the St. Martin River,
and phytoplankton density increased in the tributaries
of the Isle of Wight Bay (Wazniak and Hall, 2005).
Certain types of algae may become harmful if they
occur in large amounts as HABs or if they produce a
toxin that can harm aquatic life or humans.
Approximately 5% of the phytoplankton species identi-
fied in the Maryland Coastal Bays represent potential
HAB species. The presence of these species is richest in
the polluted tributaries of St. Martin River and
Newport Bay. In recent years, brown tide (Aureococcus
anophagefferens) has been the most widespread and
prolific HAB species in the area, affecting the growth of
juvenile clams in test studies and potentially impacting
seagrass distribution and growth in the Bays. Although
no evidence of toxic activity has been detected among
the phytoplankton in Maryland Coastal Bays, some of
the species found in the Bays have been responsible for
positive toxic bioassays, detectable toxin levels, and/or
fish kills in other areas along the eastern shore of the
United States. Tracking the diversity, abundance, distri-
bution, and toxic activity of potential HAB species over
time provides important indicators of environmental
change for the Coastal Bays (Wazniak and Hall, 2005).
Environmental Stressors
The Maryland DNR monitors shoreline change as
an indicator of human impacts on habitat quality in the
Maryland Coastal Bays. Evaluations of aerial photog-
raphy taken in 1989 showed that approximately 10% of
the Coastal Bays have artificially hardened shoreline
(e.g., bulkheads or riprap). The percentage of hardened
shoreline was higher in the northern Bays (Assawoman
Bay, Isle of Wight Bay, and St. Martin River), where
percentages ranged from 21% to 44% (Wazniak et al.,
2004; Wazniak and Hall, 2005).
Benthic Index Score
2002
3 _ 4 • ) Meets Goal
A Degraded
m ) Severe|y Degraded
2-3
Figure 3-110. Map of 2002 MAIA benthic index results for the
Maryland Coastal Bays (Wazniak et al., 2004).
National Estuary Program Coastal Condition Report 191
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CHAPTER 3 NORTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Maryland Coastal Bays Program
Current Projects,
Accomplishments, and Future
Goals
Some of the recent environmental success stories and
restoration efforts completed around the Coastal Bays
include the following:
• The Maryland DNR's Fish Advisory Committee
has completed fishery management plans for hard
clams and blue crabs and has also obtained a
$25,000 NOAA Coastal Services Center Grant
for developing the concepts of water zoning and
sanctuaries to manage resources.
• In April 2002, the Maryland Saltwater Sport-
fishermen's Association and local anglers coordi-
nated a cooperative angler flounder survey to
collect and assess data to promote better fishing
techniques and legislation to benefit both fish and
fishermen (Wazniak et al., 2004).
• Co-organized by the MCBP, the Delmarva Bird-
ing Weekend highlights the watershed's status as
an internationally significant route on the Atlantic
Flyway by featuring more than 27 kayaking,
boating, and walking tours through the watershed
and other parts of the Delmarva Peninsula. More
than 500 people from 20 states attended this
event in 2005 (MCBP, 2005).
• Recognizing shortcomings in state enforcement of
wetland laws, Worcester County, the MCBP, plan-
ners, regulators, and wetland delineators formed
the Wetland Planning Group to discuss projects,
laws, and issues affecting area wetlands. The group
has served as a coordinator among agencies and
spawned a wetland White Paper on ways to better
protect wetlands in the Coastal Bays' watershed.
• The Bishopville Restoration Project is funded
under the Estuary Restoration Act of 2000 and
focuses efforts to initiate restoration efforts in the
upper St. Martin River, which is considered the
most degraded waterbody in the Bays. The
restoration project is a cooperative effort among
the MCBP, Maryland DNR, USAGE, State
Highway Administration, and Worcester County
to restore about 1,000 feet of stream and stream-
side vegetation and remove the existing dam at
Bishopville to open the stream to fish passage
(MCBP, 2005).
• Worcester County government has pursued local
responsibility for achieving nutrient-reduction
goals through sub-watershed planning by
engaging stakeholders in each sub-watershed to
develop strategies for meeting reduction goals.
The new comprehensive development plan
included strategies for TMDL implementation.
• The Maryland DNR has worked with the U.S.
Department of Agriculture (USDA) Forest Service
in programs such as Rural Legacy and Stream
ReLeaf to improve forest character, develop
educational outreach programs, and identify and
promote programs that protect these areas
(Wazniak et al., 2004).
• The MCBP has developed a homeowner's guide
that provides more than 100 ways to protect the
Maryland Coastal Bays.
• The MCBP has completed more than 500 news
articles, 11 school projects, and 33 television spots
to help educate the public about the Maryland
Coastal Bays. In 2000, 11 radio shows highlighted
the MCBP's efforts (ANEP, 200 Ib).
Conclusion
The overall condition of the Maryland Coastal Bays
is rated fair based on the four indices of estuarine condi-
tion used by the NCA survey. Based on the findings of
the MCBP, water and sediment quality are generally
poorer in and near tributaries than in the open Bays,
and, in general, most streams in the MCBP study area
are degraded with excess nutrients. Higher contaminant
and organic carbon levels in sediments were restricted to
localized areas in tributaries in the northern Bays and in
Newport Creek. Seagrass acreage has been increasing,
and wetlands have been decreasing. Macroalgae
communities are abundant and well distributed
throughout the area; however, some macroalgae species
occur at harmful levels. Although finfish in the Bays are
diverse, the forage fish index has been declining over
time. Overall, benthic communities are faring poorly in
the creeks and better in the open Bays, and the presence
of HAB species is richest in the polluted tributaries of
St. Martin River and Newport Bay.
192 National Estuary Program Coastal Condition Report
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CHAPTER 4
SOUTHEAST COAST NATIONAL ESTUARY PROGRAM
COASTAL CONDITION
,-ir\,.;t,,-a \
,, -;;-
-------
CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
CHAPTER 4
SOUTHEAST COAST NATIONAL ESTUARY PROGRAM
COASTAL CONDITION
Background
The Southeast Coast region extends from southern
Virginia to Florida and includes two NEP estuaries: the
Albemarle-Pamlico Estuarine Complex in North
Carolina and Virginia and the Indian River Lagoon in
Florida (Figure 4-1). Both estuarine systems are charac-
terized by shallow lagoons located behind extensive
Atlantic Ocean
I. Albemarle-Pamlico Estuarine Complex
2. Indian River Lagoon
barrier island chains that are punctuated with one or
more narrow inlets or channels to the ocean. The flat
coastal plain, small tidal range, and barrier islands that
typify the Southeast Coast combine to minimize the
influence of tides on water circulation in the region's
two NEP estuaries; therefore, circulation within these
systems is driven by different factors than in the river-
dominated or tidally dominated estuaries found in other
regions of the United States (NOAA, 1985).
Due to the vast forested acreage that dominates the
Southeast region's coastal drainage area;;, freshwater
inflow to the NEP estuaries typically brings only small
to moderate amounts of sediment; however, sediment
loading to these estuaries can be higher in areas where
land use is dominated by intensive agriculture and
where soils that are subject to erosion are farmed.
Precipitation patterns also influence freshwater input
from rivers flowing into these estuaries. The region's
annual average precipitation of about 40 inches
decreases slightly from the north to the central portion
of the region, and then increases to up to 64 inches in
southern Florida. The Southeast Coast NEP estuaries
contribute about 35% of all freshwater discharges to
East Coast waters (NOAA, 1985).
Population Pressures
The population of the 41 NOAA-designated coastal
counties coincident with the NEP study areas of the
Southeast Coast region increased by more than 131.4%
during the past 40 years, from 1.4 million people in
1960 to 3.2 million people in 2000 (Figure 4-2) (U.S.
Census Bureau, 1991; 2001). This increase resulted in a
population density of 168 persons/mi2 in 2000 for
these coastal counties; however, the population densities
of the region's individual NEP study areas varied
considerably in 2000, from a high of 308 persons/mi2
for the Indian Pviver Lagoon to 125 persons/mi2 for the
Figure 4-1. The Southeast Coast region is home to two NEP
estuaries.
1194 National Estuary Program Coastal Condition Report
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I
CHAPTER 4 i SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Albemarle-Pamlico Estuarine Complex (U.S. Census
Bureau, 2001). Development and population pressures
are especially strong surrounding these NEP estuaries,
which are centers of commercial fishing and recreational
activity for the coastal communities of the Southeast
Coast region.
I960
2000
Figure 4-2. Population of the 41 NOAA-designated coastal
counties of the Southeast Coast NEP study areas, 1960-2000
(U.S. Census Bureau, 1991:2001).
NCA Indices of Estuarine
Condition—Southeast Coast
Region
Based on data collected by the NCA, the overall
condition of the collective NEP estuaries of the South-
east Coast region is rated good to fair (Figure 4-3). Due
to the rotating basin-monitoring schedule for Florida,
the NCA sampled only the northern portion of the
Indian River Lagoon for this assessment (approximately
230 mi2). Because of their size, the estuaries of the
Albemarle-Pamlico Estuarine Complex generally drive
the coastal condition estimates for the Southeast Coast
NEP estuarine area. The ratings for the NCA indices of
estuarine condition (water quality, sediment quality,
benthic, and fish tissue contaminants) for the Southeast
Coast NEP estuaries ranged from good to fair, and
neither estuary received a poor rating for any of the
component indicators. Figure 4-4 shows the percentage
of the Southeast Coast NEP estuarine area rated good,
fair, poor, or missing for each parameter considered.
Please refer to Tables 1-24, 1-25, and 1-26 (Chapter 1)
for a summary of the criteria used to develop the rating
for each index and component indicator.
Overall Condition
Southeast Coast
NEP Estuaries
(4.0)
Water Quality Index (5)
Sediment Quality Index (4)
\ Benthic Index (3)
\ Fish Tissue Contaminants
Index (4)
Figure 4-3. The
overall condition of
the Southeast Coast
NEP estuarine area is
good to fair
(U.S. EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80
Percent Estuarine Area
100
Missing
Figure 4-4. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Southeast Coast
region (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 1 95
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Water Quality Index
The water quality index for the collective NEP estu-
aries of the Southeast Coast region is rated good (Figure
4-5). This index was developed using NCA data on five
component indicators: DIN, DIP, chlorophyll a, water
clarity, and dissolved oxygen. Thirty-five percent of the
region was rated fair for this index, indicating that some
vigilance may be required regarding DIP and chloro-
phyll a concentrations.
Dissolved Nitrogen and Phosphorus I The
Southeast Coast region is rated good for DIN concen-
trations because 12% of the region's NEP estuarine area
was rated fair for this component indicator and none of
the area was rated poor. The Southeast Coast region is
also rated good for DIP concentrations, with 17% of
the region's NEP estuarine area rated fair and 6% of the
Water Quality Index - Southeast Coast
Site Criteria: Number of component
indicators in poor or fair condition
• Good = No more than I is fair
OFair = I is poor, or 2 or
more are fair
• Poor = 2 or more are poor
O Missing
Missing Roor
2/0 4%
area rated poor. NCA data on DIN and DIP concentra-
tions were unavailable for 1 % of the Southeast Coast
NEP estuarine area.
Chlorophyll a The Southeast Coast region is rated
fair for chlorophyll a concentrations because 71% of the
regions NEP estuarine area was rated fair for this com-
ponent indicator and 5% of the area was rated poor.
NCA data on chlorophyll a concentrations were
unavailable for 1 % of the Southeast Coast NEP estu-
arine area.
Water Clarity \ Water clarity in the collective NEP
estuaries of the Southeast Coast region is rated good.
Three percent of the region's NEP estuarine area was
rated fair for this component indicator, and only 6% of
the area was rated poor.
Dissolved Oxygen The Southeast Coast region is
rated fair for dissolved oxygen concentrations because 8%
of the region's NEP estuarine area was rated fair for this
component indicator and 7% of the area was rated poor.
Figure 4-5. Water quality index data for the Southeast Coast
NEP estuarine area, 2000-2002 (U.S. EPA/NCA).
Sediment Quality Index
The sediment quality index for the Southeast Coast
region is rated good to fair because 6% of the regions
NEP estuarine area was rated poor for sediment quality
condition (Figure 4-6). This index was developed using
NCA data on three component indicators: sediment
toxicity, sediment contaminants, and sediment TOC.
This report discusses two different approaches for
characterizing estuarine condition:
Approach I —The NCA provides unbiased, quality-
assured data that can be used to make consistent "snap-
shot" comparisons among the nation's NEP estuaries.
These comparisons are expressed in terms of the percent
of NEP estuarine area in good, fair, or poor condition.
Approach 2 - Each individual NEP collects site-specific
estuarine data in support of local problem-solving efforts.
These data are difficult to compare among NEPs, within
regions or nationally, because the sampling and evaluation
procedures used by the NEPs are often unique to their
individual estuaries. However, these evaluations are
important because NEP-collected data can evaluate
spatial and temporal changes in estuarine condition on a
more in-depth scale than can be achieved by the NCA
snapshot approach.
196 National Estuary Program Coastal Condition Report
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Sediment Quality Index - Southeast Coast
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
OFair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Poor
6%
Figure 4-6. Sediment quality index data for the Southeast
Coast NEP estuarine area, 2000-2002 (U.S. EPA/NCA).
TOC concentrations were the only sediment quality
component indicator measured in the Indian River
Lagoon; therefore, the sediment quality index for the
Southeast Coast NEP estuarine area is not based on a
full assessment of sediment toxicity or sediment
contaminant concentrations in all of the region's NEP
estuaries.
Sediment Toxicity I The Southeast Coast region
is rated good for sediment toxicity; however, this
assessment is based solely on data collected for the
Albemarle-Pamlico Estuarine Complex because NCA
data on sediment toxicity were unavailable for the
Indian River Lagoon. Eighty-three percent of the
Southeast Coast NEP estuarine area was rated good for
sediment toxicity, and only 3% of the area was rated
poor, with poor samples collected at one site in
Currituck Sound and one site in Pamlico Sound. NCA
data on sediment toxicity were unavailable for 14% of
the Southeast Coast NEP estuarine area.
Sediment Contaminants The Southeast Coast
region is rated good for sediment contaminant concentra-
tions; however, this assessment is based solely on data
collected for the Albemarle-Pamlico Estuarine Complex
because NCA data on sediment contaminants were
unavailable for the Indian River Lagoon. Based on these
parameters, 88% of the Southeast Coast NEP estuarine
area was rated good for sediment contaminant concentra-
tions, 2% of the area was rated fair, and none of the area
was rated poor. NCA data on sediment contaminant
concentrations were unavailable for 10% of the Southeast
Coast NEP estuarine area.
Total Organic Carbon \ The Southeast Coast
region is rated good for TOC concentrations. TOC
concentrations were rated good in 75% of the region's
NEP estuarine area, fair in 22% of the area, and poor in
only 3% of the area, with the sites rated poor located in
North Carolina's Little Alligator River, Slocum Creek,
and Neuse River.
National Estuary Program Coastal Condition Report 197
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Benthic Index
The benthic index for the collective NEP estuaries of
the Southeast Coast region is rated fair. The Southeast
Coast Benthic Index, developed by Van Dolah et al.
(1999), integrates measures of species diversity and
populations of indicator species to distinguish between
degraded (poor) and reference benthic communities.
Fifteen percent of the Southeast Coast NEP estuarine
area was rated poor for benthic condition, 66% was
rated good, and 16% was rated fair (Figure 4-7).
Benthic Index - Southeast Coast
Site Criteria: Southeast Coast
Benthic Index Score
• Good = > 2.5
OFair =2.0-2.5
• Poor = < 2.0
O Missing
Figure 4-7. Benthic index data for the Southeast Coast NEP
estuarine area, 2000-2002 (U.S. EPA/NCA).
Although only 15% of the Southeast: Coast NEP
estuarine area had degraded benthic resources, 80% of
the sampling sites representing this degraded area were
geographically correlated with some measure of poor
water or sediment quality (Figure 4-8). Poor benthic
condition co-occurred with equal frequency for
degraded sediment quality and water quality (60% of
the sites with poor benthic condition).
None
20%
Water
Quality Only
20%
Sediment and
Water Quality
40%
Sediment
Quality Only
20%
Figure 4-8. Percent of sampling sites in the Southeast Coast
NEP estuaries where poor benthic condition overlaps with other
indices rated poor (U.S. EPA/NCA).
Fish Tissue Contaminants Index
Fish tissue contaminants data for the Southeast Coast
NEP estuarine area were collected for the Albemarle-
Pamlico Estuarine Complex; however, data were not
collected for the Indian River Lagoon. Figure 4-9 shows
that only 10% of all stations sampled where fish were
caught exceeded the EPA Advisory Guidance values
used in this assessment, resulting in a rating of good to
fair for the region's fish tissue contaminants index (70%
of the stations were rated good). These contamination
estimates are an approximation because they are based
on the analysis of whole-body samples, rather than
fillets only. For mercury, which has a high affinity for
muscle tissue, these data may be an underestimation;
however, for the chemical contaminants that concen-
trate in fish organs and fatty tissues, the data may be an
overestimation. Although the fish sampled may not
represent the same species sought by commercial fish-
ermen and consumers, the analysis does represent the
potential for accumulation of contamination in these
estuarine environments.
198 National Estuary Program Coastal Condition Report
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
O Fair = Falls within Guidance range
• Poor = Exceeds Guidance range
Fair
20%
Figure 4-9. Fish tissue contaminants index data for the Southeast
Coast NEP estuarine area, 2000-2002 (U.S. EPA/NCA).
NEP Estuaries and the Condition
of the Southeast Coast Region
The purpose of the NEP is to identify, restore, and
protect the nationally significant estuaries of the United
States. The Southeast Coast region supports diverse
agricultural activities such as large-scale agriculture
production and aquaculture and is home to two NEP
estuaries: the Albemarle-Pamlico Estuarine Complex
and the Indian River Lagoon. The Albemarle-Pamlico
Estuarine Complex NEP study area contains large tracts
of forested and undeveloped land, including 11
National Wildlife Refuges (e.g., Great Dismal Swamp,
Back Bay, Mackay Island, Currituck, Roanoke River,
Alligator River, Pocosin Lakes, Pea Island, Mattamus-
keet, Swan Quarter, and Cedar Islands). The Complex's
watershed also contains the Cape Lookout and Cape
Hatteras national seashores; the Croatan National
Forest; and many state-owned parks, forests, and
research reserves (Martin et al., 1996). In addition,
several U.S. Department of Defense (DoD) lands are
located in this watershed. Similar to the Albemarle-
Pamlico Estuarine Complex, portions of the Indian
River Lagoon NEP study area have escaped much of the
urbanization that has overrun other portions of Florida's
coastal areas, and the estuarine area of the Lagoon
includes the Merritt Island National Wildlife Refuge,
Canaveral National Seashore, Hobe Sound National
Wildlife Refuge, Pelican Island National Wildlife
Refuge, and several state parks. The citrus industry is a
dominant agricultural land use within the Indian River
Lagoon study area.
Because the areas surrounding the Southeast Coast
NEP estuaries have not been developed as major metro-
politan urban centers, a key question when assessing
these two estuaries is whether their condition accurately
reflects the condition of all Southeast Coast estuaries
(both NEP and non-NEP). A comparison of NCA data
from the two Southeast Coast NEP estuaries and all
Southeast Coast estuaries reveals that the two groups of
estuaries have similar overall condition ratings, as well as
similar ratings for most of the NCA estuarine indices.
Based on the NCA survey results, both the collective
Southeast Coast NEP estuaries and all Southeast Coast
estuaries combined are rated good to fair for overall
condition, with both groups receiving an overall condi-
tion score of 4.0 (Figure 4-10). A comparison of NCA
data for both groups of estuaries shows that the collec-
tive Southeast Coast NEP estuaries are rated good for
the water quality index, good to fair for the sediment
quality index, fair for the benthic index, and good to
fair for the fish tissue contaminants index. The group of
all Southeast Coast estuaries combined are rated good
to fair for the water quality and sediment quality
indices, fair for the benthic index, and good for the fish
tissues contaminants index. With respect to the water
quality and sediment quality component indicators,
both groups of estuaries are rated good for DIN
concentrations and all three sediment quality compo-
nent indicators (sediment toxicity, sediment contami-
nants, and sediment TOC) and fair for chlorophyll a
concentrations. The collective Southeast Coast NEP
estuaries are rated good for DIP concentrations and
water clarity and fair for dissolved oxygen concentra-
tions, whereas the group of all Southeast Coast estuaries
National Estuary Program Coastal Condition Report 199
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Overall Condition
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue Contaminants
Index
Figure 4-10. Comparison of NCA results for Southeast Coast NEP
estuaries and all Southeast Coast estuaries (U.S. EPA/NCA).
combined are rated fair for DIP concentrations and
water clarity and good for dissolved oxygen concentra-
tions.
With respect to the two Southeast Coast NEP estu-
aries, both estuaries received higher or comparable
overall condition scores to the overall condition score
for the collective Southeast Coast NEP estuaries (4.0,
rated good to fair). The Indian River Lagoon (5.0) is
rated good for overall condition, whereas the overall
condition rating for the Albemarle-Pamlico Estuarine
Complex (4.0) is good to fair. It should be noted,
however, that the NCA survey data for the Indian River
Lagoon are incomplete because NCA data were not
available to assess the fish tissue contaminants index or
the sediment toxicity and sediment contaminants
component indicators for this estuary. In addition, only
the northern portion of the Indian River Lagoon was
surveyed by the NCA in 2000 and 2001. Much of this
area is included within the federally protected National
Aeronautics and Space Administration (NASA)/Kennedy
Space Center/Merritt Island Wildlife Refuge complex
and the Canaveral National Seashore and remains rela-
tively undeveloped. In contrast, much of the southern
portion of the Indian River Lagoon (which was not
surveyed by NCA) is suburban or urban in character;
includes extensive agricultural areas; and continues to
experience rapid development. An assessment that
includes all indices and component indicators and that
assesses both the northern and southern portions of the
Lagoon may have resulted in a different overall condi-
tion rating for the Indian River Lagoon.
The NCA survey data show that the two NEP estu-
aries of the Southeast Coast are both rated good for the
water quality index and that the ratings for all five of
200 National Estuary Program Coastal Condition Report
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CHAPTER 4 I SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
the water quality component indicators are comparable
between the two estuaries. For both the Albemarle-
Pamlico Estuarine Complex and the Indian River
Lagoon, DIN and DIP concentrations and water clarity
are rated good, and chlorophyll a and dissolved oxygen
concentrations are rated fair.
The sediment quality index ratings differ slightly
between the Albemarle-Pamlico Estuarine Complex and
the Indian River Lagoon. The sediment quality index
for the Albemarle-Pamlico Estuarine Complex is rated
good to fair, with all three component indicators (sedi-
ment toxicity, sediment contaminants, and sediment
TOC) also rated good. The sediment quality index for
the Indian River Lagoon is rated good; however, this
rating is based only on measurements of one compo-
nent indicator (sediment TOC, rated good) collected in
the northern part of the Lagoon.
The benthic index, which denotes the health of an
estuary's benthic community, is rated fair for the
Albemarle-Pamlico Estuarine Complex and good for the
Indian River Lagoon.
The fish tissue contaminants index is rated good to
fair for the Albemarle-Pamlico Estuarine Complex. The
NCA did not collect data on fish tissue contaminant
concentrations for the Indian River Lagoon; therefore, a
fish tissues contaminants index for this estuary was not
developed for this report.
Nationally, the overall condition score (4.0) for the
collective NEP estuaries of the Southeast Coast region
ranked highest when compared to the Gulf Coast
(2.75), West Coast (2.5), Northeast Coast (1.5), and
Puerto Rico (1.5) NEP regions. Population pressures,
measured as population density (number of
persons/mi2), did not correlate well with the overall
condition ratings for the Southeast Coast NEP estu-
aries. For example, although the Albemarle-Pamlico
Estuarine Complex has a lower calculated population
density of 125 persons/mi2, this estuary is rated good to
fair for overall condition, with an overall condition
score of 4.0. In contrast, the Indian River Lagoon, with
a higher population density (305 persons/mi2), is rated
good for overall condition, with a overall condition
score of 5.0; however, inclusion of the missing data for
two of the sediment quality component indicators (sedi-
ment toxicity and sediment contaminants) and for the
fish tissue contaminants index may have resulted in a
lower overall condition score for the Indian River
Lagoon.
National Estuary Program Coastal Condition Report 201
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROG RAM COASTAL CONDITION
Albemarle-Paml'tco National Estuary Progran
Albemarle-Pamlico National Estuary Program
www.apnep.org
Background
The Albemarle-Parnlico Estuarine Complex drains
approximately 30,000 mi2 of watershed and comprises
the largest lagoonal estuarine system in the United
States. This NEP has a 23,000-mi2 study area that
extends south from Prince George County, VA,
to Carteret County, NC, and includes 7 sounds
(Albemarle, Bogue, Core, Croatan, Currituck, Pamlico,
and Roanoke) (APNEP, 2006).
Freshwater inputs to this system are provided by
five major rivers — the Pasquotank, Chowan, and
Roanoke rivers that flow into Albemarle Sound and the
Tar-Pamlico and Neuse rivers that flow into Pamlico
Sound. This region features a variety of habitat types,
including significant pocosins (southeastern shrub
bogs), pine savannahs, hardwood swamp forests, bald
cypress swamps, salt marshes, brackish marshes, fresh-
water marshes, and beds of SAV (Martin et al., 1996).
On the eastern side of the Albemarle-Pamlico Estuarine
Complex, a chain of islands forms a barrier with the
Atlantic Ocean. The Complex is uniquely characterized
by random wind-driven tides, which result in less-
predictable variations in water circulation and salinity
patterns (Focazio, 2006a). Economically, this estuarine
202 National Estuary Program Coastal Condition Report
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Albemarle-Pamlico National Estuary Program
system represents the Southeast region's key resource
base for commercial fishing, tourism, recreation, and
resort development. Economic benefits are also derived
from the use of the area's natural resources for mining,
forestry, and agriculture (APNEP, 2006).
The Albemarle-Pamlico National Estuary Program
(APNEP) was among the first NEPs established by EPA
in 1987. The central focus of the APNEP is to work
closely with citizens' groups, businesses, researchers,
local governments, and state and federal agencies to
implement the key objectives of the APNEP's
Comprehensive Conservation and Management Plan
(APNEP, 1994) through the APNEP's Advisory Board
and committees. Recent APNEP projects have illus-
trated new methods of environmental protection and
restoration, including conservation easements,
stormwater-runoff control systems, greenroofs,
composting techniques that turn agriculture and crab-
processing waste into fertile soil, and the development
of new fishing gears that reduce the unintended capture
of non-target species such as sea turtles. Other APNEP
projects include opening historic spawning areas for
shad and herring that had previously been blocked by
dams and roads and replenishing scallop beds that were
decimated by a red tide event in 1987 (APNEP, 2006).
Environmental Concerns
The issues of environmental concern for the APNEP
are water quality, habitat quality, and fishery resources.
Impairment of waters in the Albemarle-Pamlico
Estuarine Complex can primarily be attributed to non-
point sources of pollution, of which agricultural and
urban runoff are the most prevalent. A smaller, but still
significant amount of water quality impairment in the
system can be attributed to point-source discharges
along the rivers flowing into the Complex. Ecological
stressors, including nutrient pollution, phytoplankton
growth, exotic species growth, and other factors, place
viable habitat areas in the region at risk, and the extent
of wetland habitat in the region is considerably dimin-
ished relative to historical distributions due to changes
in land-use patterns. Downward trends in commercial
landings are indicative of declining stocks of local popu-
lations of finfish and shellfish species, including Atlantic
croaker, Atlantic sturgeon, Eastern oyster, red drum,
striped bass, summer flounder, weakfish, and herring.
The overall CPUE from these estuaries is also declining,
despite improvements in fishing gear and methods. In
general, overfishing and habitat loss are believed to be
major causes of the declines in catch; however, a variety
of other factors, including habitat alteration, weather
events and seasonal cycles, and water quality degrada-
tion, may also play a role (APNEP, 2006).
Population Pressures
The population of the 35 NOAA-designated coastal
counties (25 coastal counties in North Carolina and
10 in Virginia) coincident with the APNEP study area
increased by more than 71.1% during a 40-year period,
from 1.1 million people in 1960 to 1.8 million people
in 2000 (Figure 4-11) (U.S. Census Bureau, 1991;
2001). This rate of growth for the APNEP study area is
low compared to the population growth rate of 131.4%
for the collective NEP-coincident coastal counties of the
Southeast Coast region. In 2000, the population density
of this study area's 35 coastal counties was 125
persons/mi2, slightly lower than the population density
of 168 persons/mi2 for the collective NEP-coincident
coastal counties of the Southeast Coast region (U.S.
Census Bureau, 2001). Population pressures for the
APNEP study area may be slightly lower than for other
NEPs, in part because a large amount of the state and
federal land surrounding this estuary is designated for
protection as national seashore, wildlife areas, or forests.
As a result, development is concentrated in the
remaining non-federal or non-state areas.
2.0
° 1.5
1.0
2 0.5
0.0
I960
2000
Figure 4-11. Population of NOAA-designated coastal counties
of the APNEP study area, 1960-2000 (U.S. Census Bureau, 1991;
2001).
National Estuary Program Coastal Condition Report 203
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Albemarle-Pamlico National Estuary Program
NCA Indices of Estuarine
Condition—Albemarle-Pamlico
Estuarine Complex
The overall condition of the Albemarle-Pamlico
Estuarine Complex is rated good to fair based on the
four indices of estuarine condition used by the NCA
(Figure 4-12). The water quality index for the Complex
is rated good, the sediment quality and fish tissue con-
taminants indices are rated good to fair, and the benthic
index is rated fair. Figure 4-13 shows the percentage of
estuarine area rated good, fair, poor, or missing for each
parameter considered. This assessment is based on data
collected by EMAP from 66 NCA sites sampled in the
APNEP estuarine area in 2000 and 2001. Please refer to
Tables 1-24, 1-25, and 1-26 (Chapter 1) for a summary
of the criteria used to develop the rating for each index
and component indicator.
Overall Condition
Albemarle-Pamlico
Estuarine Complex
(4.0)
Sediment Quality Index (4)
Benthic Index (3)
Fish Tissue Contaminants
Index (4)
Figure 4-12. The
overall condition of
the APNEP estuarine
area is good to fair
(U.S. EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Estuarine Area
Missing
Figure 4-13. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Albemarle-
Pamlico Estuarine Complex (U.S. EPA/NCA).
Water Quality Index
The water quality index for the Albemarle-Pamlico
Estuarine Complex is rated good (Figure 4-14). This
index was developed using NCA data on five compo-
nent indicators: DIN, DIP, chlorophyll a, water clarity,
and dissolved oxygen. Only 4% of the Complex's estu-
arine area was rated poor for water quality; however,
35% was rated fair.
Dissolved Nitrogen and Phosphorus I The
Albemarle-Pamlico Estuarine Complex is rated good for
DIN and DIP concentrations. Eighty-five percent of
the estuarine area was rated good for DIN concentra-
tions, 14% of the area was rated fair, and none of the
area was rated poor. Similarly, 74% of the estuarine
area was rated good for DIP concentrations, 18% of the
area was rated fair, and 7% of the area was rated poor.
204 National Estuary Program Coastal Condition Report
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CHAPTER 4 ! SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Albemarle-Pamlico National Estuary Program
Site Criteria: Number of component
indicators in poor or fair condition
• Good = No more than I is fair
I is poor, or 2 or
more are fair
• Poor = 2 or more are poor
O Missing
Fair
35%
Figure 4-14. Water quality index data for the Albemarle-
Pamlico Estuarine Complex, 2000-2001 (U.S. EPA/NCA).
The measured DIP values used in this assessment are an
approximation because these values were based on
filtered, acid-preserved phosphorus, which provides a
measure of total phosphorus, not of DIP only.
Literature suggests that DIP represents about 97% of
the total phosphorus measurement for estuaries of the
Southeast Coast region (Van Dolah et al., 2002).
Chlorophyll a I The Albemarle-Pamlico Estuarine
Complex is rated fair for chlorophyll a concentrations,
with 25% of the estuarine area rated good for this
component indicator, 70% of the area rated fair, and
5% of the area rated poor.
Water Clarity I The Albemarle-Pamlico Estuarine
Complex is rated good for water clarity. Water clarity
was rated poor at a sampling site if light penetration at
1 meter was less than 10% of surface illumination.
Eighty-three percent of the estuarine area was rated
good for water clarity, 3% of the area was rated fair,
and only 7% of the area was rated poor. NCA data on
water clarity were unavailable for 7% of the APNEP
estuarine area.
Dissolved Oxygen I The Albemarle-Pamlico
Estuarine Complex is rated fair for dissolved oxygen
concentrations. Although 86% of the estuarine area was
rated good for this component indicator, 8% was rated
poor, and 5% was rated fair.
Sediment Quality Index
The sediment quality index for the Albemarle-
Pamlico Estuarine Complex is rated good to fair, with
7% of the estuarine area rated poor and 93% of the area
rated good for sediment quality condition (Figure 4-15).
This index was developed using NCA data on three
component indicators: sediment toxicity, sediment
contaminants, and sediment TOC.
Sediment Toxicity I The Albemarle-Pamlico
Estuarine Complex is rated good for sediment toxicity.
Ninety-two percent of the estuarine area was rated good
for this component indicator, and only 3% of the area
was rated poor. NCA data on sediment toxicity were
unavailable for 5% of the APNEP estuarine area.
Sediment Contaminants The Albemarle-
Pamlico Estuarine Complex is rated good for sediment
contaminant concentrations, with 97% of the estuarine
area rated good, 3% of the area rated fair, and none of
the area rated poor.
Total Organic Carbon The Albemarle-Pamlico
Estuarine Complex is rated good for sediment TOC.
Twenty-three percent of the estuarine area was rated fair
for this component indicator, 74% of the area was rated
good, and the remaining 3% of the area was rated poor.
National Estuary Program Coastal Condition Report 205
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Albemarle-Pamlico National Estuary Program
Sediment Quality Index -
Albemarle-Pamlico Estuarine Complex
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
OFair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Site Criteria: Southeast Coast
Benthic Index Score
• Good = > 2.5
OFair =2.0-2.5
• Poor = < 2.0
O Missing
Figure 4-15. Sediment quality index data for the Albemarle-
Pamlico Estuarine Complex, 2000-2001 (U.S. EPA/NCA).
Benthic Index
As measured by the Southeast Coast Benthic Index,
benthic condition for the Albemarle-Pamlico Estuarine
Complex is rated fair. Sixty-five percent of the estuarine
area was rated good for benthic condition, 16% of the
area was rated fair, and 16% of the area was rated poor
(Figure 4-16), with sites rated poor located in portions
of the Neuse River and Albemarle Sound.
Although only 16% of the estuarine area exhibited
degraded benthic condition, 92% of the sampling sites
representing this degraded area were also associated with
some measure of adverse water quality or sediment
quality (Figure 4-17). Poor benthic condition co-
occurred most frequently with degraded sediment
quality (75% of sites with poor benthic condition).
Figure 4-16. Benthic index data for the Albemarle-Pamlico
Estuarine Complex, 2000-2001 (U.S. EPA/NCA).
Water
Quality Only
17%
Sediment
Quality Only
25%
Sediment and
Water Quality
50%
Figure 4-17. Percent of sampling sites in the Albemarle-Pamlico
Estuarine Complex where poor benthic condition overlaps with
other indices rated poor (U.S. EPA/NCA).
206 National Estuary Program Coastal Condition Report
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Albemarle-Pamlico Notional Estuary Program
Fish Tissue Contaminants Index
The fish tissue contaminants index for the
Albemarle-Pamlico Estuarine Complex is rated good to
fair. Figure 4-18 shows that 10% of stations sampled
where fish were caught exceeded risk-based EPA
Advisory Guidance values using whole-fish contaminant
concentrations and were rated poor, 20% of the stations
were rated fair, and 70% of the stations were rated
good. The only contaminants measured with elevated
concentrations in fish tissues were total PAHs and total
PCBs.
Humans can be exposed to toxic chemicals by eating contami-
nated fish (johnTheilgard).
Fish Tissue Contaminants Index -
Albemarle-Pamlico Estuarine Complex
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
O Fair = Falls within Guidance range
• Poor = Exceeds Guidance range
Figure 4-18. Fish tissue contaminants index data for the
Albemarle-Pamlico Estuarine Complex, 2000-2001
(U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 207
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Albemarle-Pamlico National Estuary Program
FerryMon A
UNC-CH / DUKE / NCDENR / NCDOT
The FerryMon Project
The Albemarle-Pamlico Estuarine Complex provides
critical foraging and nursery habitats for finfish and
shellfish populations along the mid-Adantic and south-
eastern coasts of the United States. Changes in water
quality, precipitated by rapidly changing land uses in
tributary watersheds and the increased frequency of
tropical storms, have emphasized the need for predictive
modeling to guide policy and management decisions
regarding ecosystem response to those stressors.
Compounding this need is a relative lack of monitoring
data despite the importance of the habitat.
To address this problem, the University of North
Carolina at Chapel Hill's Institute of Marine Sciences in
Morehead City, NC; Duke University's Marine Lab in
Beaufort, NC; and others joined ranks to found the
FerryMon project. The goals of the project are the
following:
• Determine ecosystem response to excess nutrient
inputs
• Quantify the relationships between the land-use
activities, hydrologic processes, and ecological
response of receiving waters
• Assess and predict ecosystem response and the
relationships between nutrient inputs, phyto-
plankton blooms, and associated water quality
changes
• Provide information critical to long-term water
quality management.
FerryMon, a ferry-based water quality monitoring
project, utilizes North Carolina Department of
Transportation (NCDOT) ferries that traverse the
Neuse River and Pamlico Sound on three routes
(see table below), following a regular schedule 365 days
a year. The ferries are fitted with automated water
quality monitoring equipment that measures tempera-
ture, conductivity, pH, dissolved oxygen, turbidity, and
chlorophyll fluorescence in surface water. Subsequent
measurement of nutrients, diagnostic algal pigments,
colored dissolved organic material, and suspended solids
is made possible by a refrigerated grab sampler, and
Information about the Ferry Routes in the FerryMon Project (FerryMon, 2006)
Ferry Route
Initiated
November 2000
February 2001
May 2001
Origination
Cherry Branch
Cedar Island
Swan Quarter
Destination
Minnesott Beach
Ocracoke Island
Ocracoke Island
Ferry Name
Floyd Lupton
Corteret
Silver Lake
Average Speed (knots)
8.0
10.7
10.4
Number of Crossings/Day
40
Number of Data Points/Day
300
200
200-300
208 National Estuary Program Coastal Condition Report
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Albemarle-Pamlico National Estuary Progran
logged data are downloaded at the laboratories via a
cellular telephone modem. Use of the ferries to monitor
water quality offers an economy of scale for the rapid
construction of databases not provided by conventional
monitoring platforms (Buzzelli et al., 2003).
Although the FerryMon project only monitors
surface waters along the route of each ferry, the project's
observing platform does have several advantages,
including the following:
• High spatial and temporal resolution
• Repetition in time and space
• Capturing of base, diel, tidal, synoptic, seasonal,
annual, and interannual scales
• Reliable data collection (i.e., data collection ceases
only when wind velocity is greater than 40 knots
or during times of dense fog)
• Professionally maintained, high-quality ferries
(U.S. Coast Guard-certified to carry passengers for
hire)
• Free use of ferries (i.e., low-cost analysis).
An initial return on the investment of retrofitting the
ferries has been the availability of an intensive temporal
and spatial water quality baseline data set for an area
holding the distinction of being the largest estuary in
the United States for which there is the least available
data. The availability of data from the FerryMon project
allows for rapid analysis of the Sound's status and
trends, thus supporting the wisest and most sustainable
use of the resource. Monitoring results and additional
information about the project are available at
http://www.ferrymon.org.
The Corteret collects water quality measurements along its route between Cedar Island and Ocracoke
Island (NCDOT).
National Estuary Program Coastal Condition Report 209
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Albemarle-Pamlico National Estuary Program
Albemarle-Pamlico National
Estuary Program Indicators of
Estuarine Condition
Although the APNEP does not currently have a set
of formalized indicators to determine estuarine condi-
tion, the APNEP STAC is expected to complete the
development of indicators in 2006. Currently, agencies
that work in partnership with the APNEP use a group
of informal indicator measures to evaluate environ-
mental conditions in the Complex. In addition, more
detailed information on environmental indicators is
collected and reported on a basin-wide level and by
individual subbasins in the Albemarle-Pamlico region.
Some stressors that have been evaluated to compare the
subbasins of the Albemarle-Pamlico Estuarine Complex
(in support of past EPA studies) include total non-point
source loadings (kg/yr) to each subbasin and the
numbers of fish consumption advisories, HAB occur-
rences, Superfund and hazardous waste sites, coastal
marinas per subbasin, and water quality exceedances.
The following section will describe some of the recent
trends and environmental measures studied on a
Complex-wide basis, as compiled by state partners
managing the Albemarle-Pamlico region for water and
sediment quality, fish and wildlife, and habitat condi-
tions.
Water Quality and Sediment Quality
Data on the water quality condition of the
Albemarle-Pamlico Estuarine Complex are collected by
a number of APNEP partners. The North Carolina
Department of Environment and Natural Resources'
(NCDENR's) Division of Water Quality (DWQ)
samples ambient stations for nutrients, dissolved
oxygen, pH, conductivity, temperature, metals,
turbidity, hardness, fecal coliform bacteria, and total
suspended solids. The North Carolina DWQ also
analyzes algal samples to document HABs and to inves-
tigate the causes offish kills (NCDENR, 2006). Water
quality data is also collected by the FerryMon project
(see Highlight article).
Although trends in nutrient concentrations in the
Complex appear to be very site-specific, the waters of
these estuaries are generally rich in phosphorus and rela-
tively nitrogen-limited (Harned and Davenport, 1990;
APNEP, 2006). Water quality measurements and trend
analysis conducted across the entire Albemarle-Pamlico
Estuarine Complex demonstrated some noticeable long-
term patterns between 1945 and 1988, including the
following:
• Increased dissolved oxygen levels (in general)
• Increased pH (in general)
• Decreased levels of suspended solids
• Increased chlorophyll a levels (Harned and
Davenport, 1990).
A major source of nutrient loading to the waters of
the Albemarle-Pamlico Estuarine Complex is runoff
from agricultural activities (Harned and Davenport,
1990). Enhanced runoff of nutrients in the spring
season has been a major contributor to nuisance HABs
during the summer months. Atmospheric deposition
accounts for an average of 27% of total nitrogen inputs
and 22% of total phosphorus inputs to the drainage
basin of the Albemarle-Pamlico Estuarine Complex
(McMahon and Woodside, 1997). Major hurricanes in
1999 (Floyd) and 2003 (Isabel) had a significant impact
on the water quality and growth of phytoplankton in
the Complex, with salinity levels in these lagoonal
estuaries decreasing dramatically after these storm
events. Chlorophyll a levels typically increased substan-
tially after the storm events, but eventually returned to
pre-storm levels (Peierls et al., 2003).
Habitat Quality
The measures that have been used in past studies to
measure habitat quality across the subbasins of the
Albemarle-Pamlico Estuarine Complex include acreages
of wetlands, SAV, nursery areas, and shellfish-harvesting
areas. An estimated 25% to 50% of the wetlands lining
the tributaries or inland areas have been lost to develop-
ment, dredging, draining, or filling of rnarsh habitat
(NCDENR, 2003). Losses and gains for the major
basins of the Albemarle-Pamlico Estuarine Complex
during 2002 and 2003 are presented in Table 4-1.
The extent and health of SAV in the Albemarle-
Pamlico Estuarine Complex is a function of several
variables, including depth, salinity, sediment texture,
concentration of suspended sediments, epiphyte
encrustation, weather, climate, and nutrient availability.
Most of these potential stresses are natural, but some are
exacerbated by human activities. Eighty percent of SAV
210 National Estuary Program Coastal Condition Report
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Albemarle-Pamlico National Estuary Program
coverage in the estuarine area is located in southern
and eastern Pamlico Sound. Eelgrass, shoalgrass, and
widgeongrass dominate these environments, and such
a mixture of species is unique to North Carolina.
Preliminary analyses suggest that the estimated area of
marine SAV in the Complex's estuarine area is approxi-
mately 200,000 acres (APNEP, 2006).
Table 4-1. Change in the Extent of Wetland Habitat
in the Major Subbasins of the Albemarle-Pamlico
Estuarine Complex, 2002-2003 (NCDENR, 2003)
Subbasin
Overall Change (%)
Pasquotank
(loss)
Chowan
0.8 (loss)
Roanoke
1.9 (loss)
Tar-Pamlico
(loss)
Neuse
25 gain
White Oak
(eastern portion only)
6.2 gain
Living Resources
Fish and wildlife living in the Albemarle-Pamilico
Estuarine Complex help serve as continuous monitors
of environmental quality and increase the likelihood of
detecting spills, non-point sources, or other highly vari-
able impacts that are often missed by chemical-sampling
water quality processes. The NCDENR pays particular
attention to monitoring the more important commer-
cial species of finfish and shellfish across the subbasins
of the Albemarle-Pamlico Estuarine Complex to esti-
mate the population structures and commercial value of
these species. The blue crab population is monitored to
help evaluate the effects of environmental stressors in
different areas of the Albemarle-Pamlico region. Of the
natural stressors examined, low dissolved oxygen and
elevated water temperatures have correlated well with
lowered concentrations of hemocyanin in blue crabs.
Hemocyanin is a substance found in crab blood, and
low concentrations are correlated with the crabs'
increased susceptibility to parasitic infections and
reproductive problems (APNEP, 2006).
Current Projects,
Accomplishments, and Future
Goals
The APNEP continues to work toward fulfilling the
goals of its CCMP and has already seen some major
accomplishments, including the following:
• Restoration of more than 1,100 miles of anadromous
fish habitat through the removal of three dams
• Enhancement of interagency and interstate coordina-
tion through creation of the APNEP
• Organizational restructuring to promote region-wide
interstate citizen involvement through collaboration
and coordination
• Development of bycatch reduction gear (e.g., sea
turtle exclusion devices) and practices to reduce
fisheries impacts
• Restoration of two miles of riparian habitat along the
Roanoke River through livestock fencing and river-
bank-stabilization practices (APNEP, 2006).
Conclusion
Based on data collected by the NCA, die overall
condition of the Albemarle-Pamlico Estuarine Complex
is rated good to fair. Data collected by NCA and the
APNEP partners indicate that the Complex is in good
condition with respect to most indicators of estuarine
health; however, factors such as chlorophyll a, dissolved
oxygen, and sediment quality may signal declining
health, especially in some tributary river areas.
National Estuary Program Coastal Condition Report 211
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Indian River Lagoon National Estuary Program
Indian River Lagoon National Estuary Program
New Smyrna Beach
Mosquito Lagoon
Banana River
Indian River
--^
Titusville
INDIAN
RIVER
LAGOON
Cape Canaveral
Cocoa Beach
PROGRAM^
.\Vero Beach
Pierce
NEP Study Area
www.sjrwmd.com/programs/outreach/irlnep
Background
Located along Florida's east coast and stretching
156 miles from Volusia County to Palm Beach County,
FL, the Indian River Lagoon is one of the most diverse
estuaries in North America and one of Florida's most
popular fishing destinations, with more than 1 million
anglers visiting the Lagoon area each year (U.S. EPA,
2000c). The Lagoon and its surrounding watershed
include a wide variety of habitats that support a diverse
assemblage of plants and animals (SJRWMD, 2004).
These habitats range from xeric scrub through pine
I Jupiter Inlet
flatwoods, tropical and temperate hardwood hammocks,
salt marshes, mangrove swamps, and other intertidal
communities to seagrass meadows and other SAV
communities (Hill, 2002).
This region's broad diversity of habitats support more
than 4,300 different species, including 700 saltwater
and freshwater fish species and 310 bird species
(SJRWMD, 2004). Thirty-six of the species found in
this region are classified as threatened or endangered,
including the Southeastern beach mouse, Atlantic salt-
marsh snake, bald eagle, and Florida scrub jay
212 National Estuary Program Coastal Condition Report
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Indian River Lagoon National Estuary Program
(SJRWMD, 2004; U.S. EPA, 2006d). In addition, an
estimated one-third of Florida's endangered West Indian
manatees live in the Indian River Lagoon. Commercially,
the estuary is one of the most important waterways in
Florida and is a productive nursery ground for an esti-
mated $300 million in annual commercial fishing
revenues, including $100 million from inshore species.
The Indian River Lagoon accounts for 50% of Florida's
total East Coast fisheries landings (SJRWMD, 1994). In
addition, tourism and recreation contribute $540
million to the local economy, and the influx of tourists
and part-time residents to the area is considerable
(SJRWMD, 2002).
In 1987, the Florida Legislature passed the Surface
Water Improvement and Management (SWIM) Act,
which designated the Indian River Lagoon as a priority
waterbody in need of restoration and special protection
(Florida Statutes, Chapter 373.451-373.4595). Created
in 1990, the Indian River Lagoon NEP (IRLNEP)
fosters active participation by other federal agencies,
notably the FWS, NASA, and USAGE. It also manages
a local government cost-share program that assists coun-
ties and municipalities with planning and implementing
pollution-abatement projects, typically small-scale
efforts with an emphasis on stormwater treatment. For
instance, both the St. John's River Water Management
District (SJRWMD) and South Florida Water Manage-
ment District (SFWMD) focus on projects designed to
improve water and sediment quality, restore or enhance
the seagrass community in the Lagoon, or rehabilitate
wetlands, recovering many of the natural functions of
these areas.
Environmental Concerns
The primary environmental concerns for the Indian
River Lagoon include the loss or alteration of habitat,
the impact of alterations to the area's hydrology, and the
discharge of pollutant-laden wastewater and stormwater
into the Lagoon. Approximately 75% of the Lagoon's
salt marshes and mangrove wetlands have been lost or
altered. In addition, the conversion of native uplands
and wetlands to urban and agricultural land uses has
negatively affected the rate, timing, volume, and quality
of water flow to the St. Lucie River and the Indian
River Lagoon, resulting in excessive discharges of fresh
water that have degraded shellfish habitat, closed
shellfish-harvesting areas, reduced water clarity,
promoted algae growth, and contributed to the destruc-
tion of seagrass beds and other valuable habitats.
Estuarine hydrology and salinity are also affected by
releases from Lake Okeechobee and other drainage
systems. Metals, pesticides, and herbicides present in
surface runoff and water from the canal system bioaccu-
mulate in the food chain and have been associated with
an increased incidence of fish abnormalities, decreases in
the health of fisheries, and impacts on the resident
bottlenose dolphin population (Sime, 2002; SJRWMD,
2006).
Population Pressures
The population of the 6 NOAA-designated coastal
counties (Brevard, Indian River, Martin, Okeechobee,
St. Lucie, and Volusia) coincident with the IRLNEP
study area increased by more than 327% during a
40-year period, from 0.3 million people in 1960 to
almost 1.4 million people in 2000 (Figure 4-19) (U.S.
Census Bureau, 1991; 2001). This rate of population
growth for the IRLNEP study area is almost four times
the rate of 71.1% calculated for the Albemarle-Pamlico
Estuarine Complex and more than twice the rate of
131.4% calculated for all NEP-coincident coastal
counties of the Southeast Coast region. In 2000, the
population density of these 6 coastal counties was 308
persons/mi2, almost double the density of 168
persons/mi2 for the collective NEP-coincident coastal
counties of the Southeast Coast region (U.S. Census
Bureau, 2001). Population pressures for the IRLNEP
area are likely higher due to the extensive development
of the area associated with the Kennedy Space Center at
Cape Canaveral and from the residential development
that has occurred in these counties. Despite the area's
high population growth, a good portion of the land
surrounding the IRLNEP study area is associated with
state and federal lands that have been designated for
protection as national seashore, wildlife areas, or forests.
National Estuary Program Coastal Condition Report 213
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Indian River Lagoon National Estuary Program
0.0
I960
2000
Figure 4-19. Population of NOAA-designated coastal counties
of the IRLNEP study area, 1960-2000 (U.S. Census Bureau, 1991;
2001).
NCA Indices of Estuarine
Condition—Indian River Lagoon
The overall condition of the Indian River Lagoon is
rated good based on three of four indices of estuarine
condition used by the NCA (Figure 4-20). The water
quality, sediment quality, and benthic indices were each
rated good for the Indian River Lagoon, and data were
unavailable to calculate a fish tissue contaminants index
for this estuary. Figure 4-21 provides a summary of the
percentage of estuarine area rated good, fair, poor, or
missing for each parameter considered. This assessment
is based on data from 45 NCA sites sampled by EMAP
in the IRLNEP estuarine area in 2001 and 2002. Due
to the rotating basin schedule in Florida, the NCA only
sampled the northern portion of the Lagoon (approxi-
mately 230 mi") in 2001 and 2002; the remainder of
the estuarine area was sampled in 2003, but these data
are not yet available. Please refer to Tables 1-24, 1-25,
and 1-26 (Chapter 1) for a summary of the criteria used
to develop the rating for each index and component
indicator.
Overall Condition
Indian River Lagoon
(5.0)
Water Quality Index (5)
Sediment Quality Index (5)
Benthic Index (5)
Fish Tissue Contaminants
Index (missing)
Figure 4-20. The
overall condition of
the IRLNEP estuarine
area is good (U.S.
EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80
Percent NEP Estuarine Area
100
Missing
Figure 4-21. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Indian River
Lagoon (U.S. EPA/NCA).
214 National Estuary Program Coastal Condition Report
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CHAPTER 4 : SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Indian River Lagoon National Estuary Program
Water Quality Index
The water quality index for the northern portion of
the Indian River Lagoon is rated good (Figure 4-22).
This index was developed using NCA data on five
component indicators: DIN, DIP, chlorophyll a, water
clarity, and dissolved oxygen. Only 3% of the Lagoon's
estuarine area was rated poor for water quality, and 36%
of the area was rated fair.
Dissolved Nitrogen and Phosphorus I The
Indian River Lagoon is rated good for nutrient concen-
trations, with 100% and 93% of the estuarine area
rated good for DIN and DIP concentrations, respec-
tively. Only 7% of the Lagoon's estuarine area was rated
fair for DIP concentrations.
Chlorophyll a \ Concentrations of chlorophyll a
in the northern portion of the Indian River Lagoon
are problematic, and the Lagoon is rated fair for this
component indicator. Overall, the Lagoon received a
fair rating because 11 % of the estuarine area was rated
poor for chlorophyll a concentrations, and the
combined value for fair and poor ratings was 93%.
Only 7% of the IRLNEP estuarine area was rated good
for chlorophyll a concentrations.
Witter Clarity I Despite the fair rating for chloro-
phyll a concentrations, the Indian River Lagoon is rated
good for water clarity. Water clarity was rated poor at a
sampling site if light penetration at 1 meter was less
than 20% of surface illumination. None of the estuarine
area of the Indian River Lagoon was rated poor for
water clarity, 4% of the area was rated fair, and 91% of
the area was rated good.
Dissolved Oxygen ! The Indian River Lagoon is
rated fair for dissolved oxygen concentrations. Although
68% of the estuarine area was rated good for this
component indicator, 5% of the area was rated poor,
and 27% of the area was rated fair.
Water Quality Index - Indian River Lagoon
Poor
3%
I
Site Criteria: Number of component
indicators in poor or fair condition
• Good = No more than I is fair
OFair = I is poor, or 2 or
more are fair
• Poor — 2 or more are poor
O Missing
Figure 4-22. Water quality index data for the Indian River
Lagoon, 2001-2002 (U.S. EPA/NCA).
•'V'.*
National Estuary Program Coastal Condition Report 215
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Indian River Lagoon National Estuary Program
Sediment Quality Index
The sediment quality index for the Indian River
Lagoon is rated good; however, this rating is based only
on NCA data for one component indicator (sediment
TOG). Data on sediment toxicity and sediment conta-
minant concentrations were not assessed in the
2001-2002 NCA surveys. All of the IRLNEP estuarine
area (100%) was rated good for the sediment quality
index (Figure 4-23).
Sediment Toxicity The NCA surveys did not
collect sediment toxicity data for the Indian River
Lagoon in 2000 and 2001; therefore, sediment toxicity
in the Lagoon has not been rated for this report.
Sediment Quality Index - Indian River Lagoon
Good
100%
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
OFair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Figure 4-23. Sediment quality index data for the Indian River
Lagoon, 2001-2002 (U.S. EPA/NCA).
Sediment Contaminants \ The NCA surveys did
not collect sediment contaminants data for the Indian
River Lagoon in 2000 and 2001; therefore, sediment
contaminant concentrations in the Lagoon have not
been rated for this report.
Total Organic Carbon I The Indian River
Lagoon is rated good for TOC concentrations, with
only 12% of the estuarine area rated fair and the
remaining 88% rated good for this component indi-
cator.
Benthic Index
Based on the Southeast Coast Benthic Index, the
benthic condition of the Indian River Lagoon is rated
good. The benthic index shows that 6% of the estuarine
area was rated poor, 20% of the area was rated fair, and
74% of the area was rated good (Figure 4-24).
Although only 6% of the estuarine area exhibited
degraded benthic condition, 33% of the sampling sites
representing this degraded area were associated with
some measure of adverse water quality (Figure 4-25).
There were no areas of degraded benthic condition asso-
ciated with poor TOC concentrations; however, no
sediments were analyzed for sediment toxicity or sedi-
ment contaminant concentrations, so the co-occurrence
of degraded benthic condition with either of these
component indicators could not be evaluated.
The roseate spoonbill feeds on shrimp, small fish, and aquatic
insects (Ryan Hagerty FWS).
216 National Estuary Program Coastal Condition Report
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CHAPTER 4 i SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Indian River Lagoon National Estuary Program
Benthic Index - Indian River Lagoon
Poor
6%
Fair
20%
Site Criteria: Southeast Coast
Benthic Index Score
• Good = > 2.5
OFair =2.0-2.5
• Poor = < 2.0
O Missing
Figure 4-24. Benthic index data for the Indian River Lagoon,
2001-2002 (U.S. EPA/NCA).
Fish Tissue Contaminants Index
The NCA survey did not assess the level of fish tissue
contaminants in the northern portion of the IRLNEP
study area during 2001 or 2002; therefore, a fish tissue
contaminants index for the Indian River Lagoon was
not developed for this report.
None
67%
Water Quality
Only
33%
I
Figure 4-25. Percent of sampling sites in the Indian River
Lagoon where poor benthic condition overlaps with other indices
rated poor (U.S. EPA/NCA).
Hands-on educational activities help children learn about the Indian River Lagoon estuary
(Ed Garland).
National Estuary Program Coastal Condition Report 217
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Indian River Lagoon National Estuary Program
Seagrass Monitoring in
the Indian River Lagoon
The primary habitat of concern within the Indian
River Lagoon is the Lagoon's seagrass community.
Seagrass beds are valuable because they provide habitat
and nursery areas for estuarine animals, enhance water
quality by removing nutrients and stabilizing sediments,
and serve as one of the planet s most productive ecosys-
tems (Dawes, 1981; Zieman, 1982; Lewis, 1984;
Virnstein et al., 1987). The seagrass community is sensi-
tive to water quality conditions, particularly those para-
meters that afreet water clarity, such as turbidity,
suspended matter, color, and chlorophyll a concentra-
tions (a surrogate for phytoplankton). As a result, the
seagrass community in the Indian River Lagoon is an
effective indicator of water quality (IRLNEP, 1996;
Steward et al., 2003).
The IRLNEP, through the program's sponsor, the
SJRWMD, has developed a monitoring program to
assess the state of the Lagoon's seagrass community. This
monitoring program has two major components:
Lagoon-wide mapping and a series of fixed transects at
selected sites throughout the Lagoon.
Lagoon-wide seagrass mapping provides an overall
picture of seagrass resources throughout the Indian
River Lagoon. Lagoon-wide maps are produced every
two to three years, with the production process
involving several steps, including aerial photography,
ground-truthing, photo-interpretation and delineation
of polygons containing seagrass beds, registration of
these polygons to a base map, digitization of these
polygons into GIS, and production of seagrass maps
(Dobson et al., 1995). Appropriate management
measures are developed and implemented to address
problems or to provide protection for specific areas, and
both problem and healthy areas are designated based
primarily on the abundance of seagrass. Comparisons of
these maps with historic maps can be used to detect
changes in seagrass coverage, set targets for seagrass
restoration, and document seagrass recovery (Virnstein
and Morris, 1996).
Although these seagrass maps are produced every
two to three years, aerial photos are taken each year to
document any changes that occur during the period
between map development. Photos are taken at USGS
Quadrangle map scale (1:24K; 1 inch = 2,000 feet),
generally during the spring, when water clarity condi-
tions are best for photography (Virnstein and Morris,
1996). These maps have several limitations, including
(1) the interval between mapping events; (2) that
smaller seagrass beds (< 1/4 acre) are not mapped;
(3) that certain seagrass species (such as Halophila) or
areas of sparse seagrass are often not visible in aerial
photographs and are not usually mapped; and (4) that
locating the edge of a bed may have errors up to
100 feet (Virnstein and Morris, 1996).
Fixed-seagrass transects are used to determine
whether local areas are healthy or stressed; whether
conditions are stable, improving, or declining; and the
amount of change in the health or extent of seagrass
beds. Sampling fixed transects allows researchers the
ability to reliably detect small-scale changes in depth
distribution, abundance, and species composition over
time (Morris et al., 2001).
Presently, more than 80 seagrass transects have been
established in the Indian River Lagoon. These transects
are monitored twice each year—in the summer and
winter—on dates that roughly correspond to times of
maximum and minimum seagrass abundance. Measure-
ments are made every 33 feet along each transect and
include data on the depth, percent cover of seagrass,
and canopy height of each seagrass species present.
Shoot counts are made at the center and deep edges of
seagrass beds. In addition, researchers estimate percent
cover and biomass of drift algae present, measure light
attenuation at the deep edge of the seagrass bed, and
218 National Estuary Program Coastal Condition Report
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Indian River Lagoon National Estuary Program
take an underwater video as an archival record of condi-
tions at the time of sampling (Morris et al., 2001)
Data collected through transect monitoring can be
analyzed at several geographic and temporal scales.
Three geographic scales (e.g., Lagoon-wide, by segment,
and site-specific) and two temporal scales (e.g., annual
and seasonal) can be used to present and analyze the
data (Morris et al., 2001).
The use of large-scale mapping coupled with fixed
transects is an effective method of evaluating the health
of the seagrass community in the Indian River Lagoon.
Lagoon-wide maps provide information about patterns
and trends from a "big picture" perspective, whereas
individual transects provide similar information on a
localized basis. This information is valuable when devel-
oping or evaluating the effectiveness of management
strategies.
Seagrass monitoring in the Indian River Lagoon, Florida (SJRWMD).
National Estuary Program Coastal Condition Report 219
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Indian River Lagoon National Estuary Program
Indian River Lagoon National
Estuary Program Indicators of
Estuarine Condition
Water and Sediment Quality
Indicators of water quality for the IRLNEP include
the following:
• Chlorophyll a levels (ug/L)
• Reduction of muck accumulation
(extent and volume removed).
In recent years, algal blooms in the Indian River
Lagoon have been a concern. Several of these blooms
have included HAB species, which are considered
potentially harmful to human health or natural
resources. In order to track the occurrence of HABs,
chlorophyll a levels are monitored by the IRLNEP as
one of the key indicators of water quality. Increased
nutrient concentrations are reflected in elevated chloro-
phyll a concentrations found in the southern Banana
River and the Cocoa-Melbourne/Palm Bay area, where
the 10-year chlorophyll a average concentration is
greater than 8 ug/L. Although nutrient concentrations
are also elevated, chlorophyll a levels are lower in the
Vero Beach area, most likely due to increased flushing
through nearby ocean inlets. A similar reduced algal
response to elevated nutrient concentrations is seen in
the Fort Pierce and St. Lucie River areas, where shorter
residence times and increased flushing may also play a
role (Steward et al., 2003). Overall, it appears that the
fair rating assigned by the analysis of NCA data for the
northern portion of the Indian River Lagoon agrees
with the IRLNEP monitoring data for chlorophyll
-------
CHAPTER 4 ' SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Indian River Lagoon National Estuary Program
largest area of poor seagrass coverage extends from the
Cocoa area to the Melbourne/Palm Bay area. This area
has experienced the greatest loss (70%) of seagrass
coverage since the early 1940s. Across the entire
Lagoon, potential seagrass coverage is approximately
118,000 acres. In 1999, seagrass coverage was approxi-
mately 59% of the Lagoon's total potential seagrass
acreage (Steward et al., 2003).
Living Resources
Although stormwater management and enhancing
seagrass production remain the highest priorities, the
IRLNEP has identified invasive, exotic species and
aquatic animal health as emerging challenges to the
Lagoon's ecosystem. During the past several years, there
has been increasing concern over the number of
wildlife-related disease and mortality events in the
Lagoon, possibly a symptom of a wider-scale problem
regarding the overall health of the estuarine system.
Despite considerable progress and success in rehabili-
tating impounded wetlands as habitat and improving
water quality conditions in the Lagoon during the past
two decades, a number of fairly recent, possibly inter-
connected wildlife-related mysteries remain unsolved.
They include the skin disease Lobomycosis, which is
occurring on much of the Lagoon's resident dolphin
population; fibropapillomas lesions on many of the
green turtles found in the Lagoon; an increased inci-
dence of tumors in hard clams; decreases in the popula-
tion of horseshoe crabs; the recent appearance of saxi-
toxin in puffer fish in the northern Lagoon, resulting in
a ban on catching puffers throughout the Lagoon and
health advisories regarding human consumption of
these fish; the sporadic occurrence of "spicy" tasting
clams; and the appearance of invasive species, such as
the Australian spotted jellyfish (Phyllorhiza punctata) in
the central Lagoon and the exotic macroalgae Caulerpa
bmchypus in the southern portion of the estuary
(SJRWMD, 2004).
To address these problems, the IRLNEP is taking the
lead in forming an Indian River Lagoon Task Force.
The goal of this task force will be to integrate moni-
toring and research results to determine if a common-
ality of cause exists and to prevent or reduce future
occurrences. Key stakeholders in supporting CCMP
implementation have continued to respond to the
IRLNEP's priority challenges of reducing stormwater
discharges to the Lagoon and enhancing valuable
wildlife habitat through invasive plant control, endan-
gered lands acquisition, and reconnection of
impounded wetlands to the estuary (SJRWMD, 2004).
The Indian River Lagoon has a resident dolphin population (Commander GradyTuell, NOAA Corps).
National Estuary Program Coastal Condition Report 221
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CHAPTER 4 SOUTHEAST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Indian River Lagoon National Estuary Progran
Current Projects,
Accomplishments, and Future
Goals
The greatest tangible improvement to date in the
Indian River Lagoon is the hydrologic reconnection of
more than 23,000 acres of impounded wetlands since
1989 under the SWIM Act (in addition to nearly
5,000 acres reconnected through other programs).
These impoundment reconnections restore many
natural functions provided by salt marshes and
mangrove wetlands (Steward et al., 2003).
There is also a noticeable increase in public aware-
ness of the Lagoon's problems and its ecology, as well as
an understanding of the projects that are underway to
benefit the Lagoon's recovery and management. Much
has been accomplished, but the IRLNEP recognizes
that more work remains to be done to reach restoration
targets established for seagrass and coastal wetlands.
Preventative safeguards, vigilance, and education are
needed to ensure that achievements in addressing prob-
lems in the Indian River Lagoon are maintained and
that progress continues in protecting and restoring the
water quality and natural resources of the Lagoon
(Steward et al., 2003).
There is also good progress taking place within the
Indian River Lagoon watershed. More than 56,000
acres of wetlands and uplands have been acquired for
various purposes (such as water quality remediation
projects and habitat preservation). The various agencies
and local governments with jurisdiction over the Indian
River Lagoon basin have made good progress in ending
discharges of treated wastewater, removing harmful
muck deposits, and making incremental improvements
in stormwater management throughout the basin. In
recent years, the IRLNEP has tackled some of the most
important and controversial issues to address pollution
in the Indian River Lagoon basin, such as addressing
the impact of septic tanks on water quality, promoting
the acquisition of environmentally sensitive lands,
promoting the development of regional stormwater
management plans, and participating in the develop-
ment of local management plans for threatened and
endangered species.
Some of the ongoing goals of the IRLNEP include:
• Attaining and maintaining water and sediment
of sufficient quality to support a healthy, macro-
phyte-based estuarine Lagoon ecosystem
• Attaining and maintaining a functioning macro-
phyte-based ecosystem that supports endangered
and threatened species, fisheries, and wildlife
• Improving the understanding and management
of impacts of invasive and exotic species and the
emerging challenges to aquatic animal health
• Achieving heightened public awareness and coor-
dinated interagency management of the Indian
River Lagoon ecosystem (Steward et al., 2003).
Conclusion
Based on data collected by the NCA, the overall
condition of the Indian River Lagoon is rated good. In
general, the IRLNEP considers seagrass coverage in the
Indian River Lagoon to be a key indicator of trends in
environmental condition. Areas with good seagrass
coverage are located adjacent to fairly undeveloped
watersheds or close to inlets, whereas areas of extensive
SAV loss and sparse seagrass are adjacent to highly
developed watersheds or shoreline areas. The areas with
poorest water quality are Cocoa to Melbourne/Palm
Bay, the southern Banana River, and the Vero Beach,
Fort Pierce, and St. Lucie River areas. Areas of the
Indian River Lagoon adjacent to larger tributaries and
major drainages systems experience elevated levels of
nutrients and total suspended solids.
222 National Estuary Program Coastal Condition Report
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CHAPTER 5
GULF COAST NATIONAL ESTUARY PROGRAM
COASTAL CONDITION
-------
CHAPTER 5
GULF COAST NATIONAL ESTUARY PROGRAM
COASTAL CONDITION
Background
The Gulf Coast region extends from the lush tropical
southern tip of Florida, including the Florida Keys,
westward to the saline lagoons of South Texas at the
Mexican border. The Gulf of Mexico receives runoff
from almost two-thirds of the continental United States,
primarily funneled through the Mississippi River
drainage basin (NOAA, 1985). Within the Gulf Coast
region, there are seven NEP estuaries—Charlotte
Harbor, Sarasota Bay, Tampa Bay, Mobile Bay, the
Barataria-Terrebonne Estuarine Complex, Galveston
Bay, and the Coastal Bend Bays (Figure 5-1).
The entire Gulf Coast region is characterized by flat
coastal plains and high levels of sediment deposition.
Some of the estuaries in this region have large deltas at
their river mouths (e.g., Mobile-Tensaw River Delta in
Mobile Bay), where suspended sediment carried by
runoff is deposited in shallow coastal waters. In other
areas, sediment deposited by ocean currents has formed
offshore sand bars that enclose shallow saline lagoons
known as bar-built estuaries (e.g., Laguna Madre of the
Coastal Bend Bays), which are most common along the
Texas coast. The inlets to these estuaries are often
narrow, and the exchange of water with the ocean is
highly restricted; as a result, the circulation patterns in
these waterbodies are driven primarily by wind (NOAA,
1985). In general, the shallow coastal plain estuaries
characteristic of the Gulf Coast region receive little tidal
influence, and tidal range in the region is small, with a
minimum of 1 foot in Louisiana and Texas and a
maximum of 3.6 feet in Florida (NOAA, 1985).
Hurricanes and their accompanying heavy rains, an
ever-present risk during the June-to-late-November
hurricane season, have a dramatic effect on the Gulf
Coast NEP estuaries by increasing freshwater inflow
from storm precipitation and saltwater intrusion from
wind-driven storm surge. Annual rainfaJl averages 48
inches in western Florida; increases to 56 inches in
Alabama, Mississippi, and Louisiana; and then dramati-
cally decreases to 24 inches in south Texas (NOAA,
1985).
The Gulf Coast NEP estuaries provide critical
feeding, spawning, and nursery habitats for a rich
assemblage of fish, wildlife, and plant species, including
endangered species such as sea turtles, the Gulf
I. Charlotte Harbor
1. Sarasota Bay
3. Tampa Bay
4. Mobile Bay
5. Barataria-Terrebonne Estuarine Complex
6. Galveston Bay
7. Coastal Bend Bays
Figure 5-1. The Gulf Coast region is home to seven NEP estuaries.
224 National Estuary Program Coastal Condition Report
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CHAPTER 5 i GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
sturgeon, the Perdido Key beach mouse, the manatee,
the white-topped pitcher plant, and the red-cockaded
woodpecker. These estuaries also support SAV commu-
nities that stabilize shorelines from erosion, reduce
non-point source loadings, improve water clarity, and
provide wildlife habitat. Increasingly, the varied estu-
arine habitats found along the Gulf Coast region are
under pressure from human development.
Population Pressures
The population of the 48 NOAA-designated coastal
counties coincident with the study areas of the Gulf
Coast NEP estuaries increased by more than 133%
during a 40-year period, from 4.9 million people in
1960 to 11.3 million people in 2000 (Figure 5-2) (U.S.
Census Bureau, 1991; 2001). Population density for
these coastal counties was 287 persons/mi2 in 2000;
however, the population densities of the individual NEP
study areas varied considerably, from a high of 651
persons/mi2 in Galveston Bay to 53 persons/mi2 in the
Coastal Bend Bays (U.S. Census Bureau, 2001).
Development and population pressures are especially
strong in these 48 Gulf Coast counties because the
coincident NEP study areas serve as centers of
commerce, contain substantial commercial and
recreational fisheries, and provide recreational areas for
coastal communities.
.o
'
a
£
I960
2000
Figure 5-2. Population of the 48 NOAA-designated coastal
counties of the Gulf Coast NEP study areas, 1960-2000
(U.S. Census Bureau, 1991; 2001).
The following sections of this report discuss two different
approaches for characterizing estuarine condition.
Approach I -The NCA provides unbiased, quality-
assured data that can be used to make consistent "snap-
shot" comparisons among the nation's estuaries.These
comparisons are expressed in terms of the percent of
estuarine area in good, fair, or poor condition.
Approach 2 - Each individual NEP collects site-specific
estuarine data in support of local problem-solving efforts.
These data are difficult to compare among NEPs, within
regions or nationally, because the sampling and evaluation
procedures used by the NEPs are often unique to their
individual estuaries. However, these assessments are
important because NEP-collected data can evaluate
spatial and temporal changes in estuarine condition on a
more in-depth scale than can be achieved by the NCA
snapshot approach.
Atmospheric deposition is often monitored in NEP study areas
because it can contribute to estuarine nitrogen loadings (Mobile
Bay NEP).
National Estuary Program Coastal Condition Report 225
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CHAPTHtS GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
NCA Indices of Estuarine
Condition—Gulf Coast Region
The overall condition of the collective NEP estuaries
of the Gulf Coast region is rated fair based on the four
indices of estuarine condition used by the NCA (Figure
5-3). The region's water quality index is rated fair, the
sediment quality and benthic indices are rated fair to
poor, and the fish tissue contaminants index is rated
good to fair. Figure 5-4 provides a summary of the
percentage of estuarine area rated good, fair, poor, or
missing for each parameter considered. This assessment
is based on data collected by the NCA and its state
partners from 221 sites sampled in the Gulf Coast
region's NEP estuaries in 2000, 2001, and 2002.
Samples were collected during the summer, the most
stressful period of the year, and neither environmental
stressors (e.g., nutrients, TOC) nor aquatic life commu-
nities showed any major evidence of degradation. Please
refer to Tables 1-24, 1-25, and 1-26 (Chapter 1) for a
summary of the criteria used to develop the rating for
each index and component indicator.
Overall Condition
Gulf Coast
NEP Estuaries
(2.75)
Water Quality Index (3)
Sediment Quality Index (2)
Benthic Index (2)
Fish Tissue Contaminants
Index (4)
Figure 5-3. The
overall condition of
the Gulf Coast region's
NEP estuarine areas is
fair (U.S. EPA/NCA).
The sampling conducted by EPA's NCA has been designed
to estimate the percent of estuarine area (nationally or
in a region or state) in varying conditions, which are
displayed as pie diagrams. Many of the figures in this
report illustrate environmental measurements made at
specific locations (colored dots on maps); however, these
dots (color) represent the value of the indicator specifi-
cally at the time of sampling. Additional sampling may be
required to define variability and confirm impairment or
the lack of impairment at specific locations.
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 10
Percent NEP Estuarine Area
I Missing
Figure 5-4. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Gulf Coast
region (U.S. EPA/NCA).
Gulf Coast NEP estuaries provide breeding and wintering habitat for
royal terns (Sterna maxima) (Mobile Bay NEP).
226 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Water Quality Index
Based on NCA results, the water quality index for
the collective NEP estuaries of the Gulf Coast region is
rated fair (Figure 5-5). This index was developed using
NCA data on five component indicators: DIN, DIP,
chlorophyll a, water clarity, and dissolved oxygen. The
NCA survey data indicates that 21% of the Gulf Coast
region's NEP estuarine area was rated good for water
quality, 65% of the area was rated fair, and 13% of the
area was rated poor. In NOAA's Estuarine
Eutrophication Survey (NOAA, 1997), the Gulf of
Mexico as a whole was ranked poor for eutrophic
condition, with an estimated 38% of the estuarine area
having a high expression of eutrophication.
Dissolved Nitrogen and Phosphorus I The Gulf
Coast region is rated good for DIN concentrations,
with 88% of the region's NEP estuarine area rated good
for this component indicator, 8% rated fair, and 3%
rated poor. Elevated DIN concentrations are not
expected to occur during the summer in Gulf Coast
waters because freshwater input is generally lower
and dissolved nutrients are more rapidly utilized by
phytoplankton during this season. The Gulf Coast
region is rated fair for DIP concentrations because 22%
of the NEP estuarine area was rated poor for this
component indicator.
Chlorophyll a I The Gulf Coast region is rated fair
for chlorophyll a concentrations. Although poor chloro-
phyll a conditions occurred rarely in this region (6% of
the NEP estuarine area), 60% of the area was rated fair
for this component indicator, and 31 % of die area was
rated good. NCA data on chlorophyll a concentrations
were unavailable for 3% of the Gulf Coast NEP estu-
arine area.
Water Clarity I Water clarity in the Gulf Coast
NEP estuarine area is rated poor. Thirty-one percent of
the Gulf Coast region's NEP estuarine area was rated
poor, 30% was rated good, and 36% was rated fair.
NCA data on water clarity were unavailable for 3% of
the Gulf Coast NEP estuarine area.
Dissolved Oxygen I The Gulf Coast region is rated
good for dissolved oxygen conditions in its NEP estu-
aries. The NCA results for these estuaries show that
only 2% of the estuarine area was rated poor for
dissolved oxygen concentrations, 23% of the estuarine
area was rated fair, and 75% of the area was rated good.
Water Quality Index - Gulf Coast
Site Criteria: Number of component
indicators in poor or fair condition
OGood = No more than I is fair
OFair = I is poor, or 2 or
more are fair
OPoor - 2 or more are poor
O Missing
Good 1% Poor
21% -—- '™
Figure 5-5. Water quality index data for the Gulf Coast NEP estuarine area, 2000-2002 (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 227
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Sediment Quality Index
The sediment quality index for the collective NEP
estuaries of the Gulf Coast region is rated fair to poor
because 18% of the region's NEP estuarine area was
rated either fair or poor for sediment quality (Figure 5-
6). This index was developed using NCA data on three
component indicators: sediment toxicity, sediment
contaminants, and sediment TOC.
Sediment Toxicity I Sediment toxicity in the Gulf
Coast region is rated good because only 1% of the
region's NEP estuarine area was rated poor for this
component indicator. It should be noted that data on
sediment toxicity were unavailable for 38% of the Gulf
Coast NEP estuarine area, including the region's three
Florida estuaries (Charlotte Harbor, Sarasota Bay, and
Tampa Bay).
Sediment Contaminants I The Gulf Coast region
is rated fair for sediment contaminant concentrations,
with 11 % of the region's NEP estuarine area rated poor
for this component indicator. It should be noted that
NCA data on sediment contaminant concentrations
were unavailable for 21 % of the Gulf Coast NEP estu-
arine area, including the region's three Florida estuaries
(Charlotte Harbor, Sarasota Bay, and Tampa Bay).
Total Organic Carbon I The Gulf Coast region is
rated good for sediment TOC. Eighty-nine percent of
the estuarine area was rated good for TOC concentra-
tions, and 2% of the area was rated poor.
Sediment Quality Index - Gulf Coast
Site Criteria: Number and condition of
component indicators
• Good — None are poor, and sediment
contaminants is good
OFair = None are poor, and sediment
contaminants is fair
• Poor =
O Missing
Figure 5-6. Sediment quality index data for the Gulf Coast NEP estuarine area, 2000-2002 (U.S. EPA/NCA).
228 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Benthic Index
The condition of benthic invertebrate communities
in the collective Gulf Coast NEP estuaries is rated fair
to poor. The composition of benthic invertebrate
communities reflects long-term exposure to sediment
quality in estuaries, and short-term changes in benthic
communities occur in response to hypoxic events and
disturbance. Indices of biotic integrity have been devel-
oped for aquatic systems to describe the condition of
biotic communities. Engle and Summers (1999) devel-
oped a Gulf Coast Benthic Index that integrates
measures of diversity and populations of indicator
species to distinguish between degraded and reference
benthic communities. Based on NCA survey data and
the Gulf Coast Benthic Index, 20% of the Gulf Coast
region's NEP estuarine area showed degraded benthic
resources (Figure 5-7).
Field trips can be used to teach students about Gulf Coast NEP
estuaries (CHNEP).
Benthic Index - Gulf Coast
Site Criteria: Gulf Coast
Benthic Index Score
• Good = > 5.0
OFair =3.0-5.0
• Poor =<3.0
O Missing
Figure 5-7. Benthic index data for the Gulf Coast NEP estuanne area, 2000-2002 (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 229
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
A great blue heron looking for its next meal (CBBEP).
Fish Tissue Contaminants Index
The fish tissue contaminants index for the Gulf
Coast NEP estuarine area is rated good to fair. It should
be noted that fish tissue contaminants were measured in
only four of the seven Gulf Coast NEP estuaries, and
NCA fish tissue data were not collected for the three
Florida estuaries (Charlotte Harbor, Sarasota Bay, and
Tampa Bay). Figure 5-8 shows that 12% of all stations
sampled where fish were caught exceeded the EPA
Advisory Guidance values used in this assessment and
were rated poor. The whole-fish contaminant concen-
trations measured in this survey can be higher or lower
than the concentrations associated with fillets only; only
those contaminants that have an affinity for muscle
tissue (e.g., mercury) are likely to have higher fillet
concentrations. Fillet contaminant concentrations for
most other contaminants will likely be lower; however,
for some populations that consume whole fish, these
risk calculations are appropriate.
Fish Tissue Contaminants Index - Gulf Coast
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
O Fair = Falls within Guidance range
• Poor = Exceeds Guidance range
Figure 5-8. Fish tissue contaminants index data for the Gulf Coast NEP estuarine area, 2000-2002 (U.S. EPA/'NCA).
230 National Estuary Program Coastal Condition Report
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CHAPTER 5 ! GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
NEP Estuaries and the Condition
of the Gulf Coast Region
The purpose of the NEP is to identify, restore, and
protect the nationally significant estuaries of the United
States. Most of the seven NEP estuaries located in the
Gulf Coast region need this extra protection, in part
because their size and societal significance have led to
intense human development; a diversity of uses,
including municipal drinking water sources, industrial
and agricultural production, and international
commerce and shipping; and the associated environ-
mental concerns throughout their watersheds. Does the
condition of the Gulf Coast NEP estuaries accurately
reflect the condition of all Gulf Coast estuaries (both
NEP and non-NEP)? Based on the NCA survey results,
the collective Gulf Coast NEP estuaries and all Gulf
Coast estuaries combined are both rated fair for overall
condition, with both groups receiving an overall condi-
tion score of 2.75 (Figure 5-9). Although the overall
condition scores for the two groups of estuaries are the
same, and both groups received similar ratings for the
NCA estuarine indices, a comparison of NCA data
reveals that the NEP estuaries had a greater percentage
of area rated poor for almost every index than the non-
NEP estuaries of the Gulf Coast region (Engle, 2004).
A comparison of NCA data for both groups of estu-
aries shows that the collective Gulf Coast NEP estuaries
are rated fair for the water quality index; fair to poor for
the sediment quality and benthic indices; and good to
fair for the fish tissue contaminants index. In contrast,
the group of all Gulf Coast estuaries combined are rated
fair for the water quality, sediment quality, and fish
tissue contaminants indices and fair to poor for the
benthic index. In addition, the two groups of estuaries
are rated comparably for most of the water quality and
sediment quality component indicators, with both
groups of estuaries rated good for DIN and dissolved
oxygen concentrations, sediment toxicity, and sediment
TOC and fair for DIP and sediment contaminant
Overall Condition
Water Quality Index
Phosphorus (DIP)
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue Contaminants
Index
Figure 5-9. Comparison of NCA results for Gulf Coast NEP estuaries and all Gulf Coast estuaries (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 231
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
concentrations. For the remaining two component indi-
cators, the collective Gulf Coast NEP estuaries are rated
fair for chlorophyll a concentrations and poor for water
clarity, whereas the Gulf Coast estuaries combined are
rated good and fair for these indicators, respectively.
With respect to the individual NEP estuaries, four of
the seven estuaries received higher overall condition
scores than the overall condition score for the collective
Gulf Coast NEP estuaries (2.75, rated fair). These four
estuaries are Charlotte Harbor (3.0), Sarasota Bay (3.0),
Tampa Bay (3.0), and Mobile Bay (3.0) which are all
rated fair. Galveston Bay (2.5, rated fair), the Barataria-
Terrebonne Estuarine Complex (2.5, rated fair), and the
Coastal Bend Bays (1.75, rated poor) received lower
overall condition scores than the score for the collective
Gulf Coast NEP estuaries.
A review of the NCA data for the water quality index
and component indicators shows that the ratings vary
between the individual Gulf Coast NEP estuaries. None
Kayaking is a popular pastime in Gulf Coast NEP estuaries
(CBBEP).
of the NEP estuaries are rated good for the water
quality index; Sarasota Bay, Mobile Bay, the Barataria-
Terrebonne Estuarine Complex, and the Coastal Bend
Bays are rated fair; Tampa Bay is rated fair to poor,
largely driven by poor water clarity and fair concentra-
tions of chlorophyll a and DIP; and Charlotte Harbor
and Galveston Bay are rated poor, primarily due to poor
DIP concentrations and poor water clarity ratings. All
Gulf Coast NEP estuaries are rated good for DIN
concentrations, except for Galveston Bay, which is rated
fair. The Barataria-Terrebonne Estuarine Complex is
rated good for DIP concentrations; Sarasota Bay, Tampa
Bay, Mobile Bay, and the Coastal Bend Bays are rated
fair; and Charlotte Harbor and Galveston Bay are rated
poor. All the Gulf Coast NEP estuaries are rated fair for
chlorophyll a concentrations, except for the Coastal
Bend Bays, which are rated good for this component
indicator. Although most Gulf Coast NEP estuaries
(Charlotte Harbor, Tampa Bay, the Barataria-Terre-
bonne Estuarine Complex, and Galveston Bay) are
rated poor for water clarity, Sarasota Bay and the
Coastal Bend Bays are rated fair for this component
indicator, and Mobile Bay is rated good. Four Gulf
Coast NEP estuaries (Tampa Bay, the Barataria-
Terrebonne Estuarine Complex, Galveston Bay, and the
Coastal Bend Bays) are rated good for dissolved oxygen
concentrations, but the three remaining NEP estuaries
(Charlotte Harbor, Sarasota Bay, and Mobile Bay) are
rated fair.
The sediment quality index scores for the individual
Gulf Coast NEP estuaries range from good to poor. For
the three Florida NEP estuaries (Charlotte Harbor,
Sarasota Bay, and Tampa Bay), the sediment quality
index is rated good; however, it should be noted that
NCA data on the sediment toxicity and sediment
contaminants component indicators were not collected
for these estuaries. For the remaining NEP estuaries,
sediment quality index ratings decrease from east to
west, with Mobile Bay and the Barataria-Terrebonne
Estuarine Complex rated fair for sediment quality;
Galveston Bay rated fair to poor; and the Coastal Bend
Bays rated poor. Sediment toxicity is rated good for the
Barataria-Terrebonne Estuarine Complex, Galveston
Bay, and the Coastal Bend Bays and poor for Mobile
Bay. Sediment contaminant concentrations are rated
good for Mobile Bay and the Barataria-Terrebonne
232 National Estuary Program Coastal Condition Report
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I
CHAPTER 5 i GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Estuarine Complex, fair for Galveston Bay, and poor for
the Coastal Bend Bays. Sediment TOC content is rated
good for all Gulf Coast NEP estuaries, both collectively
and individually, as well as for all Gulf Coast estuaries
combined.
The benthic index scores for the individual NEP
estuaries range from poor to fair. The benthic index is
rated fair for Charlotte Harbor, the Barataria-
Terrebonne Estuarine Complex, and Galveston Bay; fair
to poor for the Coastal Bend Bays; and poor for
Sarasota Bay, Tampa Bay, and Mobile Bay. The fish
tissue contaminants index is rated good for Mobile Bay,
good to fair for Galveston Bay, and poor for the
Barataria-Terrebonne Estuarine Complex and the
Coastal Bend Bays. NCA survey data on fish tissue
contaminants were unavailable to evaluate any of the
Gulf Coast NEP estuaries in Florida (Charlotte Harbor,
Sarasota Bay, and Tampa Bay).
Nationally, the overall condition score for the collec-
tive NEP estuaries of the Gulf Coast region (2.75) is
lower than the overall condition score for the collective
NEP estuaries of the Southeast Coast region (4.0),
comparable to the score for the West Coast region (2.5),
and higher than the scores for the Northeast Coast (1.5)
and Puerto Rico (1.5) regions. Population pressures,
measured as population density (number of
persons/mi2), did not correlate well with the overall
condition ratings for the individual Gulf Coast NEP
estuaries. For example, the Coastal Bend Bays had the
lowest population density of 53 persons/mi2 in 2000,
yet this estuary is rated poor for overall condition, with
an overall condition score of 1.75. The two estuaries
with the highest population densities in 2000,
Galveston Bay (651 persons/mi2) and Tampa Bay (640
persons/mi2), are both rated fair for overall condition
and received overall condition scores of 2.5 and 2.66,
respectively. Mobile Bay (191 persons/mi2), Charlotte
Harbor (306 persons/mi2), and Sarasota Bay (364
persons/mi2), which had more intermediate population
densities in 2000, each received an overall condition
score of 3.0 and are rated fair for overall condition.
National Estuary Program Coastal Condition Report 233
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Charlotte Harbor National Estuary Program
Charlotte Harbor National Estuary Program
www.chnep.org
Background
Located on the west coast of Florida's peninsula,
Charlotte Harbor is created by the inflow and conflu-
ence of the Myakka, Peace, and Caloosahatchee rivers
and empties into the Gulf of Mexico via Boca Grande,
Gasparilla Pass, and San Carlos Bay. The fluctuations of
river flow between the wet (summer) and dry (winter)
seasons affect the Harbor's salinity and dissolved oxygen
levels (NOAA, 1985). The Harbor itself is 30 miles
long and 7 miles wide, with a total area of 270 mi2
(CHNEP, 2005a). The Charlotte Harbor watershed is
home to a highly diverse natural ecology, as well as to a
growing human population and a variety of economic
activities, including phosphate mining, residential devel-
opment, tourism, intensive agriculture, and commercial
fishing. Population growth is a major concern in the
Charlotte Harbor watershed because county popula-
tions are projected to grow by more than 33% between
2000 and 2020 (CHNEP, 2000).
The estuarine area of the Charlotte Harbor NEP
(CHNEP) contains waters listed as drinking water
supplies (e.g., Shell and Horse creeks and parts of the
Myakka River) and waters listed for shellfish propaga-
tion or harvesting (e.g., the tidal portion of the Myakka
234 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Charlotte Harbor National Estuary Program
and Peace rivers). The CHNEP estuarine area also
includes most of the Peace River (U.S. EPA, 2005c).
Those areas located within the Charlotte Harbor
Aquatic and State Buffer Preserve and the Myakka River
State Park have been designated as Outstanding Florida
Waters. Charlotte Harbor and its contiguous coastal
waters serve as a home, feeding ground, or nursery area
for more than 270 resident, migrant, and commercial
fish species of the Gulf of Mexico (CHNEP, 2005a).
For numerous species, the most critical use of Charlotte
Harbor is as a protected nursery area for both larval and
juvenile stages offish. Mangrove trees line the Harbor's
shore and provide important habitat for plants, fish,
birds, and other wildlife, such as manatees, sea turtles,
wood storks, and dolphins.
Environmental Concerns
The environmental concerns of highest priority in
Charlotte Harbor are hydrologic alterations, water
quality degradation, and habitat loss. Management chal-
lenges for the CHNEP include protecting mangrove
habitats; protecting seagrass areas from boat damage and
water pollution; securing new water supply sources for
the watershed's growing human populations and busi-
nesses; managing waste generated by septic tanks and
sewer outfalls; protecting wetland areas for water reten-
tion, groundwater recharge, and wildlife habitat; and
improving the overall efficiency of freshwater usage.
Hydrologic alterations have occurred in the Harbor's
three major tributary rivers, adversely effecting the loca-
tion, timing, and volume of freshwater flows to this
estuary (CHNEP, 2003a). The major causes of habitat
loss in Charlotte Harbor include the degradation and
elimination of headwater streams and other habitats by
commercial development; the conversion of natural
shorelines; the cumulative impacts of dock construction
and boating; the invasion of exotic species; and other
cumulative and future impacts of population growth
(CHNEP, 2005a). In general, dissolved oxygen levels
and surface water quality have declined in several areas
of the Harbor's southern basins, including the Cape
Coral peninsula south of Interstate 75, the north shore
of the Caloosahatchee River, the coastal bays near Pine
Island, and the Estero Bay watershed. Water quality in
other areas of Charlotte Harbor is stable or improving
(CHNEP, 2003b).
Population Pressures
The population of the 10 NOAA-designated coastal
counties (Charlotte, Collier, DeSoto, Glades, Hardee,
Hillsborough, Lee, Manatee, Polk, and Sarasota) coinci-
dent with the CHNEP study area increased by 251%
during a 40-year period, from 0.8 million people in
1960 to 3.0 million people in 2000 (Figure 5-10) (U.S.
Census Bureau, 1991; 2001). This rate of population
growth for the CHNEP study area was almost double
the growth rate of 133.3% for the collective Gulf Coast
NEP-coincident coastal counties and was the second-
highest rate of growth of all NEPs in the Gulf Coast
region, behind Sarasota Bay. In 2000, the population
density of these 10 coastal counties was 306 persons/mi2,
slightly higher than the population density of 287
persons/mi2 for the collective Gulf Coast NEP-coinci-
dent coastal counties (U.S. Census Bureau, 2001).
Development and population pressures are especially
strong in NEP study areas that serve as major shipping
ports and as centers for commercial and recreational
fisheries and other activities.
3.5
« 3.0
o
= 2.5
£
c 2.0
§ 1.5
I-
Q.
<£ 0.5
0.0
I960 1970 1980 1990 2000
Year
Figure 5-10. Population of NOAA-designated coastal counties
of the CHNEP study area, 1960-2000 (U.S. Census Bureau, 199 I;
2001).
National Estuary Program Coastal Condition Report 235
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Charlotte Harbor National Estuary Program
NCA Indices of Estuarine
Condition—Charlotte Harbor
The overall condition of Charlotte Harbor is rated
fair based on three of the four indices of estuarine
condition used by the NCA (Figure 5-11). The water
quality index is rated poor, the sediment quality index is
rated good, and the benthic index is rated fair; NCA
data were unavailable to calculate a fish tissue contami-
nants index for Charlotte Harbor. Figure 5-12 provides
a summary of the percentage of estuarine area rated
good, fair, poor, or missing for each parameter consid-
ered. This assessment is based on data collected by the
Florida Fish and Wildlife Research Institute, in partner-
ship with the NCA, from 30 sites sampled in the
CHNEP estuarine area in 2002. Please refer to Tables
1-24, 1-25, and 1-26 (Chapter 1) for a summary of the
criteria used to develop the rating for each index and
component indicator.
Overall Condition
Charlotte Harbor
(3.0)
Water Quality Index (I)
Sediment Quality Index (5)
Benthic Index (3)
Fish Tissue Contaminants
Index (missing)
Figure 5-11. The
overall condition of
the CHNEP estuarine
area is fair (U.S.
EPA/NCA).
Water Quality Index
The water quality index for Charlotte Harbor is
rated poor (Figure 5-13). This index was developed
using NCA data on five component indicators: DIN,
DIP, chlorophyll a, water clarity, and dissolved oxygen.
Elevated DIP concentrations and poor water clarity
contributed to the Harbor's poor water quality condi-
tion. The NOAA's Estuarine Eutrophication Survey
listed Charlotte Harbor as having low-to-high DIN
concentrations, high DIP concentrations, and medium-
to-hypereutrophic chlorophyll a levels (NOAA, 1997).
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Estuarine Area
I Missing
Figure 5-12. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Charlotte
Harbor (U.S. EPA/NCA).
Dissolved Nitrogen and Phosphorus The
Charlotte Harbor is rated good for DIN concentrations.
None of the estuarine area was rated poor for this
component indicator, 23% of the area was rated fair,
and 67% of the area was rated good. NCA data on
DIN concentrations were unavailable for 10% of the
CHNEP estuarine area. In contrast, DIP concentrations
are rated poor for Charlotte Harbor; however, it should
be noted that phosphorus levels in Charlotte Harbor are
naturally high because of a commercially mined phos-
phate deposit, the Bone Valley deposit. Fifty-seven
percent of the estuarine area was rated poor for DIP
concentrations, 20% of the area was rated good, and
13% of the area was rated fair.
236 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Charlotte Harbor National Estuary Program
Chlorophyll ft \ Chlorophyll a concentrations in
Charlotte Harbor are rated fair. Thirteen percent of
the estuarine area was rated poor for this component
indicator, 67% of the area was rated fair, and 10% was
rated good. NCA data on chlorophyll a concentrations
were unavailable for 10% of the CHNEP estuarine area.
Water Clarity Water clarity in Charlotte Harbor
is rated poor. Water clarity was rated poor at a sampling
site if light penetration at 1 meter was less than 20% of
surface illumination. Expectations for water clarity are
high for Charlotte Harbor because one of the CHNEP's
goals is to maintain SAV coverage and quality at levels
of natural variability. Fifty percent of the estuarine area
was rated poor for water clarity, 30% of the area was
rated fair, and none of the area was rated good. NCA
data on water clarity were unavailable for the remaining
20% of the CHNEP estuarine area.
Water Quality Index - Charlotte Harbor
Site Criteria: Number of component
indicators in poor or fair condition
• Good = No more than I is fair
OFair = I is poor, or 2 or
more are fair
• Poor = 2 or more are poor
O Missing
Figure 5-13. Water quality index data for Charlotte Harbor,
2002 (U.S. EPA/NCA).
Dissolved Oxygen \ The Charlotte Harbor is rated
fair for dissolved oxygen concentrations. NCA estimates
show that only 10% of the CHNEP estuarine area was
rated poor for this component indicator, 43% of the
estuarine area was rated fair, and 47% of the area was
rated good.
Sediment Quality Index
The sediment quality index for Charlotte Harbor is
rated good; however, this rating is based on measure-
ments of sediment TOC only (Figure 5-14). Ninety-
three percent of the estuarine area was rated good for
sediment quality, with NCA data unavailable for 7% of
the CHNEP estuarine area.
Sediment Toxicity I The NCA did not collect sedi-
ment toxicity data for Charlotte Harbor in 2002; there-
fore, sediment toxicity in the Harbor has not been rated
for this report.
Sediment Contaminants I The NCA did not
collect sediment contaminants data for Charlotte
Harbor in 2002; therefore, sediment contaminant
concentrations in the Harbor have not been rated for
this report.
Total Organic Carbon Charlotte Harbor is
rated good for TOC concentrations, with 90% of the
estuarine area rated good and 3% rated fair for this
component indicator. NCA data on TOC concentra-
tions were unavailable for 7% of the CHNEP estuarine
area.
National Estuary Program Coastal Condition Report 237
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Charlotte Harnor National Estuary Program
Benthic Index
The condition of benthic invertebrate communities
in Charlotte Harbor is rated fair based on the Gulf
Coast Benthic Index and data from the NCA. Benthic
index estimates indicate that 13% of the Harbor's estu-
arine area was rated poor for benthic condition, 44%
was rated fair, and 33% was rated good (Figure 5-15).
Fish Tissue Contaminants Index
The NCA did not assess the level of fish tissue conta-
minants in the CHNEP estuarine area in 2002; there-
fore, a fish tissue contaminants index for Charlotte
Harbor was not developed for this report.
Sediment Quality Index - Charlotte Harbor
Jf if C
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
OFair
None are poor, and sediment
contaminants is fair
• Poor = 1 or more are poor
O Missing
Good
93%
Figure 5-14. Sediment quality index data for Charlotte Harbor.
2002 (U.S. EPA/NCA).
Charlotte Harbor National
Estuary Program Indicators of
Estuarine Condition
The major indicators of estuarine condition used by
the CHNEP are species composition and coverage of
SAV; coverage and quality of fish and wildlife habitat;
quantity and timing of freshwater flows and ground-
water levels; and water quality conditions that lead to or
are indicative of eutrophication. The CHNEP manages
an interagency monitoring program that collects data
on a variety of parameters, including Secchi disk,
temperature, salinity, specific conductance, dissolved
oxygen, pH, color, turbidity, total suspended solids,
chlorophyll a, total nitrogen, total Kjeldahl nitrogen,
total ammonia nitrogen, total nitrite+nitrate nitrogen,
dissolved orthophosphate, total phosphorus, and TOC.
Benthic Index - Charlotte Harbor
• Good = > 5.0
OFair =3.0-5.0
• Poor =< 3.0
O Missing
Figure 5-15. Benthic index data for Charlotte Harbor; 2002
(U.S. EPA/NCA).
238 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Charlotte Harbor National Estuary Program
The results from this monitoring program can be found
at the following NEP-supported Web sites: http://
www.checflorida.org and http://wsl3.ipowerweb.com/
checflor/chec/waterquality_home.htm.
Water and Sediment Quality
The presence of algal blooms; high concentrations
of DIN, DIP, and chlorophyll a; and low levels of
dissolved oxygen are the key indicators of potential
eutrophic conditions in Charlotte Harbor. In recent
decades, population growth, stormwater runoff from
residential and commercial development, agricultural
and industrial practices, and the burning of fossil fuels
have been major sources of increased inputs of nutrients
to Charlotte Harbor. Results from March 2004 show
elevated levels ot DIN and slightly higher than normal
DIP concentrations in the Harbor, but normal chloro-
phyll a levels. Dissolved oxygen and turbidity values
were rated better than normal by the CHNEP. The
Caloosahatchee River basin has ongoing water quality
problems, with excess nutrients, low dissolved oxygen,
and noticeable increases in levels of copper and lead
(CHNEP, 2005a). Recent maps of water and sediment
quality indicators, as reported by the CHNEP on a
monthly basis, can be found at http://www.chnep.org.
Declines in dissolved oxygen levels and worsening
surface water quality were observed in the southern
basins of Charlotte Harbor. Overall, there have been
major increases in total suspended solids in the entire
southern portion of the CHNEP estuarine area,
including the full extent of Charlotte Harbor. Florida
surface water standards have been exceeded frequently
for dissolved oxygen (both instantaneous readings and
daily average readings) and ammonia in many basins,
and to a lesser extent, for chlorophyll a and bacteria
levels (CHNEP, 2003b).
Habitat Quality
The natural habitats of the Charlotte Harbor estu-
arine area span a wide range of environments, from
xeric oak scrubs to subtidal soft-bottoms to mangrove
forests. Mangrove forests provide habitat for more than
2,300 species of animals, including at least 42 federally
listed and state-listed endangered or threatened animal
species, such as the Florida black bear, manatee, bald
eagle, wood stork, Florida scrub jay, and American croc-
odile. In Charlotte Harbor, the acreage, type, and health
of seagrass systems are monitored as one of the major
indicators of estuarine condition. Informal habitat indi-
cators monitored by the CHNEP include shellfish-area
closures, number of fish kills, presence of fish lesions,
acres of stable seagrass areas, and presence or lack of
HABs (red tides). Some other useful response indicators
include the effectiveness of riprap under docks, the
effectiveness of artificial reefs in enhancing habitat value
along seawalls, the length of shoreline restored, and the
effectiveness of exotic vegetation removal (CHNEP,
2005a).
Seagrasses within the northern portion of the
CHNEP study area have been found to be stable, and
analysis is still being conducted on the southern portion
of the area (CHNEP, 2005a). Seagrass habitats exist
throughout all of the riverine and estuarine regions of
the CHNEP study area, providing food sources, solid
foundations, and protective structures for living
resources. Historically, dredge-and-fill activities within
coastal bottom and wetland areas have reduced the
extent of these habitats. One specific goal of the
CHNEP is to reduce propeller damage to SAV by 2010
(CHNEP, 2000). At the present time, the CHNEP's
data is sufficient to evaluate significant losses of SAV
acreage due to direct impacts, such as water manage-
ment (e.g., losses in the Caloosahatchee Rivers
Vallisneria americand) and channel and causeway island
construction (e.g., losses in IntraCoastal Waterway and
Sanibel Causeway). Dissolved and suspended matter
within the water column, rather than chlorophyll a,
largely limit light availability for seagrass beds in
Charlotte Harbor, and water clarity in the Harbor
increases with salinity and distance from the tributaries
(McPherson and Miller, 1987; McPherson and Miller,
1994; Dixon and Kirkpatrick, 1999; Doering and
Chamberlain, 1999; Tomasko and Hall, 1999); thus,
seagrass coverage shows inter-annual variability largely
due to inter-annual freshwater flow changes (Corbett et
al., 2005). In some areas of Charlotte Harbor, unre-
stricted development has resulted in large losses of habi-
tats, such as high marshes and salterns.
National Estuary Program Coastal Condition Report 239
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Charlotte Harbor National Estuary Program
Hurricanes and Hypoxia in 2004
Over a two-month period in 2004, four major hurri-
canes and five named tropical storms battered Florida,
with three hurricanes directly impacting the CHNEP
study area (CHNEP, 2005b; Everham 2005). On
August 13, 2004, Hurricane Charley—the strongest
hurricane to hit the United States since Hurricane
Andrew in 1992—passed through the heart of
Charlotte Harbor (Pasch et al., 2005). The destruction
from Hurricane Charley was not limited to the land
and homes of the Charlotte Harbor watershed, but
included damage to the Harbor and its rivers, creeks,
and tributaries. Many of Charlotte Harbor's local
islands, man-made canals, tributaries, and other water-
ways are lined with homes and boat docks. In calm
weather, these settings provide an idyllic existence and
magical vistas; however, the scenario changed in the face
of Hurricane Charley, as waterways were made impass-
able by fallen trees, uprooted vegetation, and enormous
quantities of debris (Fletcher, 2005).
One week after Hurricane Charley moved through
Florida, state agencies began receiving complaints of
foul-smelling water, prompting an unscheduled
sampling effort that measured low dissolved oxygen
levels for many areas of the estuary. Although the
sampling found that turbidity and total suspended solid
values for the estuary were not unusual, and that color
was typical of values normally found during the wet
season the biological oxygen demand (BOD) for the
estuary was very high. The low dissolved oxygen values
in Charlotte Harbor were associated with the decompo-
sition of large amounts of dissolved organic matter that
resulted in the high levels of BOD (see bar graph)
(Tomasko et al., 2005b). Although hypoxia is a normal,
wet season phenomenon in the Harbor (Camp Dresser
& McKee, 1998) and a hypoxic zone was apparent in
Charlotte Harbor two weeks after Hurricane Charley
passed through the area (see map), hypoxia has never
been recorded over such an extensive area of the
Charlotte Harbor watershed (Tomasko et al., 2005b).
Satellite image of Hurricane Charley at landfall (NOAA National Climatic Data Center).
240 National Estuary Program Coastal Condition Report
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CHAPTER 5 ; GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Charlotte Harbor National Estuary Program
Subsequently, Hurricane Frances passed
through Florida over the Labor Day weekend.
Three weeks later, on National Estuary Day,
Hurricane Jeanne followed Frances over the
Peace River basin. The impacts of this string
of hurricanes on the water quality of
Charlotte Harbor were felt for months
following the storms. Water quality character-
istics in Charlotte Harbor, such as dissolved
oxygen and water clarity, were degraded into
the fall of 2004, but were showings signs of
recovery by 2005 (Beever, 2005).
g
6
4
2
n
-
.
.
Top 10%
Median
"Bb
s^
a
o
CO
Prmrwsa Joshua Horse Crk. Horse Crk. Peace R. Peace R.
Intake Crk. at at at at
MyakkaHead Arcadia Arcadia Wauchula
Five-day BOD values one week after Hurricane Charley (Tomasko et al.,
2005a).
Large hypoxic zone (ca. 30 mi2) apparent two weeks after Hurricane Charley. BLUE TRIANGLE: Sites with no hypoxia (DO < 2 mg/L)
in surface or bottom waters. RED TRIANGLE POINTING UP: Sites with hypoxia in bottom waters only. RED TRIANGLE
POINTING DOWN: Sites with hypoxia in both bottom and surface waters. YELLOW TRIANGLE: Sites not visited due to an
oncoming storm.The red line delimits area believed to exhibit hypoxia for this event, based on event data and historical monitoring
data demonstrating that hypoxia is associated with flows out of the Peace River and along the western "wall" of Charlotte Harbor.
Some smaller areas (unknown in size) exhibited hypoxia in both bottom and surface waters (Tomasko et al., 2005a).
National Estuary Program Coastal Condition Report 241
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Charlotte Harbor National Estuary Program
Living Resources
Charlotte Harbor provides habitat for 39 species of
mammals, 331 species of birds, 67 species of reptiles, 27
species of amphibians, and 452 species of fish (CHNEP,
2005a); however, the growing human population and
increasing urban development have resulted in habitat
loss throughout the study area. This loss of habitat can
negatively affect plant communities and wildlife. For
example, since the 1920s, pine flatwoods habitat acreage
has decreased; communities of pines, wax myrtle, and
saw palmetto have been lost; and animals, including
pileated woodpeckers, American kestrels, sandhill
cranes, black bears, panthers, indigo snakes, and gopher
tortoises, have been displaced (CHNEP, 2000).
Shellfish are a reliable measure of the environmental
health of an estuary. Because they feed by filtering
estuary water, shellfish assimilate and concentrate the
materials carried in the water in their tissues. More than
275 species of shellfish are found throughout the waters
of Charlotte Harbor. People have been harvesting shell-
fish in the area since the Calusa Indians of southwest
Florida gathered enormous amounts of shellfish by
digging canals and constructing immense shell mounds.
In the more recent past, oysters, clams, and scallops
have been harvested commercially and recreationally
throughout Lemon Bay, Gasparilla Sound, Charlotte
Harbor, and Pine Island Sound. The height of the shell-
fish industry in the Charlotte Harbor area occurred
during the 1940s, and the commercial harvest of shell-
fish has declined since that time (CHNEP, 2000).
Environmental Stressors
Adverse changes in the location, timing, and volume
of freshwater flows; overall function of flood plain
systems; and natural river flows are the major hydro-
logic concerns in Charlotte Harbor. Man-made canals
and waterfront lots are two major developments that
alter surface water hydrology and degrade estuarine
conditions in Charlotte Harbor. The construction of
drainage channels for transportation, agricultural activi-
ties, urbanization, and hurricane flood relief have been
just as prevalent. Although changes to groundwater
systems in the Charlotte Harbor watershed have been
less obvious, the increased drainage of surface systems
reduces recharge to groundwater, altering the general
flow of underground aquifers. Saltwater intrusion is an
indicator of these changes.
Hydrologic alterations have occurred in many
regions of the Charlotte Harbor area. For example, the
Caloosahatchee River was channelized and artificially
connected to Lake Okeechobee in the late 1800s and
early 1900s to provide flood protection, serve as a navi-
gational channel, and supply water for agricultural and
Prop roots of mangrove trees below the water surface provide substrate for many other organisms (CHNEP)
242 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Charlotte Harbor National Estuary Program
urban use. Three locks and dams have been constructed
along the Caloosahatchee River, one of which artificially
truncates the river's estuarine system by blocking the
natural gradient of fresh water to salt water that histori-
cally had extended upstream during the dry season. The
flow through this river is highly manipulated because
water management juggles the often conflicting needs
of estuary resources, public water supply, and agricul-
tural uses (CHNEP, 2003a). In addition, the upper
Peace River has changed from a gaining stream with
flow all year long to a losing stream with river flows
being lost in sinkholes along the upper Peace River.
Kissingen Springs, located along the upper Peace River,
ceased flowing in the early 1950s, which is a sign of a
lowered groundwater table in the Charlotte Harbor
watershed (Corbett, 2003). The Myakka River flows
have been artificially augmented because of the overland
surface flow of groundwater pumped for agricultural use
in the dry season. Also, the upper Myakka River
demonstrates an increasing trend in specific conduc-
tivity (sulfate and calcium levels), and an extensive tree
die-off has occurred in this area due to hydrologic stress
(CHNEP, 2003b; Minnis, 2003).
Current Projects,
Accomplishments, and Future
Goals
The CHNEP set a variety of goals in Committing to
Our Future: A Comprehensive Conservation and
Management Plan for the Greater Charlotte Harbor
Watershed, Volume 1 (CHNEP, 2000). A goal of the
CHNEP is to increase conservation, preservation, and
stewardship lands by 25% by the year 2018. To combat
hydrological alterations, the CHNEP plans to improve
waterbodies affected by artificial structures by the year
2020. To help improve water quality, the program will
gather information for the State of Florida to use in
developing TMDLs (except for mercury) for high-
priority, 303(d)-listed water segments by 2004 and for
all remaining 303(d) waters in the CHNEP estuarine
area by 2009. The CHNEP also plans to develop a
sense of stewardship by providing information on living
resources and water quality to the public, as well as by
maintaining environmental education efforts with part-
ners (CHNEP, 2000).
Conclusion
Urban development in the Charlotte Harbor study
area has been rapid and has contributed to water quality
degradation, habitat loss, and hydrologic changes. In
addition, there have been ongoing declines in water
quality in many of the Charlotte Harbor basins. NCA
data classify the overall condition of Charlotte Harbor
as fair. Water quality in the Harbor is rated poor, with
DIN concentrations rated good; chlorophyll a and
dissolved oxygen concentrations rated fair; and DIP
concentrations and water clarity rated poor. Sediment
quality in the Harbor is rated good; however, this rating
is based only on measurements of one sediment quality
component indicator (sediment TOC). The benthic
index is rated fair, and 2002 NCA data were unavailable
to develop a fish tissue contaminants index for
Charlotte Harbor.
A young student conducts water quality tests in Charlotte Harbor
(CHNEP).
National Estuary Program Coastal Condition Report 243
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Sarasota Bay Estuary Program
Sarasota Bay Estuary Program
SARASOTA BAY
ESTUARY PROGRAM
www.sarasotabay.org
Background
Sarasota Bay is a small, subtropical estuary that is
located on the southwestern coast of Florida and covers
52 mi2 of surface water area. The Bay's watershed
spreads across Manatee and Sarasota counties and covers
150 mi2 of land area. This watershed extends from
Venice Inlet to Anna Maria Island and includes the
barrier islands and mainland east to Interstate 75
(SWFWMD, 2002). Sarasota Bay is classified as an
Outstanding Florida Water Body and was classified as
an Estuary of National Significance in 1987 (SBNEP,
2000; FDEP, 2005). The Sarasota Bay Estuary Program
(SBEP) estuarine area includes Sarasota, Roberts, Little
Sarasota, and Blackburn bays, which are characterized
by stretches of barrier islands. The Bay region is home
to a wide variety of marine life, including dolphins,
manatees, black mullet, red drum, spotted sea trout,
snook, blue crab, stone crab, bait shrimp, and the
endangered loggerhead sea turtle. Common birds in this
region include the great blue heron, cattle egret, great
egret, white ibis, brown pelican, osprey, wood stork,
yellow-crowned night heron, bald eagle, and the
endangered Florida scrub jay.
244 National Estuary Program Coastal Condition Report
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CHAPTER 5 ; GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Sorasofo Bay Estuary Program
Sarasota Bay proper is the largest and deepest bay
between Tampa Bay and Charlotte Harbor. The Bay is
well flushed by three passes (Big Sarasota, New, and
Longboat), and its water is much clearer than the waters
of the smaller bays to the south (Roberts, Little
Sarasota, and Blackburn bays) (Florida Center for
Community Design and Research, 2004). Improved
drainage levels in the urban watersheds around Sarasota
Bay provide more fresh water than historical levels, and
numerous improvements have been made in the Bay's
water quality, seagrass coverage, and natural habitat
areas. Most of the waterbodies in the SBEP estuarine
area are designated as recreational-use waters, which
means that waters should be fishable and swimmable.
Some waterbodies, including Palma Sola Bay and parts
of Sarasota Bay, are suitable for shellfish propagation or
harvesting (U.S. EPA, 2005c). Of all of the Gulf Coast
NEP estuaries, the Sarasota Bay watershed has the
greatest percentage of urban land use.
The tourism industry is the largest industry in
Sarasota County and the second-largest industry in
Manatee County. Seasonal residents are estimated to
represent up to 25% of the study area's total population
and more than 70% of the population on the barrier
islands. Although this multi-million dollar industry
helps to raise the revenue used to fund monitoring and
conservation efforts, tourism and recreational activities
can also take a toll on the water quality, habitat, and
wildlife of Sarasota Bay. Human activities, including the
management of waste and the operation of automobiles
and watercraft, can contribute nitrogen and other cont-
aminants to Sarasota Bay and degrade the Bay's water
quality. In addition, dredging has been conducted in the
area to create navigable waterways and new home sites
and has destroyed habitat and reduced the populations
offish and shellfish in the Bay (SBNEP, 2000). Tourism
and recreational activities can also directly harm
wildlife; for example, more than 30% of the annual
manatee deaths in Sarasota Bay are caused by collisions
with boats (Sarasota Dolphin Research Program, 2005).
Environmental Concerns
Population increases and the accompanying develop-
ment around Sarasota Bay between 1930 and 1990
resulted in the loss of historic seagrass habitat and
mangrove wetlands (SBNEP, 2000). For example, 2,495
acres of tidal wetlands were lost between 1950 and
1990 due to dredge-and-fill activities, construction, and
invasive species (SBNEP, 1992). Over time, loss of
habitat areas has been accompanied by declines in
marine life, fish, birds, and shellfish. Increased develop-
ment has also resulted in excess nitrogen pollution and
stormwater runoff, both priority concerns of the SBEP.
Nitrogen is the major pollutant of concern in Sarasota
Bay, with nitrogen loads transported to the Bay through
baseflow, wastewater, stormwater, and atmospheric
deposition (Figure 5-16) (SBNEP, 2000). In 1990,
nitrogen loadings were approximately 300% of the
levels that existed prior to development of the region
(U.S. EPA, 2005b), and loadings are projected to
increase by another 8% during the next 20 years and by
16% when the area is fully developed according to
existing plans. Tributaries to Sarasota Bay act as
pipelines for dispensing stormwater and suspended
matter into the estuary. Although the overall trophic
status index for Sarasota Bay is good, the Bay segments
that receive water from the tributaries have the poorest
water quality. Chlorinated pesticides, PAHs, and metals
have been found in tributary sediments; those tribu-
taries with the highest levels of these contaminants are
Hudson Bayou, Cedar Hammock Creek, and Whitaker
Bayou (Lowrey et al., 1992).
Atmospheric
15%
Baseflow
10%
Wastewater
20%
Surface
Runoff
55%
Figure 5-16. Percentages of nitrogen distributed to Sarasota
Bay (SBNEP, 2000).
National Estuary Program Coastal Condition Report 245
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CHAPTER 5 1 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Sorosofa Bay Estuary Program
Population Pressures
The population of the 2 NOAA-designated coastal
counties (Manatee and Sarasota) coincident with the
SBEP study area increased by 304% during a 40-year
period, from 0.14 million people in 1960 to 0.59
million people in 2000 (Figure 5-17) (U.S. Census
Bureau, 1991; 2001). This rate of population growth
for the SBEP study area substantially exceeded the
population growth rate of 133.3% for the collective
NEP-coincident coastal counties of the Gulf Coast
region and was the highest rate of population growth
for any of the individual Gulf Coast NEPs. In 2000, the
population density of these 2 coastal counties was 447
persons/mi2, significantly higher than the population
density of 287 persons/mi2 for the collective NEP-coin-
cident coastal counties of the Gulf Coast region (U.S.
Census Bureau, 2001). Development and population
pressures are especially strong in NEP study areas that
serve as major shipping centers for commercial and
recreational activities.
0.8
° 0.6 -
0.4
0.2
0.0
I960
2000
Figure 5-17. Population of NOAA-designated coastal counties
of the SBEP study area, 1960-2000 (U.S. Census Bureau, 1991;
2001).
NCA Indices of Estuarine
Condition—Sarasota Bay
The overall condition of Sarasota Bay is rated fair
based on three of the four indices of estuarine condition
used by the NCA (Figure 5-18). The water quality
index for Sarasota Bay is rated fair, the sediment quality
index is rated good, and the benthic index is rated poor;
no data were available to calculate a fish tissue contami-
nants index for this estuary. Figure 5-19 provides a
summary of the percentage of estuarine area rated good,
fair, poor, or missing for each parameter considered.
This assessment is based on data collected by the
Florida Fish and Wildlife Research Institute, in partner-
ship with the NCA, from 20 stations sampled in the
SBEP estuarine area in 2000. Please refer to Tables 1-24,
1-25, and 1-26 (Chapter 1) for a summary of the
criteria used to develop the rating for each index and
component indicator.
Overall Condition
Sarasota Bay
(3.0)
Water Quality Index (3)
Sediment Quality Index (5)
Benthic Index (I)
Fish Tissue Contaminants
Index (missing)
Figure 5-18. The
overall condition of
the SBEP estuarine
area is fair (U.S.
EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Eistuarine Area
Missing
Figure 5-19. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Sarasota Bay
(U.S. EPA/NCA).
246 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Sarasofo Bay Estuary Program
Water Quality Index
Based on NCA survey results, the water quality index
for Sarasota Bay is rated fair (Figure 5-20). This index
was developed using NCA data on five component
indicators: DIN, DIP, chlorophyll a, water clarity, and
dissolved oxygen. In NOAA's Estuarine Eutrophication
Survey, Sarasota Bay was listed as having medium DIN
concentrations, high DIP concentrations, and high
chlorophyll a levels (NOAA, 1997). Results from the
2000 NCA survey show some improvement over the
previous study, with low DIN, moderate DIP, and
moderate chlorophyll a concentrations measured.
Dissolved Nitrogen and Phosphorus I Sarasota
Bay is rated good for DIN concentrations, with 100%
of the estuarine area rated good for this component
indicator. NCA data for Sarasota Bay were collected in
the summer, when elevated DIN concentrations are less
likely to occur because freshwater inputs are low and
dissolved nutrients are more rapidly utilized by phyto-
plankton populations. Sarasota Bay is rated fair for DIP
concentrations, with 15% of the estuarine area rated
poor, 10% of the area rated fair, and 75% of the area
rated good for this component indicator.
Chlorophyll tl I Chlorophyll a concentrations in
Sarasota Bay are rated fair. Although only 5% of the
estuarine area was rated poor for this component indi-
cator, 75% was rated fair, and 20% was rated good.
Water (.larity \ Water clarity in Sarasota Bay is also
rated fair; however, expectations for water clarity are
high because one of the goals of the SBEP is to re-estab-
lish SAV. Water clarity in Sarasota Bay was rated poor at
a sampling site if light penetration at 1 meter was less
than 20% of surface illumination. Ten percent of the
estuarine area was rated poor for water clarity, 15% of
the area was rated good, and 65% of the area was rated
fair. NCA data on water clarity were unavailable for
10% of the SBEP estuarine area.
Dissolved Oxygen I Dissolved oxygen conditions
in Sarasota Bay are rated fair. NCA estimates show that
5% of the estuarine area was rated poor for dissolved
oxygen concentrations, 15% of the area was rated fair,
and 80% of the area was rated good.
Water Quality Index - Sarasota Bay
Site Criteria: Number of
component indicators in poor or
fair condition
• Good — No more than I is fair
O Fair = I is poor, or 2 or
more are fair
• Poor = 2 or more are poor
O Missing
Good
40%
Figure 5-20. Water quality index data for Sarasota Bay, 2000
(U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 247
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Sarasota Bay Estuary Program
Sediment Quality Index
The sediment quality index for Sarasota Bay is rated
good; however, this rating is based on measurements of
sediment TOC only (Figure 5-21). Sediment quality
was rated good in 100% of the Bay's estuarine area.
Sediment Toxicity I The NCA surveys did not
collect sediment toxicity data for Sarasota Bay in 2000;
therefore, sediment toxicity in the Bay has not been
rated for this report.
Sediment Contaminants I The NCA surveys did
not collect sediment contaminants data for Sarasota Bay
in 2000; therefore, sediment contaminant concentra-
tions in the Bay have not been rated for this report.
Sediment Quality Index - Sarasota Bay
Site Criteria: Number and condition
of component indicators
• Good = None are poor, and sediment
contaminants is good
O Fair — None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Figure 5-21. Sediment quality index data for Sarasota Bay, 2000
(U.S. EPA/NCA).
Total Organic Carbon I Sediment TOC concen-
trations were the only sediment quality component
indicator monitored in Sarasota Bay by the NCA in
2000. TOC concentrations in Sarasota Bay sediments
are rated good, with 100% of the estuarine area rated
good for this component indicator.
Benthic Index
The condition of benthic invertebrate communities
in Sarasota Bay is rated poor, based on the Gulf Coast
Benthic Index and data from the NCA. Benthic index
estimates indicate that 35% of the estuarine area in
Sarasota Bay has degraded benthic resources and is rated
poor (Figure 5-22).
Benthic Index - Sarasota Bay
Site Criteria: Gulf Coast
Benthic Index Score
• Good = > 5.0
OFair =3.0-5.0
• Poor = < 3.0
O Missing
Figure 5-22. Benthic index data for Sarasota Bay, 2000
(U.S. EPA/NCA).
248 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Sarasota Bay Estuary Program
Fish Tissue Contaminants Index
The NCA did not assess the level of fish tissue conta-
minants in the SBEP estuarine area in 2002; therefore,
a fish tissues contaminants index for Sarasota Bay was
not developed for this report.
Sarasota Bay Estuary Program
Indicators of Estuarine Condition
Water and Sediment Quality
The SBEPs specific indicators for measuring water
quality in Sarasota Bay are the following:
• Chlorophyll a
' Nitrogen (e.g., DIN levels, total nitrogen levels,
nitrogen load)
• Inorganic phosphorus
• Transparency (as measured using Secchi depth).
In general, water quality trends for Sarasota Bay have
shown improvements with time. Data from 1968
through 1991 indicate that nutrient and chlorophyll a
levels are decreasing in the Bay, and Secchi depths are
increasing over time. For northern Sarasota Bay,
regional trends in chlorophyll a levels, inorganic
nitrogen, organic nitrogen, total nitrogen, and inorganic
phosphorus have been declining since 1980; however,
Manatee County data have shown significant increases
in these parameters. The middle portion of Sarasota Bay
has displayed declining trends similar to those observed
in the northern portion of the Bay, with the exception
of chlorophyll a and total phosphorus concentrations,
which were increasing. SBEP data for the southern
portion of Sarasota Bay indicate a regional increase in
both chlorophyll a and ammonium nitrogen levels.
Other significant improvements observed in the trend
analysis for the southern portion of the Bay were long-
term declines in nitrate-nitrite, total nitrogen, and inor-
ganic phosphorus. The transparency of Sarasota Bay
waters is measured by Secchi depth and can be used to
help indicate overall water quality or the effects of
erosion and increased rainfall. Data from 1968 to 1991
show that Secchi depth has increased (greater water
transparency) in all segments that demonstrated signifi-
cant trends (Lowrey et al., 1992), and recently collected
monthly data show that Secchi depth generally fluctu-
ates between 4 and 8 feet (Florida Center for Commu-
nity Design and Research, 2004). Trend analyses that
examined data from 1980 to 2002 suggest that inor-
ganic nitrogen and chlorophyll a levels have declined
during the long term; inorganic phosphorus levels have
also declined, although increases were noted in total
phosphorus, particularly from 1995 to 2002 (Dixon,
2003).
In addition to the SBEPs formal indicators, other
water quality parameters monitored for the Bay include
salinity, temperature, dissolved oxygen, pH, Enterococci,
and fecal coliform. Salinity in the Bay has increased over
time, except for the period from 1995 to 1998, when
salinity declined (Dixon, 2003). Beach water samples
are collected every 2 weeks at 14 different beach sites in
Sarasota County and are analyzed for Enterococci and
fecal coliform bacteria (Florida Center for Community
Design and Research, 2004).
A great egret (Ardeo alba) hunts in the waters of an SBEP
restoration site (SBEP).
National Estuary Program Coastal Condition Report 249
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Sarasota Bay Estuary Program
Improving Water Quality in the
Sarasota Bay Watershed
Reducing nitrogen inputs to Sarasota Bay has been
recognized as a primary water quality concern since the
1980s. A central tenet of these reduction efforts has
been to address all contributors to water quality degra-
dation in the restoration of Sarasota Bay. Nutrient loads
in Sarasota Bay in 1988 were approximately 400%
higher than those expected from a pristine, undeveloped
watershed (SBNEP, 2000). By comprehensively
addressing the sources of nitrogen and other pollutants,
the water quality throughout most of Sarasota Bay has
steadily improved during the past decade.
The SBEP and its partners have been working with
the community to cost-effectively limit and control the
amount of nitrogen entering Sarasota Bay. The integra-
tion of different water quality improvement compo-
nents that address wastewater, stormwater, groundwater,
and atmospheric deposition as a whole is an important
step to ensure that issues of timing, cost, and effective-
ness are considered.
The widespread implementation of advanced waste-
water treatment, required by federal legislation in 1990,
resulted in reductions of more than 80% of nitrogen
loadings from wastewater to Sarasota Bay. At the
present time, stormwater from all areas is the primary
source of nitrogen pollution, with stormwater from
residential areas estimated to contribute more than
Urban stormwater runoff deposits large amounts of sediments and other pollutants into Sarasota Bay through drainage ditches
(above) and tributaries (Gary Raulerson, SBEP).
250 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Sarasota Boy Estuary Program
one-third of the total nitrogen load to Sarasota Bay.
Currently, an unquantified number of stormwater
pipelines that discharge directly into Sarasota Bay or its
tributaries do not receive any type of wastewater treat-
ment (SBNEP, 2000). Beginning in September 2005, a
new SBEP project will identify and prioritize water
quality control retrofits for urban stormwater, especially
in direct-discharge locations. Information to be gained
will include project price, maintenance accessibility, and
a receiving water of high resource value. This informa-
tion can be used by local, state, and federal agencies to
help determine where to direct resources to continue
the restoration of Sarasota Bay.
The Florida Yards and Neighborhoods (FYN)
Program was developed in 1993 to promote environ-
mentally friendly landscaping using plants suited to the
southwest Florida climate, natural conditions, and
wildlife. Using FYN's principles, homeowners can
reduce fertilizer and pesticide use, thereby helping to
maximize the quality of stormwater runoff.
Improvements in stormwater conveyance and treatment
systems also impact water quality. Designed primarily
for flood and sediment control, these systems have an
important effect on toxic loading, as well as a smaller,
but significant impact on nutrients.
The SBEP is also pursuing other management strate-
gies, including septic tank replacement (such as that
currently underway within the Phillippi Creek water-
shed). This strategy is being pursued primarily from a
public health perspective, but should also reduce
nitrogen loadings to Sarasota Bay. Regionally instituted
water conservation policies can also help improve the
water quality of Sarasota Bay. Through the creation and
implementation of a master reuse plan, the discharge of
wastewater to die Bay is being substantially reduced. At
the same time, this wastewater is offsetting withdrawals
from the Floridian aquifer.
Human-related atmospheric deposition (from auto
emissions, industry, and other sources) plays a role
within the Sarasota Bay watershed; however, this role is
not as large as previously believed. Although nitrogen
emissions from automobiles and other mobile sources
(such as lawn mowers) may not be as great as originally
thought, this may become an important area for further
reductions.
National Estuary Program Coastal Condition Report 251
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Sarasota Bay Estuary Program
Habitat Quality
The following indicators are used to evaluate habitat
quality in Sarasota Bay:
• Freshwater wetlands coverage
• SAV (seagrass) coverage
• Intertidal habitat coverage
• Abundance of juvenile fish in restored areas vs. abun-
dance in natural areas
• Effectiveness of artificial reef construction.
Freshwater wetlands have declined 16% since 1975,
and non-forested freshwater wetlands have declined by
35% (U.S. EPA, 2005b). Since 1950, the area of salt-
water wetlands in Sarasota Bay has declined 39%, and
seagrass acreage has generally declined by 30%, mainly
due to nitrogen pollution and dredging impacts
(SBNEP, 2000). Seagrass coverage in the Bay is an
indicator of the success or failure of restoration activities
and the area of suitable habitat, as well as an indirect
indicator of the effects of water quality changes, sedi-
ment contamination, or other human-induced impacts
on the ecosystem.
Approximately every 2 years, the Southwest Florida
Water Management District (SWFWMD) uses aerial
photography to analyze seagrass communities in water-
bodies (including Sarasota Bay) located within its
watershed. The SWFWMD's analysis distinguishes
between patchy seagrass beds (less than 75% coverage
within a given area) and continuous seagrass beds
(greater than 75% coverage within a given area). Since
1988, approximately 600 new acres of seagrasses have
appeared in the Sarasota Bay estuarine area.
Additionally, the amount of continuous seagrass beds in
Sarasota Bay has increased by more than 120% (SBEP,
2006). Figure 5-23 illustrates the percent changes in
seagrass coverage in Sarasota Bay (from the Anna Maria
Sound at State Road 64 to Venice Inlet), both for
continuous and patchy distributions of seagrass.
At least 15 artificial reefs are being established in
Sarasota Bay to help create additional juvenile fish
habitat (U.S. EPA, 2005b). To help monitor the abun-
dance of fish species in natural areas in comparison with
fish abundance in restored areas, the SBEP continues to
study the effectiveness of artificial structures in provid-
ing juvenile fish nursery habitat. The SBEP, with
funding from EPA and the Florida Department of
Environmental Protection (FDEP), has sponsored the
development of inexpensive seawall modules to attract
larval, juvenile, and adult fish. An early pilot project
demonstrated the potential benefit of deploying artifi-
cial reefs along hardened seawalls, with some types of
structures showing fish abundances more than 100
times that of nearby areas without artificial reefs
(SBNEP, 2000). In a recent shoreline survey, researchers
found that more than 200 miles of armored and altered
shoreline exist in Sarasota Bay (U.S. EPA, 2003); altered
shorelines typically do not provide enough complex or
suitable habitat for fish.
14,000
D Patchy
• Continuous
Total acreage
1950
2003
Figure 5-23. Changes in continuous, patchy, and total seagrass
coverage areas in Sarasota Bay (SBER 2006).
Living Resources
Sarasota Bay is home to a variety of fish and wildlife,
including the great blue heron, cattle egret, bald eagle,
Florida scrub jay, red drum, spotted seatrout, flounder,
blue crab, manatee, and bottlenose dolphin. The SBEP
and other organizations monitor the populations of fish
and wildlife in the SBEP study area.
Aerial surveys used to monitor manatee populations
in Sarasota Bay indicate that the number of manatees in
the Bay has increased since the early 1990s (Florida
Center for Community Design and Research, 2004).
Manatees are typically found along the fringes of the
Bay from April to December, with seasonal migration
patterns reducing the number of manatees in the Bay
between January and February.
252 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Sorasofa Bay Estuary Program
The bottlenose dolphins that use Sarasota Bay have
been monitored since the 1970s, and mark-recapture
estimates in 1976 and 1983 indicated that about 100
dolphins were present on a regular basis. Since 1984,
researchers have monitored individual dolphins using
distinctive dorsal fin features. The bottlenose dolphin
population in Sarasota Bay has increased since the mid-
1990s due to the dolphin immigration from other areas,
seasonal migration patterns of dolphins from Tampa
Bay, and high birth rates of native dolphins. These
increases correlate with presumed fish stock increases
since the net ban, but cause-effect relationships have not
been conclusively established (Florida Center for
Community Design and Research, 2004).
Current Projects,
Accomplishments, and Future
Goals
Much of Sarasota Bay's habitat for young fish was
recently destroyed when the natural mangrove shoreline
was replaced by concrete seawalls during the develop-
ment of waterfront communities. As a result, the SBEP
is embarking on an artificial habitat enhancement and
wetland restoration strategy to increase its young fish
population and overall fishery production. A recent
study by the SBEP indicated that intertidal restoration
sites less than 10 years old provide habitat for more
than 68,000 fish per acre (Serviss and Sauers, 2003).
Because most of the seawalls cannot be removed
without causing severe damage to homes, the SBEP
seeks to convert them into an asset for the Bay rather
than a liability. Four different styles of small artificial
reefs attached to seawalls are being tested for their
ability to provide a home for young fish (SBNEP,
2000). Early results show more than 400 young fish
living near these artificial reefs (U.S. EPA, 2006d),
whereas only a few young fish have been seen in similar
areas without reefs.
EPA plans to restore or create at least 18 acres of
intertidal wetlands and 11 acres of non-forested, fresh-
water wetlands per year, as well as to increase the quan-
tity, improve the quality, and protect the diversity of
freshwater and saltwater wetlands in the Sarasota Bay
watershed (U.S. EPA, 2005b). Twenty-one wetland-
enhancement projects have been proposed and funded
since 1989, and 13 significant habitat-restoration
initiatives have been completed, with 12 more initia-
tives currently in the design phase (SBNEP, 2000; U.S.
EPA, 2005b). In addition, new channel markers are
being installed in Sarasota Bay (with artificial reefs built
on each) to protect seagrass beds. The SBEP and the
surrounding community has achieved a number of
environmental success stories:
• Nitrogen pollution to the Bay has been reduced by
47% since 1990
• Seagrass habitat has increased by 7% (592 acres)
since 1988
• More than 200 acres of intertidal wetland habitat
have been restored since 1990
• More than 20 artificial reef projects have been
permitted and constructed
• The Bay supports an estimated 110 million more
fish, 71 million more crabs, and 330 million more
shrimp than it did in 1988
• Several urban watershed areas around Sarasota Bay
have been retrofitted for improved stormwater
management
• Scallops have been reintroduced to the Bay to re-
establish stocks
• SBEP policies have been integrated into local govern-
ment CCMPs (SBNEP, 2000; SBEP, 2006).
Conclusion
Based on NCA survey results, the overall condition
of Sarasota Bay is rated fair. SBEP analyses have shown
that although temporal trends by segment indicate that
water quality in Sarasota Bay is improving, water quality
problems still exist in the tributaries and the Bay
segments receiving water from the tributaries. Seagrass
coverage in Sarasota Bay has improved substantially in
the past few years, with declines in SAV occurring at a
much slower rate. Although there is no substitute for
natural habitat with respect to the diversity and produc-
tivity of organisms, engineering options for some envi-
ronments (e.g., dredge holes, canal communities, and
channel markers) exist to create artificial habitats for
juvenile and adult finfish, shellfish, and other
invertebrates.
National Estuary Program Coastal Condition Report 253
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tampa Bay Estuary Program
Tampa Bay Estuary Program
www.tbep.org
Background
Tampa Bay, Florida's largest open-water estuary,
spans almost 400 mi2 and drains 2,300 mi2 of land
(TBEP, 2003). The Tampa Bay watershed extends north
of the Bay to the upper reaches of the Hillsborough
River, east to the headwaters of the Alafia River, and
south to the headwaters of the Manatee River. The Bay
receives freshwater inflow from the Lake Tarpon Canal
and the Hillsborough, Palm, Alafia, Little Manatee, and
Manatee rivers. Tampa Bay empties into the Intracoastal
Waterway via Boca Ciega Bay and into the Gulf of
Mexico via the Southwest Channel and Passage Key
Inlet.
Tampa Bay is an important nursery for young fish,
shrimp, and crabs, and provides habitat for many other
types of wildlife, including wading birds, dolphins, sea
turtles, and manatees. In addition to its ecological
diversity, Tampa Bay boasts three major seaports and
contributes more than $5 billion annually from trade,
tourism, development, and fishing (TBEP, 2005). More
than 100,000 boats are registered to anglers and sailing
enthusiasts in the Tampa Bay area, and more than
2 million people live in the Bay's watershed, with the
population expected to grow 10% to 20% during the
254 National Estuary Program Coastal Condition Report
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CHAPTERS I GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tampa Bay Estuary Program
next 10 years (U.S. Census Bureau, 2001; TBEP, 2005).
Developing a plan to deal with the region's growth and
the associated pollution and stress on natural habitats is
the primary mission of the Tampa Bay Estuary Program
(TBEP) (TBEP, 2005).
Environmental Concerns
Habitat loss, declines in living resources, and the
atmospheric deposition of nitrogen are major concerns
for the TBEP. Since population growth began to soar in
1950, nearly half the Bay's marshes and 40% of its
seagrass areas have disappeared (TBEP, 2005). Although
the abundance of many Bay species has increased in
recent years, populations of other native species have
declined as their habitats have shrunk. For example, the
destruction of vital seagrass meadows caused a rapid
decline in spotted seatrout and other fish populations in
the Bay from the early 1970s through the 1980s
(Murphy, 2003). In addition, atmospheric deposition of
total nitrogen directly to the surface of Tampa Bay
accounts for about one-quarter of the nitrogen loadings
to the Bay (about 780 tons/year) (Poor et al., 2001).
This estimate does not include total nitrogen from
atmospheric sources deposited in the watershed and
washed to the estuary as stormwater. When both direct
and indirect pathways are considered, more than half of
the total nitrogen loading originates from atmospheric
sources (Poe et al., 2005a). The prevention of future
nitrogen loading to the Bay will continue to be a chal-
lenge because population growth in the Bay area is
projected to continue at a high rate.
Population Pressures
The population of the 6 NOAA-designated coastal
counties (Hillsborough, Manatee, Pasco, Pinellas, Polk,
and Sarasota) coincident with the TBEP study area
increased by more 190% during a 40-year period, from
1.2 million people in I960 to 3.3 million people in
2000 (Figure 5-24) (U.S. Census Bureau, 1991; 2001).
This rate of population growth for the TBEP study area
exceeded the population growth rate of 133.3% for the
collective NEP-coincident coastal counties of the Gulf
Coast region and was the third-highest growth rate for
all of the Gulf Coast NEPs. In 2000, these 6 counties
had a population density of 640 persons/mi2, more
than double the density of 287 persons/mi2 for the
collective NEP-coincident coastal counties of the Gulf
Coast region (U.S. Census Bureau, 2001).
Development and population pressures are especially
strong in NEP study areas that serve as major shipping
centers for commercial and recreational activities.
I
1
I '
£
I960 1970 1980 1990 2000
Year
Figure 5-24. Population of NOAA-designated counties of the
TBEP study area, 1960-2000 (U.S. Census Bureau, 1991; 2001).
Rare white-phase reddish egret.
Tampa Bay boasts about 60 nesting
pairs of reddish egrets, the largest
population in Florida (Gerold
Morrison).
National Estuary Program Coastal Condition Report 255
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tampa Bay Estuary Program
NCA Indices of Estuarine
Condition—Tampa Bay
The overall condition of Tampa Bay is rated fair
based on three of the four indices of estuarine condition
used by the NCA (Figure 5-25). The water quality
index for Tampa Bay is rated fair, the sediment quality
index is rated good, and the benthic index is rated poor;
no data were available to calculate a fish tissue contami-
nants index for Tampa Bay. Figure 5-26 provides a
summary of the percentage of estuarine area rated good,
fair, poor, or missing for each parameter considered.
This assessment is based on data collected by EMAP
from 25 NCA stations sampled in the TBEP estuarine
area in 2000. Please refer to Tables 1-24, 1-25, and 1-26
(Chapter 1) for a summary of the criteria used to
develop the rating for each index and component indi-
cator.
Water Quality Index
The water quality index for Tampa Bay is rated fair
(Figure 5-27). This index was developed using NCA
data on five component indicators: DIN, DIP, chloro-
phyll a, water clarity, and dissolved oxygen. In NOAA's
Estuarine Eutrophication Survey, Tampa Bay was listed
as having medium-to-very-high chlorophyll a levels and
medium-to-high DIN and DIP concentrations (NOAA,
1997). Results from the 2000 NCA survey show some
improvements over the previous study, with low DIN,
moderate DIP, and moderate chlorophyll a concentra-
tions measured.
Dissolved Nitrogen and Phosphorus I Tampa
Bay is rated good for DIN concentrations, with concen-
trations rated good throughout the TBEP estuarine
area. Elevated DIN concentrations are not expected to
occur during the summer in Gulf Coast waters because
freshwater input is lower and dissolved nutrients are
more rapidly utilized by phytoplankton during this
season. Tampa Bay is rated fair for DIP concentrations,
with 12% of the estuarine area rated poor for this
component indicator, 72% of the area rated fair, and
16% of the area rated good.
Overall Condition
Tampa Bay
(3.0)
Fab-
Water Quality Index (3)
Sediment Quality Index (5)
Benthic Index (I)
Fish Tissue Contaminants
Index (missing)
Figure 5-25. The
overall condition of
the TBEP estuarine
area is fair (U.S.
EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Estuarine Area
Missing
Figure 5-26. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators —Tampa Bay (U.S.
EPA/NCA).
256 National Estuary Program Coastal Condition Report
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CHAPTER 5 i GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tampa Bay Estuary Program
Water Quality Index -Tampa Bay
Site Criteria: Number of component
indicators in poor or fair condition
• Good = No more than I is fair
O Fair = ! is poor, or 2 or
more are fair
• Poor - 2 or more are poor
O Missing
Figure 5-27. Water quality index data forTampa Bay, 2000
(U.S. EPA/NCA).
C hlorophyll n i Tampa Bay is rated fair for chloro-
phyll a concentrations, with 16% of die estuarine area
rated poor for this component indicator, 52% of the
area rated fair, and 32% of the-area rated good.
Vi'ttfer ( li/r/f}' Water clarity in Tampa Bay is rated
poor. Water clarity was rated poor at a sampling site if
light penetration at 1 meter was less than 20% of
surface illumination. Expectations for water clarity are
high because one of the TBEP's goals is to re-establish
SAV. Twenty-eight percent of the TBEP estuarine area
was rated poor for water clarity, 36% of the area was
rated good, and 36% of the area was rated fair.
/)/',v/>//!•<-'<••/ Dissolved oxygen conditions
in Tampa Bay are rated good. NCA estimates for Tampa
Bay show that none of the Bay's bottom waters exhib-
ited hypoxia in late summer. Twelve percent of the estu-
arine area was rated fair for dissolved oxygen concentra-
tions, and 88% of the area was rated good.
Sediment Quality Index
The sediment quality index for Tampa Bay is rated
good; however, this index is based on measurements
of sediment TOC only (Figure 5-28). One-hundred
percent of the TBEP estuarine area was rated good for
sediment quality.
Sediment Toxicity I The NCA did not collect
sediment toxicity data for Tampa Bay in 2000; there-
fore, sediment toxicity in the Bay has not be rated for
this report.
Sediment Contaminants I The NCA did not
collect sediment contaminants data for Tampa Bay in
2000; therefore, sediment contaminant concentrations
in the Bay have not been rated for this report.
Sediment Quality Index - Tampa Bay
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
OFair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Figure 5-28. Sediment quality index data forTampa Bay, 2000
(U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 257
-------
CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tampa Bay Estuary Program
Total Organic Carbon I TOC concentrations in
Tampa Bay sediments were rated good throughout
100% of the TBEP estuarine area; therefore, Tampa Bay
is rated good for sediment TOC.
Benthic Index
The condition of benthic invertebrate communities
in Tampa Bay is rated poor, based on the Gulf Coast
Benthic Index and data collected by the NCA. Benthic
index estimates indicate that 36% of the estuarine area
has degraded benthic resources (Figure 5-31).
Fish Tissue Contaminants Index
The NCA did not assess the level of fish tissue conta-
minants in the TBEP estuarine area in 2000; therefore,
a fish tissue contaminants index for Tampa Bay was not
developed for this report.
Benthic Index -Tampa Bay
Tampa Bay Estuary Program
Indicators of Estuarine Condition
The Tampa Bay resource management community
has developed monitoring programs and environmental
indicators to measure progress towards adopted measur-
able goals for three major areas of concern: (1) water
and sediment quality; (2) habitat restoration and
protection; and (3) fish and wildlife protection. In
many cases, the TBEP also uses target indicators to help
assess progress towards these goals. Although some of
these indicators are similar to those evaluated by the
NCA, other indicators have been customized to suit the
ecology and ecosystems that are unique to Tampa Bay.
The TBEP's major indicators are chlorophyll a concen-
trations, water clarity, nitrogen loading (tons/year), acres
of seagrass, and habitat restoration and protection (acres
of oligohaline/brackish habitat). The TBEP also moni-
tors other indicators, including bacteria; metals;
organochlorine pesticides and other organic chemicals;
benthic resources; boater compliance with posted speed
zones; and trends in fishery stocks.
Site Criteria: Gulf Coast
Benthic Index Score
• Good = > 5.0
OFair =3.0-5.0
• Poor =<3.0
O Missing
Figure 5-31. Benthic index data for Tampa Bay, 2000
(U.S. EPA/NCA).
Local high school students plant marsh grass as part of a habitat
restoration project coordinated by Tampa Bay Watch (Tampa Bay
Watch).
258 National Estuary Program Coastal Condition Report
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CHAPTER 5 I GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tampa Bay Estuary Program
-So
o
_o
U
Water and Sediment Quality
Chlorophyll a concentrations and light attenuation
data help the TBEP track its progress toward improving
water clarity to meet seagrass habitat goals for Tampa
Bay. The TBEP calculates that sufficient water clarity
will be maintained for the desired level of seagrass
recovery if average annual chlorophyll a concentrations
can be maintained at levels adequate to support seagrass
recovery to depths observed in 1950 and equal to those
measured between 1992 and 1994 (TBEP, 2003;
Greening and Janicki, 2006). Similarly, light attenua-
tion (a measure of water clarity) goals that are needed to
maintain a minimum of 20% light to target depths
have been adopted for seagrass recovery. Although this
is the same light attenuation level used by the NCA, the
TBEP uses the average annual estimate from monthly
measurements taken throughout the year rather than
the summertime index period used by the NCA. Based
on the most recent assessment by the TBEP, all four
18-,
16-
14
12-
10-
8-
Old Tampa Bay
Mean Annual Chlorophyll a Concentration
! T
1970 1975 1980 1985 1990 1995 2000 2005
20-,
18
16-
14-
12
10-
8-
6-
Middle Tampa Bay
Mean Annual Chlorophyll a Concentration
1970 1975 1980 1985 1990 1995 2000 2005
major Bay segments met target levels for chlorophyll a
concentrations in 1999 through 2002, and three of four
segments met these targets in 2003 and 2004; however,
none of the segments met chlorophyll a targets during
the El Nino year (1998). Figure 5-29 shows that mean
annual chlorophyll a concentrations in the Bay have
generally declined during the past 20 years. From 1998
to 2001, light attenuation did not meet target levels in
three of the four major Bay segments (Figure 5-30).
This indicates that particles in the water, including non-
chlorophyll particles, were preventing enough light from
reaching seagrass growing on the Bay's floor, likely
hindering the growth and expansion of seagrass beds
(Poe et al., 2005b). These data correlate well with the
NCA component indicator ratings of poor for water
clarity and fair for chlorophyll a concentrations. The
TBEP has been able to track the trends in these condi-
tions because the program collects data from multiple
seasons and for multiple years, rather than the snapshot
approach used by the NCA.
Hillsborough Bay
-3
~W)
~>*
-C
CL.
2
Ic
U
36n
32
28-
24-
20-
16-
12-
R-
\
/ /I
/U / \
1 /'"' *
/ i y !
i i i \
\ , 1
A H
/ • /i
1 / \ / \ 1
1 _VA^_J_1 M _
• • v v ^J'"
1970 1975 1980 1985 1990 1995 2000 2005
Lower Tampa Bay
Mean Annual Chlorophyll a Concentration
^......
1970 1975 1980 1985 1990 1995 2000 2005
Figure 5-29. Mean annual chlorophyll a concentrations have generally declined over the past 20 years.The solid line indicates adopted
target levels, with + I and 2 standard deviation (dashed lines) (Poe et al., 2005b).
National Estuary Program Coastal Condition Report 259
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tampa Bay Estuary Program
2.0-1
.9-
.8
.7-
.6-
.5-
.4-
.3-
.2-
.1-
.0-
0.9-
0.8-
0.7
Old Tampa Bay
Mean Annual Light Attenuation
3.0-,
2.5-
2.0-
1.5-
Hillsborough Bay
Mean Annual Light Attenuation
I.O-V
1970 1975 1980 1985 1990 1995 2000 2005
2.1 -|
2.0-
1.9-
1.8-
1.7-
1.6-
1.5-
1.4
1.3-
1.2-
l.l-
1.0-
0.9-
0.8-
0.7-
Middle Tampa Bay
Mean Annual Light Attenuation
1970 1975 1980 1985 1990 1995 2000 2005
Lower Tampa Bay
Mean Annual Light Attenuation
T 0.9-
S 0.8-
0.7-
0.6-
0.5
1970 1975 1980 1985 1990 1995 2000 2005
1970 1975 1980 1985 1990 1995 2000 2005
Figure 5-30. Light attenuation indicators met target levels only in one major Bay segment (Middle Tampa Bay).The solid line indicates
light attenuation targets for each major Bay segment; dashed lines indicate I and 2 standard deviation (Poe et al., 2005b).
The TBEP uses nitrogen loading as an indicator of
overall water quality because excess nitrogen can lead to
algal blooms and decreased water clarity. The TBEP's
goal is to prevent increases in the Bay's nitrogen loading
to maintain levels measured between 1992 and 1994.
The TBEP's estimates showed that nitrogen loading
from 1995 to 2003 was higher than for the previous
period (1985-1994), primarily due to heavy rains and
runoff associated with El Nino in 1997-1998; however,
when adjusted for rainfall, nitrogen loadings showed no
change since 1985 (Poe et al., 2005a).
Elevated levels of bacteria in Tampa Bay waters can
result from septic system malfunctions and stormwater
runoff, especially during rainfall events. These elevated
levels are a potential public health concern to people
who use Tampa Bay for recreational swimming and
boating activities. In 2000, the Healthy Beaches Tampa
Bay one-year survey showed that the human health risk
from bacterial contamination was low throughout the
Bay; however, samples from 2 of the 22 sites around the
Bay and its beaches consistently exceeded suggested
guidelines for human health (Rose et al., 2001).
Although the TBEP has not yet finalized specific indica-
tors for tracking changes in bacterial contamination
levels, it is considering several indicators, including fecal
coliform bacteria and Enterococci. For areas where iden-
tifying the source of contamination is important, the
TBEP is considering conducting multiple antibiotic
resistance (MAR) tests for fecal coliform bacteria.
Bacteria develop patterns of resistance to antibiotics that
they are exposed to by their host organisms, and MAR
tests can identify the source of the bacteria based on
260 National Estuary Program Coastal Condition Report
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CHAPTER 5 | GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tampa Bay Estuary Program
these patterns of resistance. When the source of conta-
mination is known, it becomes easier to target specific
areas for cleanup and pollution prevention.
To improve sediment quality, the TBEP's goal is to
reduce toxic chemicals in contaminated sediments and
to protect clean areas. Despite the input of chemical
contaminants, including metals, organochlorine pesti-
cides, and the organic chemicals PCBs and PAHs,
TBEP data show that the overall benthic condition of
the Bay is good, with elevated contaminant levels
typically found in only a few areas (TBEP, 2003). NCA
data on sediment contaminants and sediment toxicity
were not collected for Tampa Bay.
Both the TBEP and NCA collected monitoring data
on the condition of benthic resources. During the past
10 years, TBEP partners and a national advisory group
have worked together to implement a probabilistic
benthic monitoring program based on EPA's EMAP
design and to develop narrative and numerical sediment
quality targets for key indicators of sediment quality.
The newly developed Tampa Bay Benthic Index (TBBI)
classifies sediments as healthy or degraded based on the
diversity and abundance of the observed benthos. Using
the TBBI, "hot spots" of contaminated sediments have
been found to occur in relatively concentrated areas
around large marinas, ports, and urban stormwater
outfalls (Malloy et al., in press) (Figure 5-32). No trends
in sediment quality have been observed since monitoring
was initiated in 1993 (Karlen, 2003). Although the
TBEP collected more sediment samples than the NCA,
both programs used the same benthic index method to
determine the health of the benthic community.
Healthy
Indeterminant
Degraded
Index Score
10
Healthy
Degraded
Figure 5-32. Tampa Bay Benthic Index classification (David Wade,
Janicki Environmental, Inc.).
National Estuary Program Coastal Condition Report 261
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tampa Bay Estuary Program
Summary: Tampa Bay Habitat
Restoration/Protection Master Plan
TBEP participants have agreed to the implementa-
tion of a watershed strategy for coastal habitat restora-
tion and protection, with a focus on preventing habitat
"bottlenecks" for the survival and growth of estuarine-
dependent fauna. Since die 1950s, more dian 20% of
Tampa Bay's saltwater marsh and mangrove habitat has
been lost to development, and more dian 50% of die
shoreline has been altered by seawalls, dredge-and-fill,
or other hardening activities (Lewis and Robison,
1995).
Step 1: Identify Estuarine-dependent
"Indicator" Faunal Guilds
Although the TBEP Technical Advisory Committee
(TAG) attempted to identify indicator species and their
habitat requirements, the group was not comfortable
with selecting individual species to drive this process. A
total of 38 species were identified as potential indica-
tors, ranging from filter-feeding zooplankton species to
manatees —an unmanageable number for determining
specific habitat requirements. Each species was consid-
ered to be a critical indicator by at least one TAG
member, and determining the relative importance of
one species over another proved an impossible task
within the group (Lewis and Robison, 1995).
To address this problem, members of the TAG agreed
on 10 faunal guilds (based roughly on trophic guilds
and taxonomic groups) in which all the potential indi-
cator species could be grouped. Several species were
separated into different guilds, depending upon life
stage. For example, larvae of some fish may be classified
as open-water filter feeders, but then reclassified as
shallow-water forage fish as they mature. The 10
adopted Tampa Bay guilds were the following:
• Open-water filter feeders
• Shallow-water forage fish
• Recreational/commercial finfish and shellfish
• Subtidal invertebrates
• Intertidal invertebrates
• Estuarine mollusks
• Estuarine-dependent birds
• Estuarine-dependent birds requiring freshwater
forage areas
• Estuarine reptiles
• Marine mammals (Lewis and Robison, 1995).
Step 2: Identify Habitats Critical
to Support Guilds
Based on the habitat requirements of each of the 10
guilds, 6 habitat types were identified as critical to
support the full suite of guilds:
• Open estuarine water
• Oligohaline (low-salinity) marsh
• Mangrove/Spartina
• Salt barrens
• Associated uplands
• Freshwater "frogponds" (Lewis and Robison, 1995).
Step 3: Compare Historic and Existing
Extent of Habitats
In 1950, Tampa Bay coastal areas were flown to
collect aerial photographs to examine the potential for
draining coastal wetlands with mosquito ditches to
combat an ongoing malaria epidemic at that time.
Using these historic aerial photographs, the area! extents
of each of three target habitat types (mangrove/marsh,
oligohaline marsh, and salt barren) in 1950 were esti-
mated. Current areal estimates for each of these habitat
types were similarly constructed using 1995 aerial
photographs (Lewis and Robison, 1995).
262 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tampa Bay Estuary Program
Change in Acres of Mangrove/Marsh, Oligohaline Marsh, and Salt Barren Habitat between 1950
and 1995 (Lewis and Robison, 1995)
1950 1950 1995 1995 Net Change Net Change
Habitat Type Acres Percent Acres Percent (Acres) (Percent)
Mangrove/marsh 15,894
67%
13,764
73%
-2,130
-13%
Oligohaline marsh 6,621
28%
4,117
22%
-2,504
-38%
Salt barren
1,371
5%
877
-494
-36%
Total
23,886
100%
18,758
100%
-5,128
-21%
The table compares the acreage of these three target
habitats in 1950 and 1995. Although a total of 21% of
the total acreage for these three habitats was lost
between 1950 and 1995, oligohaline habitat and salt
barren acreage losses were approximately 38% and 36%
of the 1950s acreage, respectively. Marsh and mangrove
acreage loss was approximately 13% of the 1950s
acreage. If mangrove/marsh habitat acreage remains
constant, an increase of 1,800 acres of oligohaline
habitat would be necessary to restore the historic
balance of coastal habitats to support estuarine-depen-
dent fauna! guilds in Tampa Bay (Lewis and Robison,
1995).
Step 4: Focus Efforts on Restoring the
Balance
Existing habitat-restoration efforts by agencies and
local governments in Tampa Bay from 1990 to 1995
were successful in procuring funds for the restoration of
86 acres of coastal habitat. It was expected in 1995 that
some additional funds would be available through
2005. Based on the results of this analyses and the
recognized need for a reasonable expectation of funding
sources, a target of restoring 100 acres of oligohaline
habitat every 5 years was considered equivalent to the
current rate of restoration. Thus, it was not assumed
that additional funds would be available, but rather that
funds be directed toward oligohaline marsh where
possible. Mangrove/marsh habitat restoration has
continued on an opportunity basis when appropriate
sites are available and public support and funding exist
(Lewis and Robison, 1995).
Between 1995 and 2003, the TBEP partners met
and exceeded the adopted goal to restore at least 100
acres of oligohaline habitat every 5 years. A total of
2,357 acres of estuarine habitat was restored through
2003, including 378 acres of oligohaline habitat (see
figure) (Greening et al., 2005).
Oligohaline
(378)
Marsh/
Mangrove
(1450)
Freshwater
Wetlands
(133)
Coastal
Upland
(625)
Total acres of Tampa Bay estuarine habitat restored
between 1995 and 2003 (Greening et al., 2005).
National Estuary Program Coastal Condition Report 263
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tampa Bay Estuary Program
Habitat Quality
The TBEP monitors Bay acreage and changes in
acreage over time to assess the quality of coastal
wetland, salt marsh, and mangrove and seagrass habitats
in the study area. The preservation of salt marsh and
mangrove habitats in Tampa Bay is focused on 28
priority sites. These 28 sites were given the highest
priority for Florida's Save Our Rivers and Preservation
2000 land-acquisition programs conducted by the
SWFWMD. A total of 11,494 acres of estuarine habitat
was preserved through direct land acquisitions between
1996 and 2003 (Figure 5-33) (Greening et al., 2005).
The area of historical seagrass coverage in Tampa Bay
has been reduced as a result of excessive nitrogen
loading and dredge-and-fill activities. To track and
quantify changes in the seagrass beds, aerial
photographs and mapping have been conducted every
2 years since 1988 to assess recovery trends. As shown
in Figure 5-34, seagrass acreage in Tampa Bay declined
between 1950 and 1982. Figure 5-35 illustrates the
areas of seagrass cover lost between 1950 and 1990.
Since 1992, overall seagrass acreage in the Bay has been
increasing at a average rate of about 500 acres per year.
Data from the 2004 survey show an increase in Bay-
wide seagrass coverage by 2,183 acres between 1999 and
2004 (Tomasko et al., 2005c). One exception is the Old
Tampa Bay area, which has experienced a 24% loss of
seagrass during this time period and sustained previous
losses between 1994 and 1996, suggesting a more
serious condition could exist in this area. In addition to
aerial photography and interpretation every 2 years, the
Seagrass Condition Monitoring Program (70 transects
Bay-wide) is conducted to better assess seagrass changes
in the Bay (Avery and Johansson, 2004).
Coastal Upland
(474)
Riparian
(8,754)
Marsh/Mangrove
(2,261)
Figure 5-33. Total acres of habitat acquired through land
acquisitions from 1996-2003 (Greening et al., 2005).
SEAGRASS RESTORATION AND PROTECTION:
2004 UPDATE
1950 1982 1988 1990 1992 1994 1996 1999 2002 2004
Year
Figure 5-34. Decline in seagrass acreage in Tampa Bay between 1950
and 1982 and restoration after 1982 (Tomasko et al., 2005c).
Seagrass cover
lost between
1950 and 1990
Figure 5-35. Seagrass cover lost between 1950 and 1990 in
Tampa Bay (Janicki et al., 1994).
264 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tampa Bay Estuary Program
Living Resources
The TBEP has been working to protect manatees
and ensure healthy fishing stocks in Tampa Bay. The
program uses boater compliance with posted speed
zones and trends in fishery stocks as indicators for
monitoring the success of these activities.
Manatees, which graze on seagrass beds, are often
injured or killed by power boats in shallow areas of
Tampa Bay. Boater-education efforts and a number of
different manatee-protection efforts, such as signs
marking mandatory and voluntary "go slow" areas, may
reduce the number of manatee deaths each year. The
TBEP's Manatee Awareness Coalition (MAC) has devel-
oped intensive boater-education programs aimed at
protecting manatees and the seagrass habitats they
depend upon. The MAC has also assisted in the devel-
opment of federal, state, and local boating speed zones
in Tampa Bay. The success of these efforts is being
assessed by monitoring the numbers of boaters
complying with posted speed zones, including both
voluntary and mandatory compliance.
The TBEP is also interested in ensuring that healthy
fishery stocks are maintained in the Bay. Although no
target population levels have been designated, fish and
shellfish population estimates, as measured by the
Florida Wildlife Commission's Fisheries Independent
Monitoring Program, have shown species-specific
patterns in fish abundance since 1989. The results of
monitoring efforts have documented the Bay's yearly
fluctuations in major fish species and have not recorded
any overall declining trends in the fishery stocks of
Tampa Bay (Matheson et al., 2005).
Current Projects,
Accomplishments, and Future
Goals
Since the Tampa Bay master plan was first adopted
in f 996, the TBEP has made aggressive strides toward
defining goals and taking actions for the restoration and
protection of Tampa Bay. The program has set goals for
water quality, habitat restoration and protection, and
fish and wildlife.
The TBEP's goals for water quality are to reduce
nitrogen loadings, improve water quality in the Bay for
recreation, and improve water clarity for the protection
of seagrass habitat. The TBEP is measuring its progress
toward these goals through the monitoring of water
clarity and bacteria, chlorophyll a, and nitrogen concen-
trations. The TBEP also aims to gain a better under-
standing of atmospheric deposition and to identify
sources of air pollution that are adding excess nitrogen
to the Bay (Poor et al., 2001). To learn more, the TBEP
plans to continue supporting the careful monitoring
needed to identify and track any changes in atmos-
pheric deposition to the Bay.
Habitat restoration and protection goals for Tampa
Bay are directed primarily toward restoring the historic
balance of coastal wetland habitats, preserving the Bay's
salt marsh and mangrove acreage, and protecting and
restoring the Bay's seagrass beds. The primary indicators
of success toward these goals involve tracking the
acreage of each habitat and the changes in acreage over
time. In some cases, the TBEP has set specific goals for
habitat preservation. For example, one of the program's
estuarine habitat protection goals is to preserve the Bay's
18,800 acres of salt marsh and mangrove habitat
(TBEP, 2003).
Fish and wildlife goals for Tampa Bay are directed
primarily toward developing recommendations for local
manatee protection zones and improving on-water
enforcement of fishing and environmental regulations.
The improvement of on-water enforcement was greatly
facilitated by the merger of the Florida Fish and
Wildlife Commission and the Florida Game and
Freshwater Fish Commission. This merger increased the
on-water presence in Tampa Bay.
Conclusion
The overall condition of Tampa Bay is rated fair
based on three indices of estuarine condition used by
the NCA. The TBEP has taken strong actions to estab-
lish short- and long-term goals for the protection and
restoration of this estuary. NCA and TBEP monitoring
data show that many aspects of environmental quality
in the Bay are improving, such as nitrogen load and
chlorophyll a levels and seagrass coverage. Attaining die
TBEP's ambitious goals will require continued strong
scientific involvement through monitoring, research,
and pollution management, as well as the cooperation
and dedication of a wide spectrum of stakeholders,
including the public.
National Estuary Program Coastal Condition Report 265
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Mobile Bay National Estuary Progran
Mobile Bay National Estuary Program
www.mobilebaynep.com
Mississippi Sound
Gulf of /Mexico
Mobile Boy
NEP Study Area
Background
Mobile Bay is a submerged river valley that acts as a
coastal transition zone between the Mobile Bay water-
shed and the Gulf of Mexico. The Mobile Bay water-
shed covers approximately 44,600 mi2, including
two-thirds of Alabama and portions of Mississippi,
Georgia, and Tennessee (NOAA, 1985; Mobile Bay
NEP, 2002a). It is the nation's fourth-largest watershed
in flow volume and the sixth-largest river system in area
(Mobile Bay NEP, 2002a).
Although the Mobile Bay watershed covers a vast
area, the Mobile Bay NEP study area is limited to the
portions of the watershed in Baldwin and Mobile coun-
ties in Alabama. The study area also includes Mobile
Bay, the Mobile-Tensaw Delta, the surface waters
between the Mississippi Sound and Alabama-Mississippi
state line, and the Alabama state marine waters in the
north-central portion of the Gulf of Mexico, which
extend three miles south of Dauphin Island and the
Fort Morgan Peninsula. The surface waters of Mobile
Bay cover 409 mi2, and the average depth of the Bay is
about 10 feet, which is very shallow for a bay of this size
(NOAA, 1985; Mobile Bay NEP, 2002a). Fresh water
flows into the Bay through the Mobile-Tensaw, Blakely,
266 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Mobile Boy National Estuary Program
Apalachee, Dog, Deer, Fowl, and Fish rivers. The Bay's
primary opening to the Gulf of Mexico is the Main
Pass, located between Dauphin Island and the Fort
Morgan Penninsula. The Mobile-Tensaw River Delta is
the largest intact delta in the United States and covers
approximately 289 mi of marsh, swamp, and forested
wetlands (Wallace 1994; Auburn University, 2004). The
Bay basin is characterized by barrier islands, tidal
marshes, cypress swamps, bottomland hardwoods, and
oyster reefs. The Mobile Bay NEP study area is home to
49 species of mammals, 126 species of reptiles and
amphibians, 337 species of freshwater and saltwater
fish, and 355 species of birds (Mobile Bay NEP, 2002a).
Portions of Mobile Bay and the Mobile-Tensaw Delta,
including the Tennessee-Tombigbee Waterway and the
Port of Alabama, are subject to a number of human
uses with national implications, such as commercial
fisheries, industry, tourism and recreation, and coastal
development.
An estimated 4.85 million metric tons of sediment
enter this estuary annually, with 33% being deposited
in the Mobile-Tensaw Delta, 52% in Mobile Bay, and
the remainder flowing through to the Gulf of Mexico
(Mobile Bay NEP, 2002a). Mobile Bay's salinity regime
is complex. At times, the predominant influence is
freshwater inflow from the large Mobile Bay watershed;
however, salinity levels are highly variable in Mobile Bay
because winds and tidal regimes affect the inflow of
salty Gulf of Mexico waters into the Bay from the
south. A recent hydrologic study indicated that salinity
also varies with depth in the Bay and in the major river
channels, shallower embayments, and stream channels
of the Mobile-Tensaw Delta (Braun and Neugarten,
2005).
Environmental Concerns
Habitat loss is a high-priority environmental concern
for the Mobile Bay NEP. Development, natural erosion
processes, sedimentation, dredge-and-fill practices,
exotic species, and hydrologic modifications are some of
the causes of habitat loss in the Mobile Bay NEP study
area (Mobile Bay NEP, 2002a). Between the mid-1950s
and the late 1970s, 34% of the wetlands in northern
Mobile Bay were lost, compared to the national and
southeastern wetland loss average of 8% (U.S. EPA,
1998). Loss of habitat can result in a decreased number
and/or diversity of faunal species in the Bay, increased
flooding, and impaired water quality (Mobile Bay NEP,
2002a). For example, the Mobile Bay Causeway, a
major hydrologic modification in the Mobile-Tensaw
Delta, was built in the 1920s and acts as an uninten-
tional barrier between the Delta waters to the north and
the saline waters to the south. Recent studies indicate
that the causeway has significantly impacted the ecolog-
ical function of the lower Mobile-Tensaw Delta and
may also have impacted the region's biodiversity
(Mobile Bay NEP, 2002a; Valentine et. al., 2004).
Coastal cleanup along the Mobile Bay Causeway (Mobile Bay NEP).
National Estuary Program Coastal Condition Report 267
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Mobile Bay National Estuary Program
Population Pressures
The population of the 2 NOAA-designated coastal
counties (Baldwin and Mobile) coincident with the
Mobile Bay NEP study area increased by 49% during a
40-year period, from 0.36 million people in 1960 to
0.54 million people in 2000 (Figure 5-36) (U.S. Census
Bureau, 1991; 2001). This population growth rate for
the Mobile Bay NEP study area was less than half the
population growth rate of 133.3% for the collective
NEP-coincident coastal counties of the Gulf Coast
region. The population density of these two counties in
2000 was 191 persons/mi2, which was about one-third
less than the population density of 287 persons/mi2 for
the collective Gulf Coast NEP-coincident coastal coun-
ties (U.S. Census Bureau, 2001). Development and
population pressures are especially strong in NEP study
areas that serve as major shipping centers for commer-
cial and recreational activities.
0.6
0.5
e 0.4
0.3
0.2
£ o.i
0.0
I960 1970 1980 1990 2000
Year
Figure 5-36. Population of NOAA-designated counties of the
Mobile Bay NEP study area, 1960-2000 (U.S. Census Bureau,
I99I;200I).
NCA Indices of Estuarine
Condition—Mobile Bay
The overall condition of Mobile Bay is rated fair
based on the four indices of estaurine condition used by
the NCA (Figure 5-37). The water quality and sedi-
ment quality indices are rated fair, the benthic index is
rated poor, and the fish tissue contaminants index is
rated good. Figure 5-38 provides a summary of the
percentage of estuarine area rated good, fair, poor, or
missing for each parameter considered. This assessment
is based on data collected by the Alabama Department
of Environmental Management (ADEM), in partner-
ship with the NCA, from 66 sites sampled in the
Mobile Bay NEP estuarine area in 2000 and 2001.
Please refer to Tables 1-24, 1-25, and 1-26 (Chapter 1)
for a summary of the criteria used to develop the rating
for each index and component indicator.
Overall Condition
Mobile Bay
(3.0)
Water Quality Index (3)
Sediment Quality Index (3)
Benthic Index (I)
Fish Tissue Contaminants
Index (5)
Figure 5-37. The
overall condition of
the Mobile Bay NEP
estuarine area is fair
(U.S. EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminant Index
20 40 60 80 100
Percent NEP Estuarine Area
[| [Missing
Figure 5-38. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Mobile Bay
(U.S. EPA/NCA).
268 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY-PROGRAM COASTAL CONDITION
Mobile Bay National Estuary Program
Water Quality Index
Based on NCA survey results, the water quality index
for Mobile Bay is rated fair (Figure 5-39). This index
was developed using NCA data on five component
indicators: DIN, DIP, chlorophyll a, water clarity, and
dissolved oxygen. In NOAA's Estuarine Eutrophication
Survey, Mobile Bay was listed as having medium levels
of chlorophyll a and medium-to-low DIN and DIP
concentrations (NOAA, 1997).
Dissolved Nitrogen and Phosphorus -DIN
concentrations in Mobile Bay are rated good, whereas
DIP concentrations are rated fair. Concentrations of
DIN were rated good in 89% of the estuarine area and
fair in the remaining 11 %. Eleven percent of the
estuarine area was rated poor for DIP concentrations,
53% of the area was rated fair, and 36% of the area was
rated good.
Chlorophyll a \ Chlorophyll a concentrations in
Mobile Bay are rated fair. Although no poor chlorophyll
a conditions occurred in Mobile Bay, 73% of the estu-
arine area was rated fair, and the remaining 27% of the
area was rated good for this component indicator.
Water Clarity Water clarity in Mobile Bay is
rated good. Expectations for water clarity in Mobile Bay
are low due to high river flow and naturally high
turbidity. Water clarity was rated poor at a sampling site
if light penetration at 1 meter was less than 5% of
surface illumination. Water clarity was rated poor in
only 6% of the estaurine area, 11 % of the area was
rated fair, and 83% of the area was rated good.
Dissolved Oxygen \ Dissolved oxygen conditions
in Mobile Bay are rated fair. NCA estimates show that
9% of the estuarine area was rated poor for this compo-
nent indicator, 41% of the area was rated fair, and 50%
of the area was rated good.
Water Quality Index - Mobile Bay
Site Criteria: Number of component
indicators in poor or fair condition
• Good = No more than I is fair
O Fair = I is poor, or 2 or
more are fair
• Poor = 1 or more are poor
O Missing
Figure 5-39. Water quality index data for Mobile Bay,
2000-2001 (U.S. EPA/NCA).
Throwing a cast net for bait fish, shrimp, and mullet is a popular
local tradition (Mobile Bay NEP).
National Estuary Program Coastal Condition Report 269
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Mobile Bay National Estuary Program
Sediment Quality Index
Sediment Quality Index - Mobile Bay
The sediment quality index for Mobile Bay is rated
fair because 9% of the estuarine area was rated poor for
sediment quality (Figure 5-40). This index was devel-
oped using NCA data on three component indicators:
sediment toxicity, sediment contaminants, and sediment
TOC.
Sediment Toxicity I Mobile Bay is rated poor for
sediment toxicity because 6% of the estuarine area was
rated poor for this component indicator.
Sediment Contaminants I Only 2% of the estu-
arine area was rated poor for sediment contaminant
concentrations; therefore, this component indicator is
rated good for Mobile Bay.
Total Organic Carbon I Mobile Bay is rated good
for sediment TOC. Eighty-seven percent of the estu-
arine area was rated good for this component indicator,
11 % of the area was rated fair, and only 2% of the area
was rated poor.
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
OFair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Figure 5-40. Sediment quality index data for Mobile
2000-2001 (U.S. EPA/NCA).
Navy Cove along Fort Morgan Peninsula, Alabama (Mobile Bay NEP).
270 National Estuary Program Coastal Condition Report
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CHAPTER 5 ! GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Mobile Bay National Estuary Program
Benthic Index
Based on the Gulf Coast Benthic Index and data
from the NCA, the condition of benthic invertebrate
communities in Mobile Bay is rated poor. Benthic index
estimates indicate that 30% of the estuarine area has
degraded benthic resources and another 24% of the area
is rated fair (Figure 5-41).
Benthic Index - Mobile Bay
Fish Tissue Contaminants Index
The fish tissue contaminants index for Mobile Bay is
rated good, based on concentrations of contaminants in
fish tissues (whole fish). Figure 5-42 shows that 2% of
all stations sampled where fish were caught exceeded the
EPA Advisory Guidance values used in this assessment
and were rated poor.
Fish Tissue Contaminants Index - Mobile Bay
Site Criteria: Gulf Coast
Benthic Index Score
• Good= > 5.0
OFair = 3.0-5.0
• Poor = < 3.0
O Missing
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
O Fair = Falls within Guidance range
• Poor = Exceeds Guidance range
Figure 5-41. Benthic index data for Mobile Bay, 2000-2001
(U.S. EPA/NCA).
Figure 5-42. Fish tissue contaminants index data for Mobile Bay,
2000-2001 (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 271
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CHAPTER S GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Mobile Bay National Estuary Progra
Invasive Species of Coastal
Alabama and Mississippi
The invasion of non-indigenous aquatic species is
recognized as one of die five most-critical environ-
mental issues facing die ocean's marine life (NRC,
1995). Broad efforts are underway nationwide to
combat the entry of new species into our country and
to effectively control and manage those that have
already made their way here. This is particularly impor-
tant in Gulf Coast waters because numerous vectors
exist for the introduction of non-native aquatic plant
and animal species in this region. These invasive species
pose ecological, economic, and even human health
threats.
Identifying these "alien" species was the goal of the
newly formed Alabama-Mississippi Rapid Assessment
Team (AMRAT) during the largest coast-wide rapid
assessment of living resources ever held in the Gulf of
Mexico. This team carried out rapid assessment surveys
of non-native plant and animal species in Mobile Bay
over several days in September 2003, as well as along
the Mississippi coast in August and September 2004.
The result was a "snapshot" inventory of coastal species
from which potentially invasive or nuisance species
could be identified. Such surveys offer an opportunity
for the early detection of newly introduced non-native
species, can result in early actions to curb the spread of
invasive species, and provide insight into the ways these
plants and animals arrive in a region. The assessments
can also serve as a basis for the development of manage-
ment plans to deal with potential nuisance species. The
data collected provides a baseline against which future
status and trends in non-native populations can be
assessed (Mobile Bay NEP, 2005).
During die assessment surveys, researchers used a
variety of sampling techniques to collect and identify as
many different non-native organisms as possible. These
techniques included aerial surveys, diving, elec-
troshocking, plankton and algae sampling, trawling,
seine netting, hand netting, hand picking, and scraping
fouling organisms from surfaces. Ballast water was also
sampled from ships in port and analyzed for pathogens
by an FDA laboratory. Collectively, more than 120
researchers, technicians, and support personnel from 22
state, federal, and research institutions and agencies took
part in these intensive field and laboratory efforts
(Mobile Bay NEP, 2005).
The AMRAT is a continuing effort led by a unique
partnership between co-founders Harriet Perry, Director
of die Center for Fisheries Research and Development at
the University of Mississippi's Gulf Coast Research
Laboratory (GCRL), and David Yeager, Director of the
Mobile Bay NEP. The team was founded is based on die
premise diat few individual organizations have all the
resident scientific expertise or logistical ability to carry
out a survey of this scale. The AMRAT partnership
represents an innovative way to provide diis capability.
The surveys were coordinated with the Gulf and South
Atlantic Regional Panel on Aquatic Invasive Species. The
Gulf States Marine Fisheries Commission administers
this panel and manages the data from die surveys.
More than 730 samples were collected during the
AMRAT assessment surveys (Yeager and Perry, 2004).
Many native and non-native animals and plants were
classified and accessioned into the GCRL museum to
serve as type specimens and aid in future study and
identification. The surveys validated the presence of
previously identified or suspected non-native plants and
animals and added some new information. New arrivals
include a population of Nile tilapia (Oreochromis
niloticus) and the wild taro plant (Colacasia antiquorum),
both noted in Mississippi, and the Asian clam
(Corbicula flumined), noted in both Alabama and
Mississippi. In addition, two new state records for
molluscs in Alabama were established: a marine snail
(Turbonilapuncta) and a bicolor purse-oyster (Isognomon
bicolor). Changes in the distribution of certain native
plants such as smooth cord grass (Spartina alterniflora)
and their replacement by an invasive, Phmgmites, were
also noted. This was also the first time seaweeds and
benthic algae in Alabama coastal waters were cataloged.
272 National Estuary Program Coastal Condition Report
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!
CHAPTER 5 ! GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Mobile Bay Notional Estuary Program
A researcher collects samples during AMRAT 2004 (Pam Fuller, USGS).
The AMRAT assessment surveys were unqualified
successes and were highly acclaimed by participants,
observers, and reviewers. In 2006, the AMRAT
program was awarded a first place Gulf Guardian
Award by EPA's Gulf of Mexico Program. The survey
is identified by the Gulf and South Atlantic Regional
Panel on Aquatic Invasive Species in their current
strategic plan as a model for Gulf—wide assessment
efforts, and other areas of the Gulf Coast are consid-
ering implementing similar programs. Current plans
for coastal Louisiana surveys, led by the Louisiana Sea
Grant Program and the Barataria-Terrebonne NEP
(BTNEP), are using the lessons learned from AMRAT.
Discussions also are underway to extend the AMRAT
surveys into areas of the Florida panhandle as early as
2006. Additional information about AMRAT and a full
list of its partners and participants is available from the
following Web sites: http://www.mobilebaynep.com,
http://nis.gsmfc.org, and http://www.gsmfc.org.
National Estuary Program Coastal Condition Report 273
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Mobile Bay National Estuary Program
Mobile Bay National Estuary
Program Indicators of Estuarine
Condition
The Mobile Bay NEP has not yet finalized indicators
for tracking the health of Mobile Bay, but will complete
this task in 2006. Several successful public participation
workshops resulted in a preliminary list of indicators
that may be used to easily communicate the ecological
condition of the Bay to the public. These indicators are
either currently monitored or considered sufficiently
important to warrant additional monitoring. Progress
has also been made in developing status and trends data
in preparation for a future report on the five issue areas
identified in the Mobile Bay NEP Comprehensive
Conservation and Management Plan, Volume I—A Call
to Action (Mobile Bay NEP, 2002a). This progress
includes initiating a new sub-estuary water quality
monitoring project; instituting a continuous Bay-wide
time series monitoring project; performing rapid assess-
ments to monitor invasive species; analyzing more than
20 years of collected fish population data to evaluate
trends; performing the first comprehensive modern
survey of SAV and a comparison with historical data;
establishing a completely updated NWI wetland survey
and upland habitat survey for Mobile and Baldwin
counties; utilizing a land-use cover map for Baldwin
County; and performing other baseline data collection
to provide a solid scientific basis for evaluating status
and trends.
Water and Sediment Quality
The Mobile Bay NEP has established explicit goals
and objectives for Mobile Bay and its subbasins,
including developing allowable water quality-based
loadings sufficient to maintain water quality standards
(or TMDLs) for pathogens, nutrients, toxic chemicals,
and other pollutants. Water quality indicators for
Mobile Bay include chlorophyll a, total phosphate,
ammonia, nitrates+nitrites, dissolved oxygen, salinity,
pH, biochemical oxygen demand, turbidity, and water
temperature. ADEM also monitors the Bay for several
toxic chemicals, including mercury, cadmium,
chromium, DDT, and PAHs (Hutchings and Yokel,
2000).
Portions of some rivers in the Mobile Bay NEP study
area do not fully support their current or proposed
water-use classifications because of nutrient enrichment
and/or low dissolved oxygen levels; however, dissolved
oxygen standards were actually achieved in 95% of the
coastal waters across the Bay (Baya et al., 1998).
Nutrient levels in the Bay are affected by point and
non-point sources of nitrogen and phosphorus, rainfall
levels, freshwater flows in the Mobile Bay River Delta,
and a variety of cycling processes between the sediment
and water column. Data collected between 1993 and
1995 show that more than 55% of Mobile Bay had
bottom dissolved oxygen levels below 4 mg/L and that
30% of the Bay had levels below 2 mg/L, indicating
poor conditions for dissolved oxygen (Mobile Bay NEP,
2002a). Eight percent of the sites monitored by the
Alabama Monitoring and Assessment Program
(ALAMAP) indicated dissolved oxygen deficiencies
(below the 5-mg/L criteria) (ADEM, 2004).
ADEM's pathogen indicators for Mobile Bay are
fecal coliform and Enterococci. Existing pathogen data
have been deemed insufficient for developing a true
status and trends relationship because these data have
focused on short time frames and narrow geographic
regions. In 1996, 412 of 451 mi2 (91%) of shellfish
waters in the study area did not fully support their
intended use classifications due to pathogen indicators
(Mobile Bay NEP, 2002a). The 2002 303 (d) list of
impaired stream segments in the Mobile Bay NEP
study area indicates that, of the 23 stream segments
listed, 11 were listed in part due to pathogen contami-
nation (ADEM, 2002).
Metals and chemicals that are slow to break down in
the environment accumulate in Mobile Bay sediments
over time, and the Mobile Bay NEP uses a variety of
indicators to assess the Bay's sediment quality. These
indicators include analyzing sediments for metals and
pesticides, monitoring human activities such as fuel
spills and pesticide use, and assessing shellfish contami-
nation levels (Mobile Bay NEP, 2002b). Of the 23
303(d)-listed streams located in the Mobile Bay NEP
study area, 8 were impaired, in part due to mercury
contamination (ADEM, 2002).
274 National Estuary Program Coastal Condition Report
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CHAPTER 5 | GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Mobile Bay National Estuary Program
Habitat Quality
The Mobile Bay NEP monitors indicators of habitat
quality and habitat loss, including upland habitat extent
and conversion. Changes in SAV habitat acreage,
wetland areas, beach and dune extent, and shoreline
habitats are all indicators that have been monitored to
evaluate habitat loss in the Mobile Bay system (Hutch-
ings and Yokel, 2000). Probable impacts of habitat loss
include population declines and/or the extinction of
native species. More than 50% of Alabama's wetland
acreage was lost between 1780 and 1980 (Mobile Bay
NEP, 2002a). In 2002, the Mobile Bay NEP used aerial
photography and CIS technology to assess the extent of
SAV in Mobile Bay. The study showed that Mobile
Bay's SAV acreage decreased by more than 55% in
Mobile County (1940-2002) and by more than 88% in
Baldwin County (1955-2002) (Barry A. Vittor &
Associates, Inc., 2005). In light of this trend, the rela-
tionship between water quality (including nutrient
loading and water clarity) and SAV loss is a subject for
further evaluation by the Mobile Bay NEP and its
partners.
Living Resources
Indicators for monitoring living resources include
distribution, diversity, and composition of benthic
assemblages; distribution and diversity of native fishes;
abundance of exotic species; number of rare listed
species by year and habitat acreage; and other measures.
The population of many wildlife species in the Mobile
Bay NEP study area have been diminished due to over-
harvesting, pollution, and habitat loss. The Bay and
coastal waters of the study area are home to many rare
and endangered species of wildlife, including five species
of sea turtles; the West Indian manatee; sperm whales;
bottlenose dolphins; and the American bald eagle.
Thirty-six of the Bay's 337 fish species are listed as at
risk (Mobile Bay NEP, 2002a).
More than 350 species of birds can be found in the
Mobile Bay NEP study area each year. Some of the
birds are year-round residents, whereas others pass
though the area during migrations or reside in the area
for part of the year. These birds include waterfowl, colo-
nial wading birds, and seabirds. Gaillard Island supports
the only nesting colonies of the brown pelican, laughing
gull, Caspian tern, and sandwich tern in Alabama.
Nests of brown pelicans on the island increased from 4
in 1983 to 4,597 in 1997 (Stout et al., 1998).
Although there are no fish advisories specific to
Mobile Bay, the State of Alabama has issued a statewide
advisory for mercury in king mackerel from all estu-
arine/coastal Alabama waters (U.S. EPA, 2005a). The
State of Alabama currently employs the FDA standards
set for the sale of seafood in issuing fish consumption
advisories based on mercury contamination. Discussion
is underway to adopt the stricter EPA standards for fish
tissue contamination. Using EPA standards would
significantly expand the number of streams in Alabama
with fish consumption advisories based on mercury
contamination (Bouma, 2005).
The brown pelican population has made a remarkable recovery
on Gaillard Island (Mobile Bay NEP).
National Estuary Program Coastal Condition Report 275
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Mobile Bay National Estuary Program
Environmental Stressors
A variety of human activities are used as indicators to
help evaluate environmental stressors in Mobile Bay.
These indicators include population growth, sanitary
waste per capita, changes in land use and land cover,
increase in impervious surfaces, the number and type of
development permits, the number of boating and
fishing licenses, the number of municipal sewage viola-
tions, and the air pollution index for Mobile Bay.
Indicators of hydrologic modification are also moni-
tored and include the acres of floodways impacted by
development, extent of bulkheading, areal extent of
dredging activities, areal extent of wetland filling and
excavation, linear extent of stream and creek channeliza-
tion, shoreline loss and erosion, and other parameters
(Hutchings and Yokel, 2000).
Current Projects,
Accomplishments, and Future
Goals
Major goals of the Mobile Bay NEP include
attaining and maintaining water and sediment quality
that is sufficient to support healthy aquatic communi-
ties and designated human uses; providing optimum
fish and wildlife habitat; and restoring historic plant
and animal populations. The Mobile Bay NEP is also
concerned with providing consistent and enforceable
land- and water-use management that ensures smart
growth for sustainable development. High-priority
issues of the Mobile Bay NEP are habitat loss, rapid
coastal growth and development and attendant non-
point source pollution, water quality, growth manage-
ment, municipal treatment facilities, public education,
and industrial impacts on the Bay. Several of the Mobile
Bay NEP's current projects and accomplishments are
described below:
• The Mobile Bay NEP, in partnership with the
Dauphin Island Sea Lab, the University of South
Alabama's Center for Estuarine Studies, and the
Weeks Bay NERR, has established the first long-
term network of real-time, continuous time-series
water monitoring stations in Mobile Bay. This
project provides basic data from three new sites in
Mobile Bay and links an established site at the
Weeks Bay NERR. The most recent addition to
the network, the site at Middle Bay, is unique in
that its vertical water-profiling system provides
information throughout the water column. The
measured meteorological and hydrographic para-
meters include wind speed and direction, air
temperature, barometric pressure, solar radiation,
quantum radiation, precipitation, water tempera-
ture, water height, salinity, dissolved oxygen, and
turbidity.
A major GIS study and water monitoring
program is now underway to identify the sources
of pathogen introduction into one of the local
303(d)-listed streams, with an aim toward taking
necessary remediation or corrective actions.
Two major habitat-restoration grants have been
awarded to local organizations by the Mobile Bay
NEP. The first grant helped eliminate the world's
second-most invasive weed, cogori grass, on a
portion of a 2,400-acre site bordering theTensaw
River. The second grant provides for purchase and
further restoration of an 8-acre marsh on Mon
Luis Island.
A SAV restoration manual has been completed
and printed, and a SAV restoration project
involving numerous volunteers is in progress
(Turner et al., 2005).
In concert with the USAGE and other partners,
several restoration projects are in the planning
stages, including the use of dredge material to
restore nesting habitat on a barrier island; the
creation of additional oyster bottom, emergent
marsh, and SAV habitat; and the examination of
the feasibility of increased public access.
In partnership with the Nature Conservancy, the
Mobile Bay NEP has completed an assessment of
habitat-protection needs and identified priority
sites for acquisition and conservation protection,
as well as other priority sites for restoration efforts.
The first efforts toward implementing these goals
are underway. In addition, a database is being
created in partnership with the Mississippi-
Alabama Sea Grant to catalogue restoration and
acquisition efforts on the Mississippi and Alabama
coasts and to help better direct and refine efforts
in this area.
276 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Mobile Bay National Estuary Program
The Mobile Bay NEP facilitated discussions and
planning between conservation, recreational, and
commercial interests through a public process.
These activities resulted in the closure of a portion
of the upper reaches of Mobile Bay to shrimp
trawling, thereby reducing the impacts of bycatch
on juvenile fmfish and of trawling on SAV
habitat.
The Mobile Bay NEP is partnering with the City
of Mobile and the State Lands Division on the
creation of a significant public access site and the
restoration of its adjoining marsh area.
A preliminary report has been prepared
concerning the probable impacts of the Mobile
Bay Causeway on freshwater and saltwater
hydrology in the Mobile-Tensaw River Delta, as
well as its attendant impact on aquatic living
resources (Valentine et al., 2004).
Since 2001, the Mobile Bay NEP has helped to
conduct an Oyster Gardening Program. This
program has many purposes, including collecting
data on oysters, improving water quality through
oyster filtration, protecting young oysters by
improving their conditions, creating habitat for
other marine species that form the base of the
food chain, and educating the community about
oysters.
Conclusion
Based on data collected by the NCA, the overall
condition of Mobile Bay is rated fair. The Mobile Bay
NEP has not yet finalized its indicators for tracking the
health of Mobile Bay, but this task will be completed in
2006. The preliminary list of indicators includes a
variety of parameters used to assess water, sediment, and
habitat quality; habitat loss; living resources; hydrologic
modifications; and the effects of human activities on the
estuary. Several of these parameters are currently being
monitored in the study area, and the Mobile Bay NEP
is making progress towards developing status and trends
data for these indicators.
National Estuary Program Coastal Condition Report 277
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barataria-Terrebonne National Estuary Program
Barataria-Terrebonne National Estuary Program
BARATARIA-TERREBONNE
NATIONAL ESTUARY PROGRAM
Background
The study area of the Barataria-Terrebonne National
Estuary Program (BTNEP) is located between the
Mississippi and Atchafalaya rivers in southern Louisiana
and covers approximately 6,500 mi2 (Caffey and
Breaux, 2000). Bayou Lafourche separates this area into
two basins: Barataria Basin to the east and Terrebonne
Basin to the west. The integration of salt water and
fresh water begins offshore, where water, sediment,
nutrients, and pollutants from the Mississippi River mix
with the salt water of the Gulf of Mexico. Approxi-
mately 735 species of birds, finfish, shellfish, reptiles,
Terrebonne Bay
amphibians, and mammals spend all or part of their life
cycle in the estuary, with several of these species catego-
rized as either threatened or endangered (BTNEP,
2005).
Significant industrial and municipal effluents enter
the Mississippi River between Baton Rouge and New
Orleans, contributing to nutrient and contaminant
loadings in the estuary system. Several natural and man-
made waterways transect the estuary system, including
the Gulf Intracoastal Waterway and the Barataria
Waterway. Open water and wetlands are the predomi-
nant land-use classifications in the region and have been
278 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barataria-Terrebonne Notional Estuary Program
increasing in area since 1956 (Figure 5-43). More than
three quarters of the BTNEP study area (3.2 million
acres) is classified as open water or wetlands, leaving
approximately one million acres for urban and agricul-
tural uses (Moore and Rivers, 1996).
100%
1956 I960 1964 1968 1972 1976 1980 1984 1988 1992 1996 2000
Year
Figure 5-43. Change in the total area of water in the BTNEP
estuarine area between 1956 and 2000 (BTNER 2002).
Environmental Concerns
The priority issues affecting the BTNEP study area
include habitat loss, hydrological modification, reduced
sediment flows (reduction in sediment inputs), eutroph-
ication, pathogen contamination from untreated sewage
and stormwater discharges, toxic substances, and
declines in living resources (Battelle, 2003). Sediment
loss (depletion), in conjunction with the subsidence
(sinking) of marshes, is the most significant problem in
the Barataria-Terrebonne Estuarine Complex. The
construction of levees to protect human communities
from floods has eliminated vital inputs of fresh water
and sediments from reaching the estuaries; these inputs
are needed to keep the marshes above water. Sea-level
rise, erosion, canal dredging, and the construction of
navigation and oil-exploration channels further
contribute to this problem. The impacts of hydrological
modifications in the BTNEP study area are numerous;
man-made canals create paths for waters of higher
salinity to intrude inland, destroying freshwater plants
and forcing animals either to adapt or to relocate. Each
year, about 15 mi2 of wetlands in the study area are lost,
and a half-acre of the Complex's coastal wetlands turns
to open water every 15 minutes (BTNEP, 2002;
Focazio, 2006b). Because this coastal marsh habitat
provides a considerable buffer from the flooding,
storms, and hurricanes that threaten the Louisiana
coastline, this loss of habitat is detrimental to the health
of fish and wildlife populations and to human develop-
ment. Many species that depend on habitat in the
Barataria-Terrebonne Estuarine Complex are either
threatened or endangered, including the American bald
eagle, brown pelican, piping plover, least tern, Louisiana
black bear, and American alligator.
Population Pressures
The population of the 16 NOAA-designated coastal
parishes coincident with the BTNEP study area
increased by 28% during a 40-year period, from
1.3 million people in 1960 to 1.6 million people in
2000 (Figure 5-44) (U.S. Census Bureau, 1991; 2001).
This rate of population growth for the BTNEP study
area was the lowest growth rate of any of the Gulf Coast
NEPs and constitutes less that one-fourth of the popu-
lation growth rate of 133.3% for the collective NEP-
coincident coastal counties of the Gulf Coast region. In
addition, the population density of the BTNEP study
area in 2000 was 184 persons/mi2, the second-lowest
density of the Gulf Coast NEPs and about one-third
less than the population density of the region's collective
NEP-coincident counties (287 persons/mi2) (U.S.
Census Bureau, 2001). Development and population
pressures are moderate in this study area, which serves
as a major center for commercial fishing and shellfish,
the petrochemical industry, and recreational activities.
1.8
x-s 1.6
VI
I '•<
1 '•*
.£ 1.0
I 0.8
1 0.6
Q. 0.4
°- 0.2
0.0
I960
2000
Figure 5-44. Population of NOAA-designated counties of the
BTNEP study area, 1960-2000 (U.S. Census Bureau, 1991; 2001).
National Estuary Program Coastal Condition Report 279
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barataria-Terrebonne National Estuary Progran
NCA Indices of Estuarine
Condition—Barataria-
Terrebonne Estuarine Complex
The overall condition of the Barataria-Terrebonne
Estuarine Complex is rated fair based on the four
indices of estuarine condition used by the NCA (Figure
5-45). The water quality, sediment quality, and benthic
indices are rated fair, and the fish tissue contaminants
index is rated poor. Figure 5-46 provides a summary of
the percentage of estuarine area rated good, fair, poor,
or missing for each parameter considered. This assess-
ment is based on data collected by the State of
Louisiana and the NCA from 25 stations sampled in
the BTNEP estuarine area in 2000 and 2001. Please
refer to Tables 1-24, 1-25, and 1-26 (Chapter 1) for a
summary of the criteria used to develop the rating for
each index and component indicator.
Overall Condition
Barataria-Terrebonne
Estuarine Complex
(2.5)
Water Quality Index (3)
Sediment Quality Index (3)
Benthic Index (3)
Fish Tissue Contaminants
Index (I)
Figure 5-45. The
overall condition of
the BTNEP estuarine
area is fair (U.S.
EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80
Percent NEP Estuarine Area
100
Missing
Figure 5-46. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Barataria-
Terrebonne Estuarine Complex (U.S. EPA/NCA).
Water Quality Index
Based on NCA survey results, the water quality index
for the Barataria-Terrebonne Estuarine Complex is rated
fair (Figure 5-47). This water quality index was devel-
oped using NCA data on five component indicators:
DIN, DIP, chlorophyll a, water clarity, and dissolved
oxygen. In NOAAs Estuarine Eutrophication Survey,
Barataria Bay was listed as having high to hypereu-
trophic chlorophyll a concentrations and high DIN and
DIP concentrations (NOAA, 1997). In the same report,
the Terrebonne and Timbalier bays were listed as having
high chlorophyll a and DIP concentrations and
moderate DIN concentrations.
280 National Estuary Program Coastal Condition Report
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CHAPTER 5 i GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barataria-Jerrebonne National Estuary Program
Dissolved Nitrogen and Phosphorus I DIN
and DIP concentrations in the BTNEP estuarine area
are rated good. For both component indicators, 4% of
the estuarine area was rated poor, 16% of the area was
rated fair, and 80% of the area was rated good.
Chlorophyll ft Chlorophyll a concentrations in
the Barataria-Terrebonne Estuarine Complex are rated
fair. Although only 4% of the estuarine area was rated
poor for chlorophyll a concentrations, 64% of the area
was rated fair, and 32% of the area was rated good.
Water Clarity Water clarity in the BTNEP estu-
arine area is rated poor. Expectations for water clarity
are low due to high river flow and naturally high
turbidity for these estuaries. Water clarity was rated
poor at a sampling site if light penetration at 1 meter
was less than 5% of surface illumination. Fifty-two
percent of the estuarine area was rated poor for water
clarity, 20% of the area was rated fair, and 28% of the
area was rated good.
Dissolved Oxygen I Dissolved oxygen conditions
in the BTNEP estuarine area are rated good. NCA esti-
mates show that none of the estuarine area was rated
poor for this component indicator, 4% of the estuarine
area was rated fair, and 96% of the area was rated good.
Water Quality Index - Barataria-Terrebonne Estuarine
Complex
Site Criteria: Number of component
indicators in poor or fair condition
• Good = No more than I is fair
OFair
I is poor, or 2 or
more are fair
• Poor = 2 or more are poor
O Missing
Good
24%.
Poor
4%
Figure 5-47. Water quality index data for the Barataria-
Terrebonne Estuarine Complex, 2000-2001 (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 281
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Borotaria-Terrebonne National Estuary Program
Sediment Quality Index
Sediment Quality Index - Barataria-Terrebonne
Estuarine Complex
The sediment quality index for the Barataria-
Terrebonne Estuarine Complex is rated fair. This index
was developed using NCA data on three component
indicators: sediment toxicity, sediment contaminants,
and sediment TOG. Although all three component
indicators received good ratings for the Barataria-
Terrebonne Estuarine Complex, the index is rated fair
because greater than 5% of the estuarine area was rated
poor for sediment quality (Figure 5-48).
Sediment Toxicity I Sediment toxicity is rated
good for the BTNEP estuarine area because none of
the area was rated poor for this component indicator.
Sediment Contaminants I Only 4% of the
BTNEP estuarine area was rated poor for sediment
contaminant concentrations; therefore, the Complex
is rated good for this component indicator.
Total Organic Carbon I Sediment TOC is rated
good for the BTNEP estuarine area. Eighty-eight
percent of the estuarine area was rated good for this
component indicator, and only 8% of the area was rated
poor. NCA data on TOC concentrations were unavail-
able for 4% of the BTNEP estuarine area.
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
O Fair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Missing Poor
4/0 12%
Figure 5-48. Sediment quality index data for the Barataria-
Terrebonne Estuarine Complex, 2000-2001 (U.S. EPA/NCA).
Eroding marsh peninsula between Bayous Perot and Rigolettes, Barataria Basin (DrTerry McTigue, NOAA, NOS, ORR).
282 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Borotoria-Terrebonne National Estuary Program
&
Benthic Index
*•»«
Fish Tissue Contaminants Index
Based on NCA survey data and the Gulf Coast
Benthic Index, the condition of benthic invertebrate
communities in the Barataria-Terrebonne Estuarine
Complex is rated fair. Benthic condition index estimates
indicate that 16% of the area had degraded benthic
resources, and NCA data on benthic condition were
unavailable for 20% of the BTNEP estuarine area
(Figure 5-49).
Benthic Index - Barataria-Terrebonne Estuarine
Complex
The fish tissue contaminants index for the Barataria-
Terrebonne Estuarine Complex is rated poor. Figure
5-50 shows that 27% of all stations sampled where fish
were caught exceeded the EPA Advisory Guidance
values used in this assessment and were rated poor.
Fish Tissue Contaminants Index -
Barataria-Terrebonne Estuarine Complex
Site Criteria: Gulf Coast
Benthic Index Score
• Good = > 5.0
OFair =3.0-5.0
• Poor = < 3.0
O Missing
Missing
20%
Poor
16%
~
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
O Fair = Falls within Guidance range
• Poor = Exceeds Guidance range
Poor
.27%
Figure 5-49. Benthic index data for the Barataria-Terrebonne
Estuarine Complex, 2000-2001 (U.S. EPA/NCA).
Figure 5-50. Fish tissue contaminants index data for the
Barataria-Terrebonne Estuarine Complex, 2000-2001 (U.S. EPA/
NCA).
National Estuary Program Coastal Condition Report 283
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barataria-Terrebonne National Estuary Progra
Maritime Forest Ridge and Marsh
Restoration at Port Fourchon,
Louisiana
The Maritime Forest Ridge and Marsh Restoration
(MFRMR) at Port Fourchon, LA, is a vital migratory
bird habitat-restoration project that is intended to serve
as an example for similar coastal ridge restoration work
and to provide useful scientific data for future coastal
restoration projects. To achieve these goals, the BTNEP
has offered its assistance in many capacities. For
example, the BTNEP and its Migratory Bird Action
Plan Team worked as liaisons between the bird-
watching community and the Greater Lafburche Port
Commission to encourage the project. The BTNEP has
also served as a liaison between the Greater Lafburche
Port Commission and various federal and state agencies
during the permitting process.
The project's vision includes plans to restore a
historic maritime forest ridge that has eroded and
subsided since the 1950s; vegetate the ridge with woody
plant species that provide excellent habitat for migratory
birds; and eventually add boardwalks, trails, and an
interpretive center.
More than 60 acres each of salt marsh and maritime
forest ridge have been created. The construction phase
of this project involved grading the land to transform a
linear mound into a sloped ridge habitat, with a eleva-
tion gradient ranging from marsh elevation at 1.6 feet
above sea level in the tidal zone to 8 feet above sea level
at the peak of the ridge. Future phases of die MFRMR
project development include plans to extend die project
area linearly by several thousand feet over the next few
years. Funding for the initial conceptualization and
construction phase came from several sources, including
$100,000 of direct project support from the Louisiana
Department of Natural Resources (LDNR); a $100,000
grant from the Shell Oil Company; and $45,000 in
project support from various project partners (Personal
communication, Blanchard, 2005). The partners for
this phase of the project listed below.
Partners for Restoring the Historic Maritime Forest Ridge
Barataria-Terrebonne National Estuary Program
Barataria-Terrebonne Estuary Foundation
Greater LaFourche Port Commission
Gulf of Mexico Foundation
Gulf of Mexico Program
The Louisiana Nature Conservancy
Louisiana Department of Natural Resources
Natural Resource Conservation Service
National Oceanic and Atmospheric Administration Orleans Audubon
Shell Oil Company
Terrebonne Bird Club
284 National Estuary Program Coastal Condition Report
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CHAPTER 5 I GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barataria-Terrebonne Notional Estuary Program
Now that this phase of the MFRMR project is
nearing completion, the BTNEP is working closely with
another group of partners (e.g., NOAA, the Gulf of
Mexico Partners) to vegetate and monitor the MFRMR
project area. The newly formed BTNEP Volunteer
Program has hosted three volunteer planting events at •
the MFRMR project area. These events involved more
than 150 volunteers who planted nearly 11,000 plants
(Personal communication, Blanchard, 2005). Because of
the logistics involved in transporting people and plants
to the MFRMR site, project partners were needed to
ferry materials and volunteers to the site by boat, as well
as to provide lunches, drinks, and T-shirts to the volun-
teers. Partners who contributed to the volunteer efforts
on the ridge include the BTNEP, Barataria-Terrebonne
Estuary Foundation, Greater Lafourche Port
Commission, USDA NRCS Plant Materials Center,
ES&H Environmental Safety Consulting, Inc.,
Louisiana Department of Wildlife and Fisheries
(LDWF), and Lafourche Parish Coastal Zone
Management (CZM). Groups that volunteered their
efforts for the different planting events on the ridge
include the Lockport Middle School, Bayou Lafourche
Marine Institute, Boy Scouts of America, Shell Oil
Company Summer Interns, and University of New
Orleans PIES Camp students. The efforts of these
volunteers are important because the vegetation
helps to stabilize the shoreline and slopes of this
restored habitat against hurricanes. A future large-
scale volunteer effort is also planned, where volun-
teers will plant woody trees and shrubs on the
crown of the ridge.
The BTNEP recognizes that any efforts to
restore the rapidly vanishing coastal lands of south
Louisiana not only require sound scientific footing,
but also the full support and involvement of the
citizens who live, work, and play in the lands and
waterways of coastal Louisiana. By engaging resi-
dents through volunteerism, die BTNEP not only
forges new community partnerships and fosters
public support for coastal restoration, but it also
puts a face on the efforts to save diis landscape by
allowing citizen volunteers to work shoulder-to-
shoulder with the biologists, geologists, engineers,
and other scientists who work on the immense
problems faced by the coastal Louisiana region.
Additional information about the MFRMR and
other restoration projects in the BTNEP study area
is available by contacting the BTNEP or by visiting
die programs Web site at: http://www.btnep.org.
BTNEP volunteers plant marsh plants to restore vegetation to the ridge site
(BTNEP).
National Estuary Program Coastal Condition Report 285
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barataria-Terrebonne National Estuary Program
Barataria-Terrebonne National
Estuary Program Indicators of
Estuarine Condition
Water and Sediment Quality
The following water and sediment quality indicators
are used by the BTNEP to assess estuarine condition:
• Eutropic conditions and nutrient levels
• Hypoxia (i.e., area of dead zone)
• Pathogens (e.g., fecal coliform at swimming and
shellfish-harvesting areas)
• Levels of toxic substances in water and sediment
• Oyster bed closures.
Eutrophic conditions and nutrient levels in the
Barataria-Terrebonne Estuarine Complex are monitored
at a series of 15 sites within the region, and trend
studies show that all sites have been classified as having
either medium or high nutrient conditions under
EPA/NOAA's guidelines for evaluating nutrient concen-
trations. Measurements of chlorophyll a levels during
the past 20 years provide strong evidence that eutrophi-
cation is occurring in this system because many sites
show an increase in chlorophyll a concentrations over
time (Rabalais et al., 1995).
The extent of mid-summer hypoxia (dissolved
oxygen levels below 2.0 mg/L) in bottom waters often
affects up to 8,000 mi of the Louisiana and Texas
continental shelf and has been associated with large fish
kills in the Barataria-Terrebonne Estuarine Complex
(Battelle, 2003). Hypoxic events are good indicators for
monitoring nutrient pollution loads associated with
wastewater treatment and agricultural runoff. Over
time, nearshore bottom dissolved oxygen concentrations
have typically varied from 4 to 8 mg/L in the Complex,
with sampling results indicating that persistent hypoxia
tends to occur from mid-May to mid-September
(Rabalais et al., 1995). Overall, data on dissolved
oxygen in bottom waters are limited, but research has
shown that hypoxic conditions (area of dead zone) in
the Complex are most likely to occur in poorly flushed
areas, deeper channels, and areas receiving organic
loading from sewage or other wastewater outfalls.
Pathogens from sewage pollution in the Complex are
associated with illnesses in humans who swim in
contaminated waters or who eat contaminated oysters.
To help reduce the consumption of pathogen-contami-
nated oysters, the Louisiana Department of Heath and
Hospitals Molluscan Shellfish Program monitors fecal
coliform bacteria levels in surface waters on a monthly
basis in the oyster bed areas of the Barataria-Terrebonne
Estuarine Complex (Battelle, 2003). Fecal coliform in
the Complex comes from a variety of sources, including
poorly functioning on-site septic systems, pasture land
runoff, and waste from marsh animals, nutria, and
waterfowl.
The presence of toxic substances in BTNEP waters
can be measured by testing the surface water and sedi-
ment or by testing the fish that feed in these waters.
Atrazine is a concern in the surface waters of the
BTNEP study area and is measured through the direct
testing of these waters. Concentrations of atrazine in
the surface waters of the Upper Terrebonne basin have
exceeded the EPA maximum contaminant level (MCL)
of 3 ppb for drinking water (Battelle, 2003). Copper,
lead, arsenic, chromium, and cadmium concentrations
have declined since the 1980s, whereas mercury levels
have remained fairly constant. Although contamination
is fairly widespread in scope, the areas of most concern
are on the periphery of the Complex, such as Oyster
Bayou and Tiger Pass. Other contaminants have been
detected in fish or shellfish, which accumulate toxic
substances from the food they eat and from the sur-
rounding water and sediments. Toxics detected in fish
and crustaceans of the Barataria-Terrebonne Estuarine
Complex include pesticides, metals, volatile organic
compounds (VOCs), and PCBs (Rabalais et al., 1995).
Habitat Quality
The LDNR, NRCS, and other programs collectively
monitor the number of acres of salt marshes and oligo-
haline (low salinity) habitat that have been restored in
the BTNEP study area since 1986; however, the data
needed to make actual assessments of habitat quality
and functionality on a Complex-wide basis do not yet
exist (Battelle, 2003). A large number of data sets
specific to individual restoration projects are available,
but these data sets can not be readily combined to
286 National Estuary Program Coastal Condition Report
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CHAPTER 5 : GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Barataria-Terrebonne National Estuary Progran
report on status and trends for habitat restoration across
the entire Barataria-Terrebonne Estuarine Complex.
The Louisiana Coastwide Reference Monitoring System
has been proposed to help make large restoration efforts
a possibility. This effort requires collecting estuary-wide
information, including land/water ratios; vegetation
composition and cover; frequency of flooding; salinity;
and sedimentation and erosion.
Living Resources
The following list of indicators is used by the
BTNEP to measure changes in living resources:
• Endangered or threatened species (e.g., abundance
and nesting success of brown pelican and
American bald eagle)
• Waterfowl (e.g., abundance of mottled duck)
• Density of alligator nests
• Invasive species (e.g., acres of marsh damaged by
invasive nutria)
• Number of fish consumption advisories and
mercury levels in fish tissue.
Both the bald eagle and the brown pelican popula-
tions show signs of recovery following near extinction in
the area due to reproductive failures associated with
pesticide exposures. Today, Louisiana's brown pelicans
occur throughout their historic range, and this reintro-
duction program is a success story in Louisiana's conser-
vation efforts. The number of successful nests in the
Barataria-Terrebonne Estuarine Complex has risen from
675 in 1990 to more than 6,500 in 2001 (BTNEP,
2002). Bald eagles are monitored for the number of
successful nests, active nests, and fledglings produced
(Battelle, 2003).
Status and trend reports indicate that 35 species of
waterfowl have been reported in the Complex, which is
of international significance as a wintering ground for
migratory waterfowl species. Drought, marsh loss,
commercial development, and predation all affect the
Complex's duck population on an annual basis and can
provide information about degradation or loss of
habitat (Condrey et al., 1995). The Audubon Society's
Christmas bird count is another indicator used by the
BTNEP, and monitoring the abundance of shorebird
species has been suggested as a priority indicator need.
The density of alligator nests in the Barataria-
Terrebonne Estuarine Complex is directly indicative
of population size and indirectly indicative of the
abundance of fresh marsh habitats. The LDWF has
been conducting an annual nest survey since 1991 to
establish quotas, measure abundance, and assess produc-
tivity. The number of alligator nests is often affected by
drought conditions and salinity levels (Battelle, 2003).
The growth of invasive species and the resultant
damage they cause is another priority concern of the
BTNEP. Among the most serious invasive species found
in the Barataria-Terrebonne Estuarine Complex are
water hyacinth, water spangle, Eurasion watermilfoil,
Hydrilla, alligatorweed, Chinese tallow tree, and zebra
mussel. The LDWF spends about $1.5 million annually
on non-native aquatic plant control (BTNEP, 2002)
and also collects data on the damage caused by nutria
herbivory using periodic aerial surveys over brackish
marsh areas (Figure 5-51). Nutria are a concern because
they damage agricultural crops and irrigation dikes and
consume the roots of marsh plants, thereby accelerating
land loss. Damage and control costs for zebra mussels is
also a good indicator of the magnitude of this invasive
species problem.
The number of fish consumption advisories issued in
the Barataria-Terrebonne Estuarine Complex is an indi-
cator of the overall human health risk associated with
toxic contaminants in seafood. Fish sampling is
conducted by the Louisiana Department of Environ-
mental Quality near facilities that have experienced
chemical spills or demonstrated poor waste manage-
ment practices. There are no waterbody-specific fish
consumption advisories within the BTNEP study area;
however, Louisiana has issued a statewide mercury advi-
sory for king mackerel in all coastal waters, which
includes BTNEP estuarine waters (U.S. EPA, 2005a).
120
£ 100
u
< 80
-8 60 ]
\ 40-
o
£ 20
1991 1993 1994 1995 1997 1998 1999 2001 2002 2004
Year
Figure 5-51. Estimated acreage damaged by nutria herbivory
(BTNER 2002).
National Estuary Program Coastal Condition Report 287
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Baratario-Terrebonne National Estuary Program
Environmental Stressors
In coastal Louisiana, more than 160,000 registered
recreational vessels share the water with thousands of
commercial vessels. Dumping sewage overboard can
contaminate surface waters, sediments, and fishery stock
with pathogens and was the suspected cause of at least
two outbreaks of illness due to the consumption of
contaminated oysters in the 1990s. To reduce instances
of overboard dumping, many marinas offer boat pump-
out stations for the collection of sewage from recre-
ational and commercial vehicles. The cumulative
number of boat pump-out stations in the Barataria-
Terrebonne Estuarine Complex is another indicator
tracked by the LDWF, and the number of stations has
risen considerably at both commercial and recreational
marinas since the early 1990s. The availability of these
stations is critical to reducing overboard discharge of
sewage to swimming and oyster-growing areas in the
region and to controlling outbreaks of gastroenteritis
that have been associated with Norwalk viruses and site
closures since 1982 (Battelle, 2003).
Current Projects,
Accomplishments, and Future
Goals
The BTNEP has produced videos, posters,
brochures, booklets, and presentations and has made
them available to teachers and other educators through
their Web site. Materials are available for kindergarten
through 12th grade and feature a range of media,
including coloring books, videos, slides, and posters.
The BTNEP has also created Action Plan Teams to
implement its CCMP, The Estuary Compact: A Public
Promise to Work Together to Save the Barataria and
Terrebonne Basins (Moore and Rivers, 1996), in each of
five different areas: Water Quality, Habitat, Living
Resources, Cultural Heritage, and Economic
Development. The BTNEP is actively implementing a
large habitat-restoration program, which includes
numerous projects to rebuild wetlands, ridges, barrier
islands, and other habitats, such as the following:
• Point Aux Chenes stormwater redirection —
This pilot-scale restoration project is diverting
stormwater discharge into the Point Aux Chenes
wetlands. These discharges are expected to reduce
salinity, stimulate the growth of emergent vegeta-
tion, and encourage sedimentation in the wetland.
• SAV research - The BTNEP is working to assess
the habitat value and to develop new methods for
restoring various SAV throughout the Complex.
• Invasive species workshops — These workshops
educate the public about which invasive species
have infiltrated the BTNEP study area, how these
species impact the region's ecosystem, and what
steps government agencies and individuals need to
take to combat these invasive species.
Conclusion
The data from the NCA suggest thai: the overall
condition of the BTNEP study area is rated fair and
that water quality is rated fair. Water quality indicators
used by the BTNEP show that eutrophication is a
continuing concern across the Complex and will require
ongoing monitoring of nutrient and dissolved oxygen
concentrations. In addition, the monitoring of chloro-
phyll a levels helps provide the more conclusive data
needed to support future analyses of eutrophic condi-
tions. Although the NCA's dissolved oxygen measure-
ments show that none of the Complex's bottom water
areas exhibited hypoxia, these measurements were made
during a relatively short time period and provide only a
snapshot of the summer dissolved oxygen concentra-
tions. The BTNEPs partner agencies conduct moni-
toring on a year-round basis rather than during a single
summer-sampling period, as is used by the NCA. The
more intensive year-round monitoring allows
researchers to evaluate more subtle changes and trends
that may only be discernable when comparing data over
a more extensive period of time. For example, NCA
sampling may not have occurred during one of the
periods of hypoxia that often occur in the Complex
during late summer; however, these hypoxic events are
sometimes detected when more frequent monitoring
intervals are used by the BTNEP. The BTNEP's indica-
tors also demonstrate that pathogens are an issue within
the estuarine system. Sediment quality tests have
provided limited information, but indicate contamina-
tion around discharge areas in the estuary basin.
288 National Estuary Program Coastal Condition Report
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CHAPTERS : GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Galveston Bay Estuary Program
Galveston Bay Estuary Program
t PROGRAM OF THE TCEQ
www.gbep.state.tx.us
Background
Galveston Bay is a subtropical estuary located on the
southeastern shore of the upper Texas Gulf coast. The
Bay is composed of five major subbays: Trinity, Upper
Galveston, Lower Galveston, East, and West bays. The
combined area of the five subbays is 384,000 acres (600
mi2), surrounded by 1,171 miles of shoreline (GBEP,
2005; HARC, 2005b). The estuary is fed by two major
rivers (Trinity and San Jacinto rivers) and is bordered by
low-lying wetlands, two barrier islands, and a peninsula.
The waters of Galveston Bay can be characterized as
East Boy
Upper Galveston Bay
'Lower Galveston Bay
Gu/fof Mexico
West Bay
NEP Study Area
well mixed and quite shallow (averaging 7 feet) and are
made shallower in some places by extensive oyster reefs
(GBEP, 2005). The Bay has increased in volume during
the past 50 years due to natural and anthropogenic
subsidence, as well as sea level rise and dredging opera-
tions (Lester and Gonzalez, 2003). Major habitats in
the Bay include estuarine and freshwater marsh, mud-
flats, seagrass beds or SAV, oyster reefs, and open water.
Galveston Bay is used extensively for recreational and
commercial activities, and the potential for large-scale
human impacts is great. Galveston Bay is one of the
National Estuary Program Coastal Condition Report 289
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Galveston Bay Estuary Program
largest sources of seafood for Texas, as well as one of the
major oyster-producing estuaries in the country. The
oysters, crabs, shrimp, and finfish harvested from
Galveston Bay are worth a combined $ 19 million
annually (Sage and Gallaway, 2002). One-third of the
state's commercial fishing income and more than half of
the state's recreational fishing expenditures are derived
from Galveston Bay (GBEP, 2005). The Port of
Houston is the second-largest port in the United States
in tonnage and the eighth-largest port in the world
(Sage and Gallaway, 2002). Along with the ports of
Texas City and Galveston, the Port of Houston supports
the region's petrochemical industries, which are the
largest in the nation and the second-largest in the world
(Port of Houston Authority, 2006). These industries
combine to produce one-half of the nation's chemicals
and one-third of the nation's petroleum refining (U.S.
EPA, 2002a).
Extending back from the river mouths, the entire
Galveston Bay watershed covers 33,000 mi2, includes
the metropolitan areas of Houston-Galveston and
Dallas-Ft. Worth, and is home to nearly half of the
population of Texas (GBEP, 2005). The surrounding
watershed is composed of a variety of habitats, ranging
from open prairies and coastal wetlands to riparian
hardwoods and pine-dominant forests, and these habi-
tats support numerous plant, fish, and wildlife species.
To increase public awareness and help address nega-
tive trends in wetland loss, habitat degradation, and
non-point source pollution, the Galveston Bay Estuary
Program (GBEP) was formed in 1989. Efforts of the
GBEP are concentrated in the 4,200-mi2 lower water-
shed, which is demarked by the dams that form Lake
Houston on the San Jacinto River and Lake Livingston
on the Trinity River. Following the establishment of its
CCMP, The Galveston Bay Plan: The Comprehensive
Conservation and Management Plan for the Galveston
Bay Ecosystem, the GBEP now continues its work as part
of the Texas Commission on Environmental Quality
(TCEQ) (GBNEP, 1995).
Environmental Concerns
With Galveston Bay in the shadow of the nation's
fourth-largest city, the environmental concerns of
highest priority for the GBEP are wetland loss and
habitat degradation, point and non-point source pollu-
tion, and chemical and petroleum product spills from
barges and industry (Sage and Gallaway, 2002).
Non-point source pollution in Galveston Bay is attrib-
uted to a variety of sources, including runoff from
thousands of gas stations, residential lawns, failing septic
systems, driveways, parking lots, industries, farms, and
other sources. Accidental spills and the deliberate
dumping of oil and other contaminants potentially
harm the habitat and living resources oi: Galveston Bay.
Other priority issues for Galveston Bay include new and
existing introductions of aquatic and terrestrial exotic
nuisance species, contaminated runoff from urbanized
areas, and the increasing and often competing demands
for fresh water. Additionally, sediment in the Houston
Ship Channel exceeds levels of concern for a number of
hazardous chemicals, including PCBs, DDT, dioxin,
and heavy metals.
Population Pressures
The population of the 7 NOAA-designated coastal
counties (Brazaria, Chambers, Fort Bend, Galveston,
Harris, Liberty, and Waller) coincident with the GBEP
study area increased by 182% during a 40-year period,
from 1.6 million people in I960 to 4.4 million people
in 2000 (Figure 5-52) (U.S. Census Bureau, 1991;
2001). This rate of population growth for the GBEP
study area exceeded the population growth rate of
133.3% for the collective NEP-coincident coastal coun-
ties of the Gulf Coast region. In 2000, the GBEP-coin-
cident coastal counties had a population density of 651
persons/mi2 (the highest of all the Gulf Coast NEPs).
.2 2
I960 1970 1980 1990 2000
Year
Figure 5-52. Population of NOAA-designated counties of the
GBEP study area, 1960-2000 (U.S. Census Bureau, 199 I; 2001).
290 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Calveston Bay Estuary Program
This density was more than double the density of 287
persons/mi2 for the collective NEP-coincident coastal
counties of the Gulf Coast region (U.S. Census Bureau,
2001). Development and population pressures are espe-
cially strong in this NEP because it serves as a major
center for international commerce; oil refinery and
other petrochemical industries; commercial fish and
shellfishing operations; and recreational activities for
these coastal communities.
NCA Indices of Estuarine
Condition—Galveston Bay
The overall condition of Galveston Bay is rated fair
based on the four indices of estuarine condition used by
the NCA (Figure 5-53). The water quality index is rated
poor, the sediment quality index is rated fair to poor,
the benthic index is rated fair, and the fish tissue
contaminants index is rated good to fair. Figure 5-54
provides a summary of the percentage of estuarine area
rated good, fair, poor, or missing for each parameter
considered. This assessment is based on data collected
by the Texas Park and Wildlife Department (TPWD)
and NCA from 28 stations sampled in the GBEP
estuarine area in 2000 and 2001. Please refer to Tables
1-24, 1-25, and 1-26 (Chapter 1) for a summary of the
criteria used to develop the rating for each index and
component indicator.
Overall Condition
Galveston Bay
(2.5)
Water Quality Index (I)
Sediment Quality Index (2)
Benthic Index (3)
Fish Tissue Contaminants
Index (4)
Figure 5-53. The
overall condition of
the GBEP estuarine
area is fair (U.S.
EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Estuarine Area
I Missing
Figure 5-54. Percentage of NEP estuarine area achieving each
rating for all indices and component indicators — Galveston Bay
(U.S. EPA/NCA).
Significant declines in the number of blue crabs have been
noted in the West Bay (Texas Sea Grant College Program).
National Estuary Program Coastal Condition Report 291
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Gaiveston Bay Estuary Program
Water Quality Index - Gaiveston Bay
Water Quality Index
Based on NCA survey results, the water quality
index for Gaiveston Bay is rated poor (Figure 5-55).
This water quality index was developed using NCA data
on five component indicators: DIN, DIP, chlorophyll a,
water clarity, and dissolved oxygen. In NOAA's Estua-
rine Eutrophication Survey, Gaiveston Bay was listed as
having medium chlorophyll a and medium-to-low DIN
and DIP concentrations, with elevated concentrations
occurring in tidal freshwater areas (NOAA, 1997).
Dissolved Nitrogen and Phosphorus I Gaiveston
Bay is rated fair for DIN concentrations and rated poor
for DIP concentrations. Thirteen percent of the estu-
arine area was rated poor for DIN concentrations,
whereas 68% of the estuarine area was rated poor for
DIP concentrations. As discussed later in this profile,
the GBEP also monitors nutrients in the bays and trib-
utaries of the GBEP estuarine area.
Chlorophyll a I Gaiveston Bay is rated fair for
chlorophyll a concentrations. Although only 4% of the
estuarine area was rated poor for chlorophyll a concen-
trations, 71% of the area was rated fair, and 13% of the
area was rated good. NCA data on chlorophyll a
concentrations were unavailable for 12% of the GBEP
estuarine area.
Water Clarity I Water clarity in Gaiveston Bay is
rated poor because 28% of the estuarine area was rated
poor. Expectations for water clarity are similar to those
for normally turbid estuaries, with water clarity rated
poor at a sampling site if light penetration at 1 meter
was less than 10% of surface illumination.
Dissolved Oxygen I Dissolved oxygen conditions
in Gaiveston Bay are rated good. Seventy-one percent of
the estuarine area was rated good for dissolved oxygen
concentrations, 29% of the area was rated fair, and
none of the area was rated poor.
Figure 5-55. Water quality index data for Gaiveston Bay,
2000-2001 (U.S. EPA/NCA).
Sediment Quality Index
The sediment quality index for Gaiveston Bay is
rated fair to poor because greater than 5% of the estu-
arine area was rated poor for sediment quality (Figure 5-
56). This index was developed using NCA data on three
component indicators: sediment toxicity, sediment
contaminants, and sediment TOG.
Sediment Toxicity \ Sediment toxicity is rated
good for Gaiveston Bay because only 3% of the estu-
arine area was rated poor; however, NCA data on sedi-
ment toxicity were unavailable to evaluate 31 % of the
GBEP estuarine area.
292 National Estuary Program Coastal Condition Report
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CHAPTER 5 i GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Calveston Bay Estuary Program
Sediment Contaminants \ Sediment contami-
nant concentrations were rated poor in 10% of the
GBEP estuarine area; therefore, this component indi-
cator is rated fair.
lotdl Organic Carbon TOG concentrations in
Galveston Bay sediments were rated good in 100% of
the estuarine area; therefore, Galveston Bay is rated
good for this component indicator.
Sediment Quality Index - Galveston Bay
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
OFair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Poor
13%
Figure 5-56. Sediment quality index data for Galveston Bay,
2000-2001 (U.S. EPA/NCA).
Benthic Index
Based on NCA survey data and the Gulf Coast
Benthic Index, the condition of benthic invertebrate
communities in Galveston Bay is rated fair. Benthic
index estimates indicate that 16% of the estuarine area
had degraded benthic resources (Figure 5-57).
Benthic Index - Gatveston Bay
Site Criteria: Gulf Coast
Benthic Index Score
• Good = >5.0
OFair = 3.0-5.0
• Poor = < 3.0
O Missing
Poor
16%
I
Figure 5-57. Benthic index data for Galveston Bay, 2000-2001
(U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 293
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Galveston Bay Estuary Program
Fish Tissue Contaminants Index
The fish tissue contaminants index for Galveston Bay
is rated good to fair. Figure 5-58 shows that 11% of all
stations sampled where fish were caught exceeded the
EPA Advisory Guidance values used in this assessment
and were rated poor.
Fish Tissue Contaminants Index - Galveston Bay
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
O Fair = Falls within Guidance range
• Poor = Exceeds Guidance range
Poor
11%
Fair
7%
Figure 5-58. Fish tissue contaminants index data for Galveston
Bay, 2000-2001 (U.S. EPA/NCA).
Galveston Bay Estuary Program
Indicators of Estuarine Condition
The GBEP implements a regional monitoring
program to foster effective cooperation by all agencies
that participate in monitoring activities for Galveston
Bay and to help prevent duplication of effort. Through
the coordination of monitoring efforts, the GBEP's
regional monitoring program ensures that data are
available to assess trends in ecological condition and
provides online access to this data at http://www.
gbep.state.tx.us. The GBEP partners include the TCEQ
Surface Water Quality Monitoring Program, which
collects data describing surface water quality, sediment
quality, and benthic organisms; the Texas Clean Rivers
Program (administered locally by the Houston-
Galveston Area Council), which collects water quality
data; and the TPWD, which collects fishery indepen-
dent and dependent data, as well as data on fish tissue
contamination, water quality, and sediment quality in
conjunction with the NCA. Other monitoring data
tracked by the GBEP include oil spill incidents (Texas
General Land Office [GLO]), colonial nesting bird
counts (FWS), freshwater inflows (Texas Water
Development Board), and fish advisories, oyster harvest
area closures, and illnesses related to seafood consump-
tion (Texas Department of State Health Services
[DSHS]).
Water and Sediment Quality
The GBEP's formal indicators for monitoring water
quality conditions in the estuary include dissolved
oxygen, nitrogen (e.g., nitrate, nitrite, ammonia), total
phosphorus, chlorophyll a, total suspended solids/
turbidity, salinity, water temperature, pH, pathogens
(e.g., Enterococri, fecal coliform), BOD, andTOC.
Of the five subbays in the GBEP study area, only
Christmas Bay exhibited a slightly increasing trend in
dissolved oxygen concentrations, which rose from 7.0
to 8.0 mg/L between 1969 and 2001 (Lester and
Gonzalez, 2003).
To help measure changes in nutrient levels over time,
the TCEQ monitors ammonia, total nitrogen, and total
phosphorus. Declines in annual average ammonia levels
have been observed in several areas of Galveston Bay,
with the most dramatic decline seen in the Houston
Ship Channel. For the most part, annual average
concentrations remain below screening levels. Nitrate-
nitrite concentrations were highest in the Houston Ship
Channel, which demonstrated an increasing trend from
about 0 mg/L in 1969 to 1.75 mg/L in 2001. The
Intracoastal Waterway East exhibited a significant
declining trend in nitrate-nitrite, and the Trinity River
had a significant declining trend in phosphorus (since
1969), which has slowed in recent years. None of the
five subbays of Galveston Bay showed trends exceeding
294 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Galveston Bay Estuary Program
the estuarinc screening levels for nutrients (Lester and
Gonzalez, 2003).
Annual average concentrations of chlorophyll a have
declined across all Galveston Bay subbays and tribu-
taries since 1969, with the largest decreasing trend in
chlorophyll a concentrations found in the Houston
Ship Channel, San Jacinto River, and Texas City Ship
Channel. Monthly average concentrations of chloro-
phyll a did not show a significant trend in any of the
five subbays in Galveston Bay. NCA data collected in
2000 and 2001 for the West Bay region had annual
averages similar to those of the TCEQ data, but chloro-
phyll a concentrations were slightly higher in this region
(Lester and Gonzalez, 2003).
The Galveston Bay Indicators Project rates the area's
subbays and tributaries based on the percentage of data
samples that exceed the state's screening criteria (Figure
5-59). Using water quality screening levels developed by
the TCEQ and indicator criteria developed specifically
for Galveston Bay, the project rates Galveston Bay water
quality (for nutrients and chlorophyll a) in the subbays
as moderate to good for the period 1990-2003, as
compared to the poor rating based on NCA survey data
for 2000-2001 (Lester and Gonzalez, 2005). It should
be noted that the DIN and DIP criteria used by the
NCA survey are much more stringent than those used
by the State of Texas; TCEQ estuarine screening levels
for nitrogen and phosphorus are 0.26 and 0.22 mg/L,
respectively. In addition, NCA sampling does not
differentiate between criteria levels for Bay versus tribu-
tary waters. Nutrients in Galveston Bay proper remain
fairly constant during the year; however, nutrient
concentrations in Galveston Bay tributaries are highest
in the summer months, when NCA data are collected.
In the Galveston Bay Indicators Project evaluation, the
tributary Buffalo Bayou was the only Bay segment to
receive a poor rating for nutrients and chlorophyll a
data because it exceeded the screening level more than
30% of the time between 2000 and 2003. It is also
worth noting the improving trend overall for Galveston
Bay since the 1970s (Lester and Gonzalez, 2005);
however, the TCEQ is currently reviewing its estuarine
nutrient criteria, which might change the results for this
indicator.
Nutrients and Chlorophyll a
Concentrations
Upper and Lower Galveston Bay
Rating
% Above Screening Level
Very Good: 0-5
Good: 6-15
Fair: 16-30
Poor: > 30
Figure 5-59. TCEQ water quality ratings for Galveston Bay nutrients and chlorophyll a concentrations
(Lester and Gonzalez, 2005).
National Estuary Program Coastal Condition Report 295
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CHAPTER 5 GULF COAST NATIONAL [ESTUARY PROGRAM COASTAL CONDITION
Galveston Bay Estuary Program
Case Study on Changes in
Freshwater Wetland Habitat
The Galveston Bay region is attracting a growing
urban and industrial sector, and the regions population
is expected to double to approximately 8 million by
2025 (Sage and Gallaway, 2002; H-GAC, 2003). The
Galveston Bay watershed contains a wealth of unique
freshwater wetland complexes that provide critical
human and ecological services, including attenuation of
water pollution, floodwater retention, wildlife habitat,
and recreational opportunities. The GBEP recognizes
that preserving these valuable resources requires a better
understanding of the status and trends of the wetland
habitat; therefore, the GBEP partnered with the Texas
Coastal Watershed Program of the Texas Cooperative
Extension in 2003 to determine the status and trends in
the wetlands of Galveston Bay.
To perform a wetlands analysis, the partners
conducted an inventory that was similar to the FWS's
NWI program. The last FWS NWI for the Galveston
Bay region was completed in 1992; however, the 1992
data are not directly comparable to those gathered
during the new wetland inventory. The methods of
identifying wetland areas have improved since the 1992
NWI, and the new inventory might identify areas that
were missed in 1992. To account for this, the GBEP
and Texas Cooperative Extension chose to consider the
1992 NWI data as a subset of the wetlands in the
region at the time. To analyze changes in the wetlands,
these data were directly compared to aerial photographs
of the same areas taken in 2000 or 2002 as part of the
new inventory.
Coastal prairie wetlands in Texas (Dr. John Jacobs.Texas Cooperative Extension/
Texas Sea Grant).
296 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Galveston Bay Estuary Prograr,
In 1992, the Galveston Bay watershed contained
294,556 acres of freshwater, non-tidal wetlands
(e.g., palustrine, lacustrine, riverine). The new inventory
results showed that 285,432 acres remained in the
subset, representing a loss of 9,124 acres or 3.1%.
These losses were attributed to industrial, commercial,
and residential development (70%); fill activities (26%);
and open-water development, such as man-made ponds
and lakes (3%). These loss estimates are conservative
figures, and resource experts believe that actual losses are
much higher due to the wetland areas that were likely
missed in the 1992 NWI. Consistent with the pattern
of urban growth spreading into more rural areas, the
greatest wetland losses (13%) occurred in Harris
County, which includes the city of Houston (see figure)
(Jacob and Lopez, 2005).
The results of the GBEP/Texas Cooperative Exten-
sion inventory study will be used to educate citizens on
the implications of wetland loss, as well as to work with
local governments and others to identify key parcels for
preservation.
Wetland Loss %
0% - S%
6% -10%
11%-25%
»26%-40%
• 41% -70%
• 7I%-IOO%
Wetland loss due to urban growth (Jacob and Lopez, 2005).
National Estuary Program Coastal Condition Report 297
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Calveston Bay Estuary Program
Total suspended solids showed declining trends in
annual average concentrations across all subbays and
tributaries of the Galveston Bay system, with the excep-
tion of Upper Galveston Bay, Lower Galveston Bay, and
Cedar Bayou (Lester and Gonzalez, 2003). Galveston
Bay is naturally turbid because of its shallow depth and
fine sediments; however, dredging activities, commercial
fisheries, and natural and man-made erosion assist in
promoting this turbid nature.
The pathogen indicators monitored by the TCEQ in
Galveston Bay are Enterococci, E. coli, and fecal coli-
form, with concentrations of fecal coliform sampled
since 1973. According to the 2005 Galveston Bay
Indicators Project, the areas of Galveston Bay with the
greatest number of TCEQ criteria-level exceedences for
fecal coliform bacteria are Buffalo Bayou, the Houston
Ship Channel, Clear Creek, and Dickinson Bayou
(Figure 5-60). In addition, Buffalo Bayou, White Oak
Bayou, and Dickinson Bayou are the subjects of
ongoing TMDL studies (Lester and Gonzalez, 2005). A
declining trend in fecal coliform was found in the East
Intracoastal Waterway area, but the other four major
subareas of the Bay did not show a significant trend for
fecal coliform. Elevated concentrations of fecal coliform
in the middle reach of Bastrop Bayou have drawn
considerable attention from the public in the past. The
areas with the highest concentrations of Enterococci were
the Houston Ship Channel, East Intracoastal Waterway,
San Jacinto River, and Trinity Bay, whereas areas with
the lowest concentrations were the Galveston Channel,
Texas City Channel, Christmas Bay, Bastrop Bayou
Complex, Dickinson Bayou/Dickinson Bay, and East
Bay (Lester and Gonzalez, 2003).
Organic matter content in Galveston Bay is
measured as TOC, and annual average TOC concentra-
tions have declined in all subbays and tributaries of
Galveston Bay since 1973. The TCEQ also reports five-
day BOD to help measure the breakdown and decom-
position of organic matter in the Bay. Sufficient data
only exist for three of the five subbays in Galveston Bay,
and none of these subbays exhibited significant trends
for BOD (Lester and Gonzalez, 2003). This finding
aligns with NCA data, which found Galveston Bay to
be in good condition for TOC concentrations.
In Galveston Bay, sediments, metals, and commonly
measured organic compounds appear to follow the same
general spatial distribution, as do most of the other
water quality parameters. Elevated concentrations of
these contaminants occur in regions of runoff, fresh-
water inflow, and waste discharges, and lower, relatively
Pathogens
% Above Screening Level
Figure 5-60. TCEQ water quality ratings for Galveston Bay pathogens (Lester and Gonzalez, 2005).
298 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Galveston Bay Estuary Program
uniform concentrations occur in the open bay. The
upper Houston Ship Channel generally has the maximal
concentration of these contaminants (Lester and
Gonzalez, 2005).
Habitat Quality
Wetland loss and declines in SAV are of significant
concern for the GBEP, but support from federal, state,
and local agencies; area non-profit organizations; and
industry activities are slowly helping to mitigate losses
through restoration and preservation. The Galveston Bay
Plan calls for the restoration of 8,600 acres of estuary
marsh and 1,400 acres of SAV (GBNEP, 1995).
Wetland loss between 1950 and 1989 has been esti-
mated to be between 700 and 1,000 acres a year, or a
net loss of over 30,000 acres (White et al., 1993). The
total acreage of wetlands lost to dredge-and-fill activities
over time has increased to 20% of the net losses esti-
mated for Galveston Bay (Sage and Gallaway, 2002). A
recent estuarine wetland inventory indicated that more
than 1,181 of the 118,072 acres of emergent marsh
identified in 1995 were lost by 2002. The loss of
approximately 830 of these acres was induced by human
activities (Webb, 2005). The GBEP continues to work
with its partners to monitor trends in wetlands loss.
Salinity, turbidity, and rainfall patterns seem to be the
controlling factors for natural seagrass growth in
BIRDS
Galveston Bay. In the 1950s, SAV was estimated at
2,500 acres; in 1989, SAV was estimated to be approxi-
mately 700 acres—more than a 70% decline. Since
1989, evidence suggests a rebound, with new areas
being established adjacent to wetland restoration sites in
West Bay (Sage and Gallaway, 2002).
Living Resources
The GBEP uses several indicators to measure trends
in living resources. Data are collected from a variety of
sources, including theTPWD, Texas DSHS, and FWS.
These indicators are the following:
• Abundance of selected colonial waterbird species
(e.g., great blue heron, white ibis)
• Abundance of selected finfish species (i.e.,
measured from bag seine, shrimp trawl, or gill
net)
• Episodes of seafood contamination and issuance
of advisories (e.g., oyster harvest-area closures, fish
consumption advisories, and elevated chemical
contaminant levels in fish tissue).
Figure 5-61 shows 20-year population trends for
several bird and finfish species monitored in the GBEP
study area. Of the 19 species of colonial nesting water
birds tracked between 1973 and 2001, 9 exhibit
negative trends, whereas others appear stable or are
FISH
I
Figure 5-61. Bird and finfish population trends in Galveston Bay (Lester and Gonzalez, 2005).
National Estuary Program Coastal Condition Report 299
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Galveston Bay Estuary Program
increasing. As with other parts of the country, brown
pelicans have been a success story in returning from the
brink of extinction (HARC, 2005a). Significant declines
in blue crab numbers have been noted in West Bay.
Gulf killifish have demonstrated a significant decline in
the estuary and could indicate a declining quantity of
fringing wetlands. Bay anchovy have demonstrated a
significant increasing trend in West Bay, and pink
shrimp have demonstrated a significant increasing trend
in Upper and Lower Galveston Bay (Lester and
Gonzalez, 2003). For areas of the Houston Ship
Channel and Upper Galveston Bay, the Texas DSHS
has issued several seafood consumption advisories for
contaminants, including PCBs and dioxins, in species
The Advisoiy for the Upper Houston Ship
Cternal includes waters from tie US Hwy 90
such as blue crab, catfish, and speckled trout (Figure 5-62)
(Lester and Gonzalez, 2005).
Environmental Stressors
The GBEP's regional monitoring program also uses
human activities as indicators to assess the health of the
estuary. The Texas GLO has monitored the amount, type,
date, and location of 11 petroleum products spilled into
the waters of 4 counties in the Galveston Bay watershed
(Brazoria, Chambers, Galveston, and Harris). Between
1998 and 2002, a total of 262,010 gallons of petroleum
products were spilled into the waters of Galveston Bay
(Lester and Gonzalez, 2003).
Bridge downstream to the Lynchburg Ferry.
pesticides, and PCBs in al species of for.
and HUB crabs.
US Hwy 90 >
Bridge
The Advisory ferine Houston Ship Channel
and Upper Gatveston Bay indu
the Lynchburg Fsrry downstream to Red Bluff
Point in Upper Galveston Bay.
OrtarnimnteindudedM
catfish and Hue crab*, ar
seatrout (speckled trout).
ns in al species of
PCBs h spotted
Upper
Galveston Bay
Red Bluff
Point
It is recommended that people not consume more than
one meal, riot to exceed 8 ounces, from these areas each
month. Children and women of cNWbearing age should
not consume any fish or blue crabs from these areas.
\
80
Figure 5-62. Seafood consumption advisory areas designated in 1990, 2001, and 2005 (Lester and Gonzalez, 2005).
300 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Galveston Bay Estuary Program
Current Projects,
Accomplishments, and Future
Goals
To protect and restore wetland habitats, the GBEP is
encouraging better use of dredge material. When
disposed of improperly, dredge materials can adversely
modify wetland habitats; however, these materials also
can be beneficial if used to create, restore, or enhance
estuary habitats (e.g., bird rookery islands). The efforts
of the GBEP and its partners have led to the restoration
of 8,000 acres of habitat (Personal communication,
Johnston, 2006). The GBEP is also working with local
governments toward increasing wetland and habitat
conservation through the promotion of water quality,
recreation, and flood-control benefits and by assisting
with grant writing and the development of stormwater
management plans. Other priorities of the GBEP
include controlling harmful exotic species; promoting
water conservation, stormwater management, and tech-
nical assistance programs; assessing the safety of
consuming seafood from Galveston Bay; and assisting
septic system owners and small WWTP operators.
Some of the invasive species of highest ecological
concern in Galveston Bay include Chinese tallow, giant
salvinia, Hydrilla, red imported fire ant, Brazilian
pepper, water hyacinth, and channeled apple snail.
Conclusion
Based on data from the NCA estuarine survey, the
overall condition of Galveston Bay is rated fair. Data
from the GBEP and its partners indicate that, in spite
of the large human population and increasing resource
demands, Galveston Bay remains productive and, for
the most part, healthy. The Bay as a whole is not threat-
ened by eutrophication, and nutrient concentrations are
decreasing in many areas of this estuary. Several aquatic
species exhibit stable trends in abundance. Galveston
Bay is not rapidly degrading in terms of increasing
concentrations of toxic or organic pollutants; rather,
trends in pollution are mixed. Concentrations of
contaminants are decreasing in the most polluted areas
of the Bay, but are rising in other areas. Even with these
stable and, in some cases, improving trends, focus
remains on strategic habitat conservation and pollution
control as the region's population continues to expand
and land-use patterns trend towards urbanization.
Extensive oyster reefs are found in Galveston Bay (Texas Sea Grant College Program).
National Estuary Program Coastal Condition Report 301
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Coastal Bend Bays ana1 Estuaries Program
Coastal Bend Bays and Estuaries Program
Aransas Bay
Redfsh&ay
Aransas Pass
Corpus Christ! Bay
www.cbbep.org
Background
The estuarine area of the Coastal Bend Bays and
Estuaries Program (CBBEP) is located within an area
known as the Coastal Bend and includes three of the
seven estuaries found in Texas. The most northerly
portion of the CBBEP study area encompasses the San
Antonio, Mesquite, Redfish, Copano, and Aransas bays.
The middle estuarine portion includes Nueces Bay and
Corpus Christi Bay (the largest of the bays) and
discharges into the Gulf of Mexico at Aransas Pass.
The most southerly estuarine portion includes Upper
Laguna Madre and Baffin Bay. The CBBEP study area
includes 75 miles of Texas coastline and 515 mi2 of
water (CBBEP, 2005a). In addition to the tidal marshes
and the barrier islands of the CBBEP estuarine area,
this area also includes seagrass meadows, open bays,
oyster and serpulid worm reefs, wind tidal flats, and
freshwater marshes.
The CBBEP study area is an important resource for
recreational, commercial, industrial, and residential uses.
Popular for sportboat fishing, bird watching, and wind-
surfing, the Bays also support a commercial fishing
industry that harvests, on average, more than 8 million
pounds of fmfish, shrimp, and crab from the area's
302 National Estuary Program Coastal Condition Report
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CHAPTER 5 i GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Coastal Bend Bays and Estuaries Program
estuarine waters (Tunnell et al., 1996). This area
contains 40% of the state's total seagrass acreage, which
provides nursery areas for fish and shellfish and habitat
for other wildlife, including birds, sea mammals, and
marine turtles (CBBEP, 1998). Corpus Christi Bay is
the nation's fifth-largest port and holds the third-largest
refinery and petrochemical complex in the United
States (CBBEP, 2005a). Although the region's popula-
tion was 550,000 in 1995, it is projected to be nearly
1 million people by 2050 (CBBEP, 1998).
Environmental Concerns
Fresh water is in short supply in semi-arid southern
Texas, and because of the state's ever-increasing coastal
population and growing industry, there will always be
competing demands for this limited resource.
Residential and business water use in this region is
expected to increase by 50% by 2050, and industrial
demand is expected to double (CBBEP, 1998). Fresh
water is not only vital to the survival of the human
population, but it is also closely tied to the survival of
the entire ecosystem. Fresh water inflows provide three
vital functions essential to an estuary. First, inflows
blend with Gulf seawater to create a range of salinities
in the Bays' waters. Second, inflows of surface runoff
carry nutrients (nitrogen, phosphorus, and decom-
posing organic matter) that are essential to the produc-
tivity of estuarine ecosystems. Phytoplankton and large
plants need these nutrients to survive, multiply, and
provide food and nursery areas for a multitude of
aquatic and terrestrial species. Lastly, inflows bring sedi-
ment to the estuaries, and these sediments are deposited
as river waters slow down upon entering the Bays.
Without the replenishing of these sediments, wave
action would eventually wash away the existing
wetlands. The annual streamflow for the Nueces River
demonstrated a declining trend from 1940—1996 due to
the construction of the Choke Canyon Reservoir, evap-
orative loss from the surface of the reservoir, increased
water use in the river basin, and a long-term regional
drought.
Population Pressures
The population of the 11 NOAA-designated coastal
counties coincident with the CBBEP study area
increased by 36% during a 40-year period, from 0.40
million people in I960 to 0.55 million people in 2000
(Figure 5-63) (U.S. Census Bureau, 1991; 2001). This
rate of population growth for the CBBEP study area
was about one-fourth of the population growth rate of
133.3% for the collective Gulf Coast NEP-coincident
counties and the second-lowest population growth rate
of the Gulf Coast NEP study areas. In addition, the
population density of these 11 coastal counties in 2000
was 53 persons/mi2, which was the lowest density of
any NEP study area in the Gulf Coast region (U.S.
Census Bureau, 2001). Development and population
pressures are less dramatic for this NEP study area,
which serves as a center for commercial fishing and
recreational activities for its coastal communities.
0.6
0.5
0.4
0.3
0.2
JS
3
Q.
,? O.I
0.0
I960
2000
Figure 5-63. Population of NOAA-designated counties of the
CBBEP study area, 1960-2000 (U.S. Census Bureau, 1991; 2001).
National Estuary Program Coastal Condition Report 303
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Coastal Bend Bays and Estuaries Progran
NCA Indices of Estuarine
Condition—Coastal Bend Bays
The overall condition of the Coastal Bend Bays is
rated poor based on the four indices of estuarine condi-
tion used by the NCA (Figure 5-64). The water quality
index is rated fair, the sediment quality and fish tissue
contaminants indices are rated poor, and the benthic
index is rated fair to poor. Figure 5-65 provides a
summary of the percentage of estuarine area rated good,
fair, poor, or missing for each parameter considered.
This assessment is based on data collected by the
TPWD and NCA from 27 stations sampled in the
Coastal Bend Bays in 2000 and 2001. Please refer to
Tables 1-24, 1-25, and 1-26 (Chapter 1) for a summary
of the criteria used to develop the rating for each index
and component indicator.
Water Quality Index
Based on NCA survey results, the water quality index
for the Coastal Bend Bays is rated fair (Figure 5-66).
This index was developed using NCA data on five
component indicators: DIN, DIP, chlorophyll a, water
clarity, and dissolved oxygen. In NOAA's Estuarine
Eutrophication Survey, the Coastal Bend Bays were
listed as having medium to hypereutrophic chlorophyll
a levels and low to high DIN and DIP concentrations,
with elevated concentrations occurring in tidal fresh-
water areas (NOAA, 1997).
Dissolved Nitrogen and Phosphorus I The
Coastal Bend Bays are rated good for DIN concentra-
tions, with 99% of the estuarine area rated good for this
component indicator. The Bays are rated fair for DIP
concentrations, with 4% of the estuarine area rated
poor, 46% of the area rated fair, and 50% of the area
rated good for this component indicator.
Chlorophyll a \ Chlorophyll a concentrations in
the Coastal Bend Bays are rated good. Although only
5% of the estuarine area exhibited poor chlorophyll a
concentrations, 40% of the estuarine area was rated fair
for this component indicator, and 55% of the area was
rated good.
Overall Condition
Coastal Bend Bays
(1.75)
Water Quality Index (3)
Sediment Quality Index (I)
Benthic Index (2)
Fish Tissue Contaminants
Index (I)
Figure 5-64. The
overall condition of
the CBBEP estuarine
area is poor (U.S.
EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Estuarine Area
I I I Missing
Figure 5-65. Percentage of NEP estuarine area achieving each
ranking for all indices and component indicators — Coastal Bend
Bays (U.S. EPA/NCA).
Water Clarity Water clarity in the Coastal Bend
Bays is rated fair because 16% of the estuarine area was
rated poor for this component indicator. In Corpus
Christi and Aransas bays, expectations for water clarity
are similar to those for normally turbid estuaries, and
water clarity was rated poor at a sampling site if light
penetration at 1 meter was less than 10% of surface
illumination. However, because one of the CBBEP's
goals is to re-establish SAV beds in Upper Laguna
304 National Estuary Program Coastal Condition Report
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CHAPTER 5 I GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
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Water Quality Index - Coastal Bend Bays
Site Criteria: Number of component
indicators in poor or fair condition
• Good = No more than I is fair
O Fair = I is poor, or 2 or
more are fair
9 Poor = 2 or more are poor
O Missing
Figure 5-66. Water quality index data for the Coastal Bend
Bays, 2000-2001 (U.S. EPA/NCA).
Madre and Baffin Bay, expectations for water clarity in
these areas are high; therefore, water clarity was rated
poor at a sampling sites in this area if light penetration
at 1 meter was less than 20% of surface illumination.
Dissolved Oxygen I Dissolved oxygen conditions
in the Coastal Bend Bays are rated good. NCA data
show that 70% of the estuarine area was rated good for
dissolved oxygen concentrations, 30% of the area was
rated fair, and none of the area was rated poor.
Sediment Quality Index
The sediment quality index for the Coastal Bend
Bays is rated poor because more than 15% of the
estuarine area was rated poor for sediment quality
(Figure 5-67). This index was developed using NCA
data on three component indicators: sediment toxicity,
sediment contaminants, and sediment TOC.
Sediment Toxicity I Sediment toxicity is rated
good for the Coastal Bend Bays because none of the
estuarine area was rated poor for this component indi-
cator; however, NCA data on sediment toxicity were
unavailable for 48% of the CBBEP estuarine area.
Sediment Contaminants \ The Coastal Bend
Bays are rated poor for sediment contaminant concen-
trations because 38% of the estuarine area was rated
poor for this component indicator.
Total Organic Carbon I The Coastal Bend Bays
are rated good for sediment TOC concentrations. None
of the estuarine area was rated poor for this component
indicator, and 75% of the area was rated good. NCA
data on TOC concentrations were unavailable for 25%
of the CBBEP estuarine area.
Sediment Quality Index - Coastal Bend Bays
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
OFair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Figure 5-67. Sediment quality index data for the Coastal Bend
Bays, 2000 2001 (U.S. EPA/NCA).
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
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Benthic Index
Fish Tissue Contaminants Index
Based on NCA survey data and the Gulf Coast
Benthic Index, the condition of benthic invertebrate
communities in the Coastal Bend Bays is rated fair to
poor. Benthic index estimates indicate that 18% of the
estuarine area had degraded benthic resources and was
rated poor and another 18% was somewhat degraded
and was rated fair (Figure 5-68).
Benthic Index - Coastal Bend Bays
The fish tissue contaminants index for the Coastal
Bend Bays is rated poor. Figure 5-69 shows that tissue
concentrations exceeded the EPA Advisory Guidance
values used in this assessment at 27% of all the stations
sampled where fish were caught.
Fish Tissue Contaminants Index - Coastal Bend Bays
Site Criteria: Gulf Coast
Benthic Index Score
• Good = > 5.0
OFair =3.0-5.0
• Poor =< 3.0
O Missing
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
OFair = Falls within Guidance range
• Poor = Exceeds Guidance range
Figure 5-68. Benthic index data for the Coastal Bend Bays,
2000-2001 (U.S. EPA/NCA).
Figure 5-69. Fish tissue contaminants index data for the Coastal
Bend Bays, 2000-2001 (U.S. EPA/NCA).
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Coastal Bend Bays and Estuaries Program
Coastal Bend Bays and Estuaries
Program Indicators of Estuarine
Condition
The CBBEP uses specific indicators to monitor the
overall health of the estuarine area, and a scoring system
is used to assign relative values for indicator measures.
This system allows analysts to assess trends and identify
the areas showing the greatest improvements. A
summary of the key resources and the types of indica-
tors used to monitor system-wide environmental trends
is presented below.
Water and Sediment Quality
The CBBEP uses a number of indicators to monitor
water quality in the study area, including temperature,
salinity, dissolved oxygen, transparency, fluorescence,
pH, nitrogen, ammonia, phosphorus, dissolved oxygen,
sulfide, chlorophyll a and b, total suspended solids, and
BOD. The program also tests waters for trace metals,
organic compounds, and pathogens, including fecal
coliform, £. coli, and Enterococci. The Inner Harbor,
which is affected by wastewater discharges, exhibits high
levels of several parameters, including ammonia
nitrogen, organic compounds, TOG, metals, and fecal
coliform. Other parameters, such as nitrate-nitrogen
and phosphorus, are typically highest in regions affected
by runoff and inflow. In general, levels of copper,
nickel, and zinc are elevated throughout Corpus Christi
Bay (Ward and Armstrong, 1997).
Hypoxic events have been documented every
summer in the southeastern region of Corpus Christi
Bay since 1988. When hypoxia occurs in the Bay, the
low dissolved oxygen levels are limited to the waters
within 3—6 feet of the Bay's bottom surface. Hypoxia is
caused by a combination of respiration, low mixing
potential, small tidal ranges, and high temperatures.
The extent and intensity of hypoxic events in the Bays
has been increasing over time, which corresponds to
rising temperatures in the region during the past
20 years. These events are primarily due to the increase
in temperature because nutrient levels in this area of the
Bay have not increased (Morehead et al., 2002).
Freshwater flow affects the quality of surface waters
in the estuary, and the CBBEP uses several freshwater-
flow indicators to help assess water quality in the region.
These indicators include the flux, volume, timing, and
locations of freshwater flows (point and river sources)
into the CBBEP area, as well as rainfall trends and
freshwater demand. Annual precipitation rates range
from 24 inches per year in the southern end of the
study area to 40 inches per year in the northern end.
Between 2% (at the southern end) and 10% (at the
northern end) of this precipitation reaches the Bays as
runoff. The non-point loadings of total nitrogen and
total phosphorus to the Bays are largely driven by
runoff from agricultural lands (Quenzer et al., 1998).
Sediment quality is also monitored in the CBBEP
study area. The CBBEP assesses sediments for grain
size, TOC, redox potential discontinuity, contaminant
levels, and toxicity. The diversity of benthic communi-
ties and other benthic community indicators are also
used to characterize sediment quality. Arsenic,
cadmium, mercury, and zinc concentrations in Corpus
Christi Bay sediments are generally elevated. The
highest levels of common pesticides have been measured
in Baffin and Copano bays (Ward and Armstrong,
1997). Elevated levels of PAHs, metals, pesticides,
PCBs, and fecal coliform have also been measured in
sediments collected near stormwater outfall sites and
other areas of concern in the CBBEP study area (Carr
et al., 1998).
Area fishermen participate in the Texas Abanded Crab Trap
Removal Project by collecting derelict crab traps in area bays
(CBBEP).
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Coastal Bend Boys and Estuaries Program
CBBEP Bacteria Source Tracking
in Copano Bay
In Copano Bay, there are a number of waterbody
segments identified in Section 303 (d) of the Clean
Water Act that are listed as having high concentrations
of coliform bacteria. The monitoring data used for this
assessment are derived from various sources. The Texas
DSHS collects data for use in assessing the health risks
of exposure to bacteria in estuarine waters and for
posting closures of shellfish harvesting areas. The
TPWD and several academic research institutions,
collect water quality monitoring data as contractors for
the Regional Coastal Assessment Program. Monitoring
data have shown that microbial contamination is occur-
ring and that elevated concentrations ol bacteria are
usually present following heavy rainfall events; however,
identifying the source or sources of the contamination is
more difficult.
The CBBEP, TCEQ, the Texas DSHS, and Texas
GLO are working with Dr. Joanna Mott at Texas A&M
University/Corpus Christi, Center for Coastal Studies,
to determine the source of bacterial contamination in
Copano Bay through bacterial DNA source tracking
and the development of a database of fecal samples
collected from numerous animals within the watershed,
Copano Bay
Bacteria Source Tracking Project
Sample Stations
Copano Bay Bacteria Source Tracking Project sampling stations (CBBEP).
308 National Estuary Program Coastal Condition Report
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Coastal Bend Bays and Estuaries Program
including humans. The University uses samples from
14 stations in Copano Bay that are part of the Texas
DSHS Shellfish Sanitation Program. Filtration of these
water samples yields isolated E. coli bacteria samples,
which are then verified using BIOLOG. Isolates from
these samples are also fingerprinted for their DNA by
Pulse Field Gel Electrophoresis. In addition, antibiotic
resistance profiling is also conducted on some of the
E. coli samples. The goal of this sampling effort is to
develop a screening tool that can be used to determine
if the coliform bacteria are coming from human,
domestic animal, or wildlife sources so that steps can
be taken to reduce the contamination.
The results of this project will assist several state
resource agencies in determining the source of bacte-
riological contamination to the Copano Bay area.
The Texas DSHS can use this data to review
needed changes to shellfish harvesting rules, and
the TCEQ can use this same data to develop a
TMDL for Copano Bay. In addition, a watershed
model for coliform bacteria is being developed by
the University of Texas, and data from the Copano
Bay Source Tracking Project will be used to assist
in model calibration. Since the project's inception
in 2003, the two major rivers (Aransas and Mission
rivers) discharging into Copano Bay have been
added to the 303 (d) list due to elevated levels of
coliform bacteria. The CBBEP plans to extend this
effort to identify and evaluate sources of coliform
bacteria throughout the entire watershed with the
hope of reducing microbial contamination of
estuarine waters and protecting and maintaining
healthy shellfishing resources.
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Coastal Bend Bays and Estuaries Program
Habitat Quality
Eight major tidally influenced habitats are repre-
sented in the CBBEP study area, including coastal
marshes, wind tidal flats, seagrass meadows, open bays,
oyster and serpulid worm reefs, barrier islands, and
freshwater marshes. Loss of habitat in the study area
results from the following contributing factors: conver-
sion to other land uses, dredge-and-fill activities, natural
erosion, altered freshwater inflow, and degraded water
quality (CBBEP, 1998).
The CCBEP monitors the acreage of each key
habitat. Although losses and gains have been observed
for specific habitat types, habitat acreage has been fairly
stable over time. Wind tidal flats have suffered the most
significant losses in the study area (CBBEP, 2002).
More than 24,500 acres of wind tidal flats were
converted to other habitat classes between the 1950s
and 1979 due to rising sea levels and dredge-and-fill
activities. The most extensive losses were observed on
Mustang Island, San Jose Island, and Harbor Island,
and in the upper portion of the Laguna Madre-Corpus
Christi estuarine complex (CBBEP, 1998; Withers and
Tunnell, 1998).
Dredge-and-fill activities also alter the region's
habitat. Maritime commerce is important to the
CBBEP's regional economy, and dredging is required to
maintain the region's more than 175 miles of navigable
waterways, including die Intracoastal Waterway and the
Corpus Christi and La Quinta Ship channels (Tunnell
et al., 1996). Between 1958 and 1994, dredging was
part of construction and maintenance activities for the
Intracoastal Waterway and other shipping channels in
Redfish Bay. During this time frame, more than
950 acres of seagrass were lost due to channel impacts
and the deposition of dredged materials on seagrass
beds (Pulich et al., 1997; CBBEP, 1998). Habitat for
nesting birds can also be created when dredged mate-
rials are stacked high enough to create islands. For
example, Pelican Island was created from dredged mate-
rial and is now the largest brown pelican nesting area in
Texas (CBBEP, 1998).
The CBBEP also measures habitat quality to assess
the overall health and productivity of the estuarine area.
Habitat quality can be affected by a variety of factors,
including changes in circulation patterns from fresh-
water inflow alterations, dredge-and-fill activities,
Black skimmer chicks exploring while the mother is out foraging
for food (CBBEP).
shoreline alterations, road construction, point and non-
point discharges, and activities associated with oil and
gas exploration. For example, historical brine discharges
have degraded habitat at White's Point in Nueces Bay
(CBBEP, 1998). Some of the indicators used to monitor
the habitat quality of SAV include maximum depth and
width of vegetative growth, shoot density, patchiness,
vegetative species composition, and percent cover
(CBBEP, 2002). Preliminary assessment activities indi-
cate that certain habitat types in the CBBEP study area
are stressed or at risk (CBBEP, 1998).
Living Resources
The CBBEP assesses the quality and quantity of the
living resources within the study area. The program
monitors the area's fisheries and several species of
concern, including species of birds, marine mammals,
and sea turtles. The fishery indicators include the rela-
tive abundance of fish and shellfish; standing crops
versus fishing pressure; CPUE for several species,
including spotted seatrout and blue crab; commercial
fish landings by type from within the system areas;
TPWD creel surveys data; catch-and-release data;
contaminant concentrations in edible tissue of fish and
shellfish; and bacteria levels in the waters where the fish
live. The program also monitors the population size and
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
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reproduction statistics for birds, colonial bird nesting
pairs, number of rookery sites visited or vandalized, the
numbers of strandings and mortalities of marine
mammals, number of strandings and sea turtle condi-
tion, and numbers of nesting sea turtles and turtle nests.
The varied habitats across the CBBEP study area
support a wide range of finfish and shellfish species that
are of commercial and recreational value. The area is
also home to many resident and migratory birds and to
marine mammals such as the bottlenose dolphin.
Although the study area is one of the richest fishery
areas in Texas, particularly for finfish, shrimp, and crab,
data suggest that some population declines have
occurred in species such as Atlantic croaker, summer
flounder, Gulf menhaden, white shrimp, and blue crabs
(Lacson and Lee, 1997). Benthic communities in some
bays (Corpus Christi, Baffin, and Nueces bays) are char-
acterized by low diversity, a dominance of pioneer
species, and a high variance of community and physical
variables (Montagna et al., 1998). Although the CBBEP
area supports almost 500 species of birds, the nesting
populations of colonial waterbirds, with the exception
of the brown pelican, have declined. The FWS is
concerned about two issues that impact migratory
species: rapid habitat loss in Latin and South American
countries and the need to preserve wooded riparian
corridors and coastal prairies along the Gulf Coast.
Some evidence also suggests that there is an increasing
trend in the number of dolphin strandings. This issue is
of particular concern for bottlenose dolphins (Tunnell
etal., 1996).
Environmental Stressors
The CBBEP monitors several human indicators in
the study area, including the length, area, and location
of hardened shoreline, bulkheads, and other hydrolog-
ical modifications; the number of vessels and amount of
cargo crossing the Bays; and the number of oil and
chemical spills in the region. Almost 200 miles of
CBBEP shoreline are protected by seawalls and other
man-made structures, whereas 1,118 miles remain in
their natural state (White et al., 1998). Approximately
80,000 vessels annually cross the Coastal Bend Bays,
and recent analysis indicates that the amount of freight
transported and the number of vessels in CBBEP waters
is increasing (CBBER 1998). More than 90% of the
region's maritime cargo tonnage is composed of oil and
petrochemicals. Although the number of oil and chem-
ical spills in the region has decreased since 1990, some
spills do occur (CBBEP, 1998). These spills have the
potential to impact the region's water, sediment, and
habitat quality, as well as to injure or kill fish and
wildlife.
Current Projects,
Accomplishments, and Future
Goals
The CBBEP and its partners are actively collecting
data that will provide a system-wide assessment of the
environmental trends in the Coastal Bend Bays
resulting from the cumulative effects of action imple-
mentation. Several CBBEP projects and numerous
partner projects are underway to quantify changes to
habitat, water and sediment quality, freshwater
resources, commercial and recreational fisheries, species
of concern, and shoreline management; however, several
factors limit the CBBEP's ability to report on system-
wide progress at this time. Some projects are still in
progress, and results may not be available for some
time. In addition, significant resources are being
directed toward water and sediment quality assessment
projects to determine the statistical confidence of these
data, and some partners have not submitted data to the
program's information clearinghouse. For these reasons,
reporting system-wide environmental changes as a result
of CBBEP or partner action is premature.
A partnership between the CBBEP and the City of
Corpus Christi will help restore freshwater flow to the
Nueces Pviver Delta and revitalize a wetland that is
crucial to the Gulf Coast. The Nueces Delta Preserve is
a dynamic ecosystem of highly productive wetlands,
open water, islands, prairie, and river and bay shore-
lines. The river provides vital riparian habitat, whereas
brackish wetlands are home to shrimp, crabs, juvenile
fish, and birds. The uplands contain an attractive
diversity of native vegetation that host a variety of
wildlife. Approximately 3,000 acres of wetlands-associ-
ated uplands have been acquired for the purpose of
habitat protection as part of a long-term regional water
and land management plan to meet human and
environmental needs for fresh water (CBBEP, 2005b).
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CHAPTER 5 GULF COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Coastal Bend Bays and Estuaries Program
The Delta provides highly productive wetlands and crit-
ical habitat for numerous shorebirds, as well as recre-
ationally and commercially important fish and shellfish
species (e.g., shrimp, crabs, and juvenile finfish). Part of
the new Nueces Delta Preserve will be purchased by the
City of Corpus Christi for use as an overflow channel
and pipeline corridor to deliver much-needed fresh
water directly to the upper Nueces River Delta.
Conclusion
The CBBEP has taken actions to establish aggressive
goals for the protection and restoration of the Coastal
Bend Bays by obtaining consensus among a variety of
different stakeholder groups. NCA monitoring data
classify the Coastal Bend Bay's overall condition as poor.
Because many of the CBBEP's own monitoring data are
still being collected or evaluated, it is not known
whether the comprehensive list of CBBEP indicators
will show a pattern similar to the NCA data. Attaining
the CBBEP's goals will require continued strong moni-
toring efforts, as well as comprehensive pollution and
resource management. Projected population increases in
the CBBEP area will require increasing cooperation
among stakeholder groups in developing a strong
regional water management plan that will balance the
long-term environmental needs of the human inhabi-
tants and living resources of the Coastal Bend Bays to
maintain a sustainable freshwater system.
Outdoor enthusiasts getting ready to hit the waves in their catamarans on North Padre Island (CBBEP).
312 National Estuary Program Coastal Condition Report
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CHAPTER 6
WEST COAST NATIONAL ESTUARY PROGRAM
COASTAL CONDITION
-------
CHAPTER 6
WEST COAST NATIONAL ESTUARY PROGRAM
COASTAL CONDITION
Background
The West Coast region extends from the Mexican
border north to the Canadian border and, due to its
unique geological history, has the fewest estuaries of any
coastal region of the United States. With the exception
of parts of the Washington coast that have become
coastal flats and islands due to the erosion of sedimen-
tary rocks, the West Coast is characterized by uplifted,
resistant rock. The proximity of coastal mountains to
the shoreline in this region has restricted the area of
coastal plain and rivers that flow to the sea (NOAA,
1985).
Within the West Coast region, there are six NEP
estuaries: Puget Sound, the Lower Columbia River
Estuary, Tillamook Bay, the San Francisco Estuary,
Morro Bay, and Santa Monica Bay (Figure 6-1). The
larger West Coast estuaries, Puget Sound and the San
Francisco Estuary, were formed when sections of the
coastline containing former river valleys sank below sea
level during mountain-building processes (NOAA,
1985). Puget Sound was further deepened and elon-
gated as a result of glacial activity, resulting in the devel-
opment of a fjord that is narrow, deep, and steep-sided,
with several internal sills. Both of these estuaries are
dominated by tidal flow rather than by freshwater
inputs. In contrast, the Lower Columbia River Estuary
is heavily influenced by freshwater riverine discharge.
During high river-flow periods, the Estuary is almost
entirely composed of fresh water that is well connected
to the ocean; however, during low-flow periods,
discharge is insufficient to maintain a good connection
with the ocean, and tidal action along the shoreline
tends to affect the entrance to the Estuary.
Sediment loads delivered to West Coast estuaries vary
considerably throughout the region, with high sediment
loading in southern California, moderate loading in
central California, and generally low loading from
northern California to Washington due to extensive
forested lands that help reduce sediment runoff
(NOAA, 1985). However, historic logging activities,
steep slopes, and heavy rainfall in some of the
Northwest Coast estuaries combine to result in high
levels of sediment and lower water clarity in some river
systems.
Pacific Ocean
I. Puget Sound
2. Lower Columbia River
Estuary
3. Tillamook Bay
4. San Francisco Estuary
S. Morro Bay
6. Santa Monica Bay
Figure 6-1. The West Coast region is home to six NEP
estuaries.
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Population Pressures
The population of the 41 NOAA-designated coastal
counties coincident with the estuarine study areas of
the West Coast NEPs increased by 100.3% during a
40-year period, from 14.7 million people in 1960 to
29.5 million people in 2000 (Figure 6-2) (U.S. Census
Bureau, 1991; 2001). This growth resulted in a popu-
lation density of 421 persons/mi in 2000 for these
NEP-coincident coastal counties; however, the popula-
tion densities of the individual NEP study areas varied
considerably, from a high of 844 persons/mi2 for the
San Francisco Estuary to a low of 22 persons/mi2 for
Tillamook Bay (U.S. Census Bureau, 2001). Develop-
ment and population pressures are especially strong
surrounding some of the West Coast NEP estuaries,
which are centers of international commerce, major
fishing ports, and recreational areas for these coastal
communities.
I960
2000
Figure 6-2. Population of the 41 NOAA-designated coastal
counties of the West Coast NEP study areas, 1960-2000 (U.S.
Census Bureau, 1991; 2001).
NCA Indices of Estuarine
Condition—West Coast Region
Researchers with the Washington State Department
of Ecology (WSDE), the Oregon Department of
Environmental Quality (ODEQ), NOAA's NS&T
Program, and the Moss Landing Marine Laboratories,
under contract to the Southern California Water
Resources Research Project, collected NCA data from
308 locations in the six West Coast NEP estuaries in
1999, 2000, and 2003. The NS&T Program also
provided sediment contaminants data from some Puget
Sound sites based on samples collected in 1997, 1998,
and 1999. With the assumption that sediment contami-
nant concentrations will change slowly, these stations
were incorporated into the 2000 sampling design and
supplemented with water quality and biological data.
The NS&T Program collected additional data during
2001 within the San Francisco Estuary, but these data
have not been included in the current report. The
Morro Bay and Santa Monica Bay estuarine areas were
not sampled until 2003.
Overall Condition
West Coast
NEP Estuaries
(2.5)
Water Quality Index (3)
Sediment Quality Index (I)
Benthic Index (5)
Fish Tissue Contaminants
Index (I)
Figure 6-3. The
overall condition of the
West Coast NEP estu-
arine area is fair (U.S.
EPA/NCA).
The following sections of this report discuss two different
approaches for characterizing estuarine condition.
Approach I -The NCA provides unbiased, quality-
assured data that can be used to make consistent "snap-
shot" comparisons among the nation's estuaries. These
comparisons are expressed in terms of the percent of
estuarine area in good, fair, or poor condition.
Approach 2 - Each individual NEP collects site-specific
estuarine data in support of local problem-solving efforts.
These data are difficult to compare among NEPs, within
regions or nationally, because the sampling and evaluation
procedures used by the NEPs are often unique to their
individual estuaries. However, these assessments are
important because NEP-collected data can evaluate
spatial and temporal changes in estuarine condition on a
more in-depth scale than can be achieved by the NCA
snapshot approach.
National Estuary Program Coastal Condition Report 315
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
The overall condition of the collective West Coast
NEP estuaries is rated fair based on the four indices of
estuarine condition used by the NCA (Figure 6-3). The
water quality index for the region is rated fair, the sedi-
ment quality and fish tissue contaminants indices are
rated poor, and the benthic index is rated good. Figure
6-4 shows the percent of estuarine area rated good, fair,
poor, or missing for each parameter considered. Please
refer to Tables 1-24, 1-25, and 1-26 (Chapter 1) for a
summary of the criteria used to develop the rating for
each index and component indicator.
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80
Percent NEP Estuarine Area
100
| [^Missing
Figure 6-4. Percentage of NEP estuarine area achieving each
ranking for all indices and component indicators —West Coast
region (U.S. EPA/NCA).
Water Quality Index
Based on NCA survey results, the water quality index
for the collective West Coast NEP estuaries is rated fair.
This index was developed using NCA data on five
component indicators: DIN, DIP, chlorophyll a, water
clarity, and dissolved oxygen. Seventy-two percent of
the estuarine area was rated fair for water quality
because of limited water clarity and elevated levels of
DIP (Figure 6-5).
Dissolved Nitrogen and Phosphorus The
West Coast region is rated good for DIN concentra-
tions, with 92% of the NEP estuarine area rated good
for this component indicator. The region is rated fair
for DIP concentrations, with 10% of the NEP estuarine
area rated poor and 80% of the area rated fair for this
component indicator. It should be noted that the
threshold for a West Coast site to be rated poor for DIN
was a concentration in excess of 1 mg/L and for DIP
was a concentration in excess of 0.1 mg/L. These values
correspond to the levels used by the NOAA/EPA Team
on Near Coastal Waters to indicate high nutrient levels
in its report on the susceptibility of West Coast estuaries
to nutrient discharges (NOAA/U.S. EPA, 1991). Along
much of the West Coast, summer wind conditions result
in an upwelling of nutrient-rich deep water, which enters
the West Coast estuaries during flood tides (Landry et
Water Quality Index -West Coast
Site Criteria: Number of
component indicators in
poor or fair condition
• Good = No more than
I is fair
= I is poor, or 2
or more are fair
Figure 6-5. Water quality index data for the West Coast NEP
estuarine area, 1999, 2000, and 2003 (U.S. EPA/NCA).
316 National Estuary Program Coastal Condition Report
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
al., 1989) and constitutes a potentially important,
natural source of nutrient inputs for many of these
estuaries.
Chlorophyll a I Chlorophyll a concentrations for
the West Coast region are rated good, with 44% of the
NEP estuarine area rated fair for this component indi-
cator and 56% of the area rated good. None of the
West Coast region's NEP estuarine area was rated poor
for chlorophyll a concentrations.
Water Clarity I NCA data show that water clarity
in the NEP estuaries of the West Coast region is rated
poor. For all of the West Coast NEP estuaries, water
clarity was rated poor at a sample site if light penetra-
tion at 1 meter was less than 10% of surface illumina-
tion. Approximately 35% of the West Coast NEP estu-
arine area was rated poor for water clarity, and 16% of
the area was rated fair. It should be noted that the West
Coast typically experiences strong seasonal variations in
freshwater flow between the wet conditions of winter
and the dry conditions of summer. In interpreting water
clarity for the West Coast NEP estuaries, the light pene-
tration levels recorded represent water clarity only in
late summer and do not represent high-flow, wet season
conditions in the winter. In addition, the large tidal
amplitude found in many estuaries along the West
Coast may result in high natural levels of turbidity in
the water column due to sediment suspension; however,
phytoplankton and other paniculate matter may also
decrease water clarity. The NOAA Eutrophication
Survey (NOAA, 1998) has previously reported high
turbidity in the West Coast NEP estuarine areas and for
the West Coast estuaries in general (20 of 38 estuaries
surveyed).
Dissolved Oxygen I The West Coast region is rated
good for dissolved oxygen conditions, with 78% of the
NEP estuarine area rated good for this component indi-
cator, 21% of the area rated fair, and only 1% of the
area rated poor. Although conditions in West Coast
NEP estuaries appear to be generally good for dissolved
oxygen, measured values reflect daytime conditions, and
some areas may still experience hypoxic conditions at
night.
Sediment Contaminant Criteria (Long et al., 1995)
ERM (Effects Range Median)—Determined for each
chemical as the 50th percentile (median) in a database of
ascending concentrations associated with adverse biological
effects.
ERL (Effects Range Low)—Determined for each
chemical as the I Oth percentile in a database of ascending
concentrations associated with adverse biological effects.
Sediment Quality Index
The sediment quality index for the collective NEP
estuaries of the West Coast region is rated poor, with
17% of the estuarine area exceeding thresholds for sedi-
ment toxicity, sediment contaminants, or sediment
TOC (Figure 6-6). The sediment contaminants compo-
nent of the sediment quality index for the West Coast
NEP estuaries excluded phenanthrene (a PAH) and
Sediment Quality Index - West Coast
Site Criteria: Number and
condition of component
indicators
• Good = None are poor,
and sediment
contaminants is
good
O Fair = None are poor,
and sediment
contaminants
is fair
• Poor = I or more are
poor
O Missing
Figure 6-6. Sediment quality index data for the West Coast
NEP estuarine area, 1997-2000, and 2003 (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 317
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
nickel. Phenanthrene was excluded because concentra-
tions were not available from all West Coast NEP estu-
aries, and nickel was excluded because its ERM value
has a low reliability for West Coast conditions, where
high natural crustal concentrations of nickel exist (Long
etal., 1995).
Sediment Toxicity I The West Coast region is
rated poor for sediment toxicity because 18% of the
NEP estuarine area was rated poor for this component
indicator. Toxicity was determined using a static 10-day
acute toxicity test with the amphipods Ampelisca abdita
or Hyalella azteca. Sediment toxicity was observed in all
West Coast NEP estuaries except Tillamook Bay and
the San Francisco Estuary.
Sediment Contaminants I The West Coast
region is rated fair for sediment contaminant concentra-
tions. Approximately 5% of the region's NEP estuarine
area was rated poor for this component indicator, and
21% of the area was rated fair.
Total Organic Carbon I The West Coast NEP
estuarine area is rated good for TOC concentrations
because concentrations in sediment were rated good in
86% of the NEP estuarine area and fair in 14% of the
area. None of the estuarine area was rated poor for this
component indicator.
Benthic Index
Currently, there is no single benthic community
index applicable to the entire West Coast region,
although work on such an index is ongoing. In lieu of a
West Coast Benthic Index, the deviation of species rich-
ness from an estimate of the expected species richness
was used as an approximate indicator of the condition
of the West Coast benthic community. The log 10 trans-
formed number of species per 0.1-square-meter grab
sample was regressed on bottom salinity. The benthic
condition of any station with fewer species than 75% of
the lower 95% confidence limit of the mean from the
regression was rated poor, whereas the condition of
stations with 75% to 90% of the lower 95% confidence
limit was rated fair.
The condition of the benthic invertebrate communi-
ties in the collective West Coast NEP estuaries is rated
good based on deviations from the expected species
richness (Figure 6-7). This analysis was based on a total
of 245 benthic samples collected in 1999 and 2000 for
the NEP estuarine areas of Tillamook Bay, Puget
Sound, the San Francisco Estuary, and the Lower
Columbia River Estuary, as well as in 2003 for Morro
Bay and Santa Monica Bay.
A significant linear regression was found between
salinity and the log of species richness that was moder-
ately strong (r2 = 0.39, p < 0.01). Based on this regres-
sion, 47 sites, representing 4% of the estuarine area,
were rated poor, and another 36 sites, representing 3%
of the area, were rated fair. Of the 47 sites rated poor,
25 sites (53%) were in the Lower Columbia River
Estuary, which may reflect the naturally low diversity of
this system, or potentially, the effects of stressors such as
channel dredging on the benthic communities.
Benthic Index -West Coast
Site Criteria: Compared
to expected diversity
• Good = > 90%
OFaiir = 75% - 90%
• Poor = < 75%
O Missing
Figure 6-7. Benthic index data for the West Coast NEP
estuarine area, 1999, 2000, and 2003 (U.S. EPA/NCA).
318 National Estuary Program Coastal Condition Report
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Fish Tissue Contaminants Index -West Coast
Fish Tissue Contaminants Index
The fish tissue contaminants index for the collective
West Coast NEP estuaries is rated poor based on fish
samples collected from 198 stations (Figure 6-8).
Thirty-two percent of all stations sampled where fish
were caught were rated poor for fish tissue contami-
nants, which most often included total PCBs, DDTs,
and mercury.
Fish tissue contaminant levels were compared to EPA
Advisory Guidance values using whole-fish contaminant
concentrations. For populations that consume whole
fish, these risk calculations are appropriate. Whole-fish
contaminant concentrations can be higher or lower than
the concentrations associated with fillets only. Only
those contaminants that have an affinity for muscle
tissue (e.g., mercury) are likely to have higher fillet
concentrations. Fillet contaminant concentrations for
most other contaminants will be lower than whole fish
analyses. In contrast to the NEP estuaries of the
Northeast, Southeast, and Gulf coasts, PAHs were not
analyzed in fish tissue samples collected from the West
Coast NEP estuaries.
NEP Estuaries and the Condition
of the West Coast Region
The purpose of the NEP is to identify, restore, and
protect the nationally significant estuaries of the United
States. The six West Coast NEP estuaries include a wide
range of estuary types, from large estuaries, such as the
San Francisco Estuary and Puget Sound, to much
smaller estuaries, such as Tillamook Bay and Morro Bay.
The larger estuaries are important to the nation as
major centers of commerce and international trade,
areas for commercial or recreational fisheries, and
centers for coastal recreational activities; however, these
diverse uses can create environmental stresses that may
result in environmental degradation. Does the condi-
tion of the West Coast NEP estuaries accurately reflect
the condition of all West Coast estuaries (both NEP
and non-NEP)? Based on the NCA survey results, the
collective West Coast NEP estuaries and all West Coast
estuaries combined are both rated fair for overall condi-
tion, with the group of NEP estuaries receiving an
overall condition score of 2.5, just slightly higher than
the overall condition score of 2.25 for all West Coast
Site Criteria: EPA
Guidance concentration
• Good = Below Guidance
range
OFair = Falls within
Guidance range
• Poor = Exceeds
Guidance range
Figure 6-8. Fish tissue contaminants index data for the West
Coast NEP estuanne area, 1999, 2000, and 2003 (U.S. EPA/NCA).
estuaries (Figure 6-9). The overall condition scores for
the two groups of West Coast estuaries were derived
from estimates presented in the NCCR II and based on
NCA data collected between 1999 and 2000 from all
West Coast estuaries, except for Morro Bay and Santa
Monica Bay, which were sampled in 2003. A higher
overall condition score for the group of collective NEP
estuaries has also been noted in some of the other
regions outlined in this report.
A comparison of NCA data shows that the collective
West Coast NEP estuaries are rated fair for the water
quality index, poor for the sediment quality index, good
for the benthic index, and poor for the fish tissue conta-
minants index. The group of all West Coast estuaries
combined are rated fair for the water quality index, fair
to poor for sediment quality index, fair for the benthic
index, and poor for the fish tissue contaminants index.
Both groups of estuaries are also rated comparably for
almost all of the water and sediment quality component
National Estuary Program Coastal Condition Report 319
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Overall Condition
Water Quality Index
Phosphorus (DIP)
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue Contaminants
Index
Figure 6-9. Comparison of NCA results for West Coast NEP estuaries and all West Coast estuaries (U.S. EPA/NCA).
indicators, with both groups rated good for DIN,
chlorophyll a, dissolved oxygen, and TOC concentra-
tions; fair for DIP concentrations; and poor for water
clarity and sediment toxicity. However, the two groups
of estuaries received different ratings for one sediment
quality component indicator (sediment contaminants).
The collective West Coast NEP estuaries are rated fair
for sediment contaminant concentrations, whereas the
group of all West Coast estuaries combined are rated
good for this component indicator. Based on these
ratings, the condition of the West Coast NEP estuaries
is relatively representative of the condition of all West
Coast estuaries, with the exception of sediment quality,
where the group of all West Coast estuaries received
better ratings.
With respect to the individual West Coast NEP estu-
aries, four of the six estuaries are rated higher for overall
condition to the overall condition score for the collec-
tive West Coast NEP estuaries (2.5, rated fair). These
NEP estuaries are Puget Sound (3.0, rated fair),
Tillamook Bay (4.5, rated good), the San Francisco
Estuary (2.75, rated fair), and Morro Bay (4.33, rated
good). Only the Lower Columbia River Estuary (2.33)
and the Santa Monica Bay (2.33), which are both rated
fair, received overall condition scores below the overall
condition score for the collective NEP estuaries of the
West Coast region.
The water quality index is rated good for two of the
six West Coast NEP estuaries (Morro Bay and Santa
Monica Bay), both of which are located in the south-
ernmost portion of the region. Three NEP estuaries
(Puget Sound, the Lower Columbia River Estuary, and
Tillamook Bay) are rated fair for the water quality
index, whereas the San Francisco Estuary is rated fair to
poor. With respect to the water quality component
indicators, all of the West Coast NEP estuaries are rated
good for DIN concentrations, except for the San
Francisco Estuary, which is rated fair. The majority of
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
the NEP estuaries (Puget Sound, the Lower Columbia
River Estuary, Tillamook Bay, and Morro Bay) are rated
fair for DIP concentrations, although the San Francisco
Estuary is rated poor and Santa Monica Bay is rated
good for this component indicator. All the estuaries are
rated good for chlorophyll a concentrations, except for
Puget Sound, which is rated fair. Four of the six West
Coast NEP estuaries (Puget Sound, the Lower Colum-
bia River, Tillamook Bay, and the San Francisco
Estuary) are rated poor for water clarity, whereas the
remaining two estuaries (Morro Bay and Santa Monica
Bay) are rated good. Finally, all six estuaries are rated
good for dissolved oxygen concentrations.
The sediment quality index ratings for the individual
West Coast NEP estuaries range from good to poor.
The sediment quality index is rated good for Tillamook
Bay; fair for the Lower Columbia River Estuary, San
Francisco Estuary, and Morro Bay; and poor for Puget
Sound and Santa Monica Bay. Sediment toxicity is rated
good in Tillamook Bay and the San Francisco Estuary
and poor in Puget Sound, the Lower Columbia River
Estuary, Morro Bay, and Santa Monica Bay. Sediment
contaminant concentrations are rated good for five of
the West Coast NEP estuaries, but poor for Santa
Monica Bay. Finally, sediment TOC is rated good in all
West Coast NEP estuaries.
The benthic index is rated good for all West Coast
NEP estuaries where a rating was applicable (Puget
Sound, Tillamook Bay, and the San Francisco Estuary).
Benthic index ratings were not applicable for the Lower
Columbia River Estuary, Morro Bay, or Santa Monica
Bay because the index used was based on deviations
from the expected species richness. The benthic index
methodology used by the NCA requires a significant
regression between salinity and the log of species rich-
ness; however, a lack of significant regression existed for
the two southernmost NEPs (Morro Bay and Santa
Monica Bay) because of the small variation in salinity.
For the Lower Columbia River Estuary, there was a lack
of significant regression because of this area's low species
richness, possibly associated with either dredging or
naturally low species diversity.
The fish tissue contaminants index is rated good for
Tillamook Bay and Morro Bay; fair for Puget Sound;
and poor for the Lower Columbia River Estuary, San
Francisco Estuary, and Santa Monica Bay.
Nationally, the overall condition score for the collec-
tive West Coast NEP estuaries (2.5) ranks higher than
the overall condition scores for the Northeast Coast (1.5)
and Puerto Rico (1.5) regions and lower than the overall
condition scores for the Southeast Coast (4.0) and Gulf
Coast (2.75) regions. Population pressures, measured as
population density (number of persons/mi2), correlated
somewhat with the overall condition score for the West
Coast NEP estuaries. For example, Morro Bay and
Tillamook Bay had the lowest population densities of 75
and 22 persons/mi2, respectively, and these estuaries had
the highest overall condition scores of 4.33 and 4.5
(both rated good). The two largest estuaries with the
highest population densities, San Francisco Estuary (844
persons/mi2) and Puget Sound (205 persons/mi2), were
both rated fair for overall condition, with overall condi-
tion scores of 2.75 and 3.0, respectively. The Lower
Columbia River Estuary and Santa Monica Bay had the
lowest overall condition scores (both 2.33 and rated fair)
of any of the six West Coast NEP estuaries and were
intermediate in population density (138 and 533
persons/mi2, respectively).
Harbor seals can be seen at sandy beaches, mudflats, bays, and estuaries along the West Coast (Jim Young).
National Estuary Program Coastal Condition Report 321
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Puget Sound Action Team
Puget Sound Action Team
PUGET SOUND ACTION TEAM
Office of the Governor, State ol Washington
www.psat.wa.gov
Background
Carved by glaciers, Puget Sound is a place where the
salt water of the ocean meets fresh water flowing from
about 10,000 rivers and streams (PSAT, 2003a).
Together, these waters commingle to form a deep,
complex system that provides invaluable habitat for fish
and wildlife, including the region's renowned Pacific
salmon and orca whales. The Sound covers 2,800 mi of
inland marine waters, with an average depth of 450 feet,
and encompasses 2,500 miles of shoreline (PSAT, 2003a;
2006).
Much of the promise and potential of the Puget
Sound estuarine area is based on natural resources and
the industries these resources support, such as tourism,
lumber, shellfish, and recreation. The region's natural
resources and high quality of life have led to good
economic growth, resulting in ever-increasing numbers
of people who live and work in the counties surround-
ing Puget Sound. By 2020, the population in the Puget
Sound basin is expected to be greater than five million
people—almost 30% more people than the present
population (PSAT, 2002). This region supports one of
322 National Estuary Program Coastal Condition Report
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Puget Sound Action Team
the leading trade centers on the West Coast and is a
gateway to some of the continent's busiest ports,
including Seattle, Tacoma, Anacortes, Everett, Port
Angeles, and Olympia. The port facilities within Puget
Sound collectively handled more than 64 million tons
of cargo during 2003 (PSAT, 2002; USAGE, 2004b).
EPA declared Puget Sound to be an Estuary of
National Significance in 1988, an action that included
the Puget Sound in the NEP (PSAT, 2003a). Created in
1996, the Puget Sound Action Team (PSAT) is
composed of state agencies and federal, tribal, and local
governments. The federal government and the State of
Washington have both adopted the 2000 Puget Sound
Water Quality Management Plan (PSAT, 2000) as the
comprehensive plan to protect and restore Puget Sound.
This partnership is leading efforts to implement the
PSAT plan and to protect and restore Puget Sound
(PSAT, 2003a).
Environmental Concerns
A growing human population means increasing stress
on Puget Sound. Human development has modified
significant portions of the Sound's shoreline, and
stormwater runoff from developed areas is a substantial
water pollution problem because of the contaminants
from those surfaces. Toxic contamination, nearshore
habitat modifications, habitat loss, declines in some fish
and wildlife populations, Endangered Species Act list-
ings of salmon and eight other species in the nearshore
habitat, and shellfish bed closures remain among the
primary concerns for Puget Sound. The Sound has
experienced significant physical changes to its nearshore
habitat, as well as population declines in some of its
most important plant and animal species (PSAT, 2002).
Population Pressures
The population of the 14 NOAA-designated coastal
counties coincident with the PSAT study area increased
by about 120% during a 40-year period, from 1.8
million people in 1960 to 4.1 million people in 2000
(Figure 6-10) (U.S. Census Bureau, 1991; 2001). This
rate of population growth for the PSAT study area
surpassed the population growth rate of 100.3% for the
collective West Coast NEP-coincident coastal counties;
however, the 2000 population density in the PSAT-
coincident coastal counties remained fairly low at
205 person/mi , well below the West Coast NEP-
coincident coastal county population density of
421 persons/mi (U.S. Census Bureau, 2001).
Development and population pressures are especially
strong in NEP study areas that serve as major shipping
centers for commercial, fishing industry, and recre-
ational activities in their coastal communities.
2000
Figure 6-10. Population of NOAA-designated coasta! counties
of the PSAT study area, 1960-2000 (U.S. Census Bureau, 199 I;
2001).
NCA Indices of Estuarine
Condition—Puget Sound
The overall condition of Puget Sound is rated fair
based on the four indices of estuarine condition used by
the NCA (Figure 6-11). The water quality and fish
tissue contaminants indices are rated fair, the sediment
quality index is rated poor, and the benthic index is
rated good. Figure 6-12 provides a summary of the
percentage of estuarine area rated good, fair, poor, or
missing for each parameter considered. This assessment
is based on data collected by the WSDE, in collabora-
tion with NOAA, from 73 sites sampled in the PSAT
estuarine area between 1997 and 2000. Please refer to
Tables 1-24, 1-25, and 1-26 (Chapter 1) for a summary
of the criteria used to develop the rating for each index
and component indicator.
National Estuary Program Coastal Condition Report 323
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Puget Sound Action Team
Overall Condition
Puget Sound
(3.0)
Water Quality Index (3)
Sediment Quality Index (I)
Benthic Index (5)
Fish Tissue Contaminants
Index (3)
Figure 6-11. The
overall condition of the
PSAT estuarine area is
fair (U.S. EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Estuarine Area
Missing
Figure 6-12. Percentage of NEP estuarine area achieving each
ranking for all indices and component indicators — Puget Sound
(U.S. EPA/NCA).
Water Quality Index
Based on NCA survey results, the water quality index
for Puget Sound is rated fair. This index was developed
using information from five component indicators:
DIN, DIP, chlorophyll a, water clarity, and dissolved
oxygen. Most (75%) of the estuarine area received fair
ratings for water quality, whereas 2% of the area was
rated poor because of limited water clarity and
moderate levels DIP and chlorophyll a (Figure 6-13).
Dissolved Nitrogen and Phosphorus I Puget
Sound is rated good for DIN concentrations, but rated
fair for DIP concentrations. Concentrations of DIN
were rated good in 100% of the PSAT estuarine area. In
contrast, fair DIP concentrations occurred in 90% of
the estuarine area, and only 1% of the area was rated
poor for this component indicator.
Chlorophyll ft \ Chlorophyll a concentrations in
Puget Sound are rated fair. Fifty-two percent of the
estuarine area was rated fair for this component indi-
cator, and the remaining 48% of the area was rated
good.
Water Clarity I Water clarity in Puget Sound is
rated poor. Approximately 37% of the estuarine area
was rated poor for water clarity, and 16% of the area
was rated fair.
Dissolved Oxygen I Dissolved oxygen conditions
in Puget Sound are rated good. Twenty-seven percent of
the estuarine area was rated fair for this component
indicator, and less than 2% of the estuarine area was
rated poor, primarily for sites located in Hood Canal.
Although dissolved oxygen conditions in Puget Sound
appear to be generally good, measured values reflect
daytime conditions, and some areas may still experience
hypoxic conditions at night.
324 National Estuary Program Coastal Condition Report
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Puget Sound Action Team
Water Quality Index - Puget Sound
Site Criteria: Number of
component indicators in
poor or fair condition
• Good = No more than
I is fair
O Fair = I is poor, or 2
or more are fair
• Poor = 2 or more are
poor
O Missing
Good
23%
Poor
2%
Fair
75%
Figure 6-13. Water quality index data for Puget Sound,
1999-2000 (U.S. EPA/NCA).
Sediment Quality Index
The sediment quality index for Puget Sound is rated
poor, with 17% of the area exceeding thresholds for one
or more of the three component indicators—sediment
toxicity, sediment contaminants, or sediment TOC
(Figure 6-14).
Sediment Toxicity \ Puget Sound is rated poor for
sediment toxicity. Sediments in 21% of the estuarine
area were rated poor; however, this percentage is based
on poor ratings at only two sites, one of which had a
79% survival rate. The effect of these two sites on the
area estimate of poor condition was augmented by the
fact that both sites were located within the statistical
stratum with the largest area and that only five other
sites had acceptable sediment toxicity data within the
stratum.
Sediment Contaminants I Puget Sound is rated
good for sediment contaminant concentrations, with
2% of the estuarine area rated poor for this component
indicator and 16% of the area rated fair.
Total Organic Carbon I Puget Sound is rated
good for sediment TOC, with sediment concentrations
rated good in 83% of the estuarine area and fair in 17%
of the area. None of the PSAT estuarine area was rated
poor for sediment TOC concentrations.
Sediment Quality Index - Puget Sound
Site Criteria: Number and
condition of component
indicators
• Good = None are poor,
and sediment
contaminants is good
O Fair = None are poor,
and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Fair
Figure 6-14. Sediment quality index data for Puget Sound,
1997-2000 (U.S. EPA/NCA).
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Puget Sound Action Team
Benthic Index
The benthic condition of Puget Sound is rated good
based on deviations from the expected species richness
(Figure 6-15). This analysis was based on 62 benthic
samples collected in Puget Sound, including 8 samples
collected in the embayments along the Strait of Juan de
Fuca in 1999 and 54 from within Puget Sound proper
in 2000.
A significant linear regression between log species
richness and salinity was found in the Puget Sound
estuary, although this regression was weak (r2 = 0.09,
p < 0.01). A potential reason for the weak relationship
between species richness and salinity is that bottom
salinity ranged only from 25.7 to 33.0 ppt among these
sites. Using this regression, four sites (representing 2%
of the estuarine area) were rated poor based on a lower-
than-predicted species richness, and another four sites,
representing 3% of the area, were rated fair. The
Benthic Index - Puget Sound
Site Criteria: Compared
to expected diversity
• Good= >90%
OFair = 75% - 90%
• Poor = < 75%
O Missing
Figure 6-15. Benthic index data for Puget Sound, 1999-2000
(U.S. EPA/NCA).
remaining 95% of the estuarine area was rated good for
benthic condition. The cause for the less-than-expected
species richness at the sites rated poor is not readily
apparent because all of these sites were rated good for
sediment contaminant concentrations. In addition, sedi-
ment TOC was rated fair at three of the four sites
surveyed, although a number of other sites with equiva-
lent TOC measurements did not display depressed
species richness.
Fish Tissue Contaminants Index
The fish tissue contaminants index for Puget Sound
is rated fair. Fourteen percent of all stations sampled
where fish were caught exceeded EPA Advisory
Guidance values using whole-fish contaminant concen-
trations (Figure 6-16). For populations that consume
whole fish, these risk calculations are appropriate. The
contaminants found in fish tissues in Puget Sound most
often included total PCBs.
Fish Tissue Contaminants Index - Puget Sound
Site Criteria: EPA
Guidance concentration
• Good = Below Guidance
range
OFair = Falls within
Guidance range
• Poor = Exceeds
Guidance range
Poor
14%
Figure 6-16. Fish tissue contaminants index data for Puget
Sound, 1999-2000 (U.S. EPA/NCA).
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Puget Sound Action Team
Efforts to Address Low Dissolved
Oxygen Levels in Hood Canal,
Washington
Hood Canal, a 60-mile-long, glacially carved fiord
(see map), is one of the most scenic marine environ-
ments of Puget Sound, a region long renowned for its
commercial and sport fishing and shellfish harvesting.
Nestled between the Olympic Mountains and the
central channel of Puget Sound, Hood Canal is experi-
encing increased growth and associated development.
This activity may be at the heart of the reoccurring
hypoxic conditions in Hood Canal, a problem that hit
the spotlight in the spring of 2002 and again in the fall
of 2003, when dead fish and other marine life washed
up on Hood Canal's beaches. During 2004, the oxygen
levels in Hood Canal dropped to all-time lows (PSAT,
2005a).
In 2005, the Washington State legislature acted on
this problem, designating the PSAT as the state's lead
agency for Hood Canal and the Hood Canal
Coordinating Council as the local management board.
The 2005 legislature charged both entities to work
together to restore marine water quality and dissolved
oxygen to levels adequate to support healthy marine life.
The legislature also designated Hood Canal as the first
Aquatic Rehabilitation Zone in Washington State. Most
significantly, the legislature and Governor approved $22
million of new funds to scale-up corrective actions for
Hood Canal (PSAT, 2005a).
Twenty-eight organizations, including state and
federal agencies, universities, local and tribal govern-
ments, non-profit organizations, and research institutes,
have formed a partnership to address low dissolved
oxygen levels in Hood Canal and the effect of this
problem on marine life. This partnership, the Hood
Canal Dissolved Oxygen Program (HCDOP), will use
data from monitoring, computer modeling, and
demonstration projects to further develop and target the
corrective actions designed to restore and maintain
healthy levels of dissolved oxygen in Hood Canal
(PSAT, 2005a).
For more information on the HCDOP's coordinated
effort to recover Hood Canal, go to http://www.psat.wa.
gov/Programs/hood_canal.htm.
Puget Sound Estuary and the Hood Canal (PSAT).
National Estuary Program Coastal Condition Report 327
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Puget Sound Action Team
Puget Sound Action Team
Indicators of Estuarine Condition
Factors such as water quality and the health of some
marine animals signal improvements in the health of
Puget Sound. Unfortunately, other environmental indi-
cators warn of concerns for the Sound's overall
ecosystem. In 2002, the PSAT issued its third biennial
report on the health of Puget Sound, Puget Sound's
Health 2002 (PSAT, 2002). This report summarizes the
condition of the Sound's marine waters, shoreline, 200
species offish, 26 species of marine mammals, 100
species of sea birds, and thousands of species of marine
invertebrates, using 19 indicators to determine whether
the Sound's health is getting better or worse. As shown
in Table 6-1, 8 of the 19 indicators classify Puget
Sound's health as improving, 2 indicators classify the
Sound's health as declining, 3 indicators show mixed
results, 4 indicators document continued concerns
about persistent toxic contamination problems, and 2
indicators are new indicators of nearshore habitat condi-
tions. Additional information about recent conditions
in Puget Sound and the PSAT's actions to restore the
estuary is available at http://www.psat.wa.gov.
Water and Sediment Quality
Freshwater quality in the streams and rivers of the
PSAT estuarine area is assessed using 8 parameters
measured at 38 sites on a monthly basis. These eight
parameters include measures of nutrients (e.g., total
nitrogen, total phosphorus), pathogens (e.g., fecal
coliform bacteria), and other physical parameters (e.g.,
water temperature, dissolved oxygen, pH, total
suspended solids, and turbidity). Trend analysis for
temperature based on data collected from 1995—2004
showed improvements in overall water quality index
scores in all areas except the Stillaguamish River. The
majority of rivers and streams monitored had good fecal
coliform conditions (28 of 38 stations), the remainder
of sites were rated fair, and none of the sites were rated
poor for coliform conditions. The same percentage of
sites were scored in good condition during wateryear
2005 as compared with wateryear 2000 (Personal
communication, Brace, 2006).
Marine water quality monitoring in Puget Sound
measures temperature, conductivity, salinity, density,
dissolved oxygen, pH, light transmission, and nutrient
(e.g., nitrate, nitrite, phosphate, silicate, and ammo-
nium) and fecal coliform bacteria concentrations.
Table 6-1. Summary of Indicator Results from Puget Sound "sHeofth 2002 (PSAT, 2002)
Rating
Improving
Mixed
Declining 1
Persistent
Toxic
Contamination
New •
Results
Area of commercial shellfish beds approved for harvesting
Beaches used by recreational shellfish harvesters
Water quality for recreation (measuring bacteria contamination)
Size and frequency of major oil spills
Reduced acreage of Sport/no infestation, an aquatic nuisance plant species
Freshwater habitat available to salmon (culverts allowing fish migration)
Water temperature in rivers and streams
Marine survival of Puget Sound wild coho salmon
Harbor seal populations
Herring populations
Marine water quality
Scoter populations
Rockfish populations
Area of contaminated sediments (bottom of waterways)
Contamination in mussels
Contamination in harbor seals
Occurrence of liver disease in English sole
Abundance and distribution of eelgrass beds
i Modifications to marine shorelines
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Puget Sound Action lean
Most of these parameters are monitored on a monthly
basis. In general, regions of high concern with respect to
marine water quality were located near urban areas or in
poorly flushed areas such as Budd Inlet, Port Gardner,
Bellingham Bay, Nisqually Reach, Carr Inlet, Case Inlet,
and Henderson Inlet (Personal communication, Brace,
2006).
As of 2001, the WSDE had identified 112 contami-
nated sediment cleanup sites, representing an estimated
3,400 acres of marine sediments in Puget Sound (Figure
6-17) (WSDE, 2001; PS AT, 2002). Twenty-two of
these sites have been cleaned up or require no further
action. In 2002, cleanup activities were underway at
11 more sites. Action was still needed at an additional
79 sites, and 65 of these sites were in the investigation
and design phases leading to cleanup. Between 1997
and 1999, 8,700 acres (1.5%) of soft sediment in Puget
Sound (excluding the San Juan Islands and the Strait of
Juan de Fuca) were contaminated, and approximately
83,000 acres were less severely contaminated. Long-
term monitoring by the WSDE indicates that concen-
trations of some contaminants (e.g., naphthalene, low
molecular-weight PAHs) have increased during the past
few years, whereas concentrations of other contaminants
(e.g., copper, mercury) have decreased (PSAT, 2002).
Commencement Bay
Areas of Contaminated Sediments Data from 1997-99
Based on three separate tests
for contamination:
- chemistry test
- toxicity test
- test of sediment-dwelling
organisms
| | No consistent evidence
of degradation
I j Degradation only in
chemistry test at all
stations
I I Degradation in two
tests at all stations
^H Degradation in three
tests at all stations
Source: Washington State
Department of Ecology, 2002
Figure 6-17. Sediment contamination map of Puget Sound (PSAT 2002).
National Estuary Program Coastal Condition Report 329
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Puget Sound Action Team
Habitat Quality
Human development significantly alters the Puget
Sound environment, and habitat loss and degradation
are major threats to the health of the Sound's fish and
wildlife. Protecting and restoring habitat is a key
element of the strategy to recover wild salmon and a
priority of the PSAT. Habitats at risk from direct
human development and construction activities include
freshwater habitat for salmon and other fish, as well as
Puget Sound's fringe of shallow subtidal, intertidal, and
shoreline habitats known as the marine nearshore. For
example, infestations of Spartina, a salt marsh grass
native to the eastern United States, can overtake native
western grass species, making these habitats less useful
to the area's fish, shellfish, and birds. Between 1999 and
2001, the Washington Department of Agriculture and
its partners reduced Spartina infestations throughout
most of the study area, except in Snohomish County
(PSAT, 2002).
Eelgrass beds are also an environment of particular
interest in considering habitat quality in Puget Sound.
Based on the first year of a new eelgrass monitoring
project, the Washington Department of Natural
Resources (WDNR) estimates that Puget Sound is
home to approximately 26,000 acres (or nearly 41 mi2)
of eelgrass. Eelgrass beds are divided into two habitat
types. A significant amount of eelgrass occurs in flats,
which can be large shallow bays or small pocket
beaches, and close to one-fifth of all the eelgrass in
Puget Sound grows in one large flat, Padilla Bay.
Eelgrass also occurs in narrow fringing beds along
steeper shorelines. These fringing beds are used as corri-
dors for migrating salmon and other wildlife, and about
one-half of all eelgrass in Puget Sound occurs in
fringing beds. Eelgrass and other seagrass species are
used as an indicator of estuary health because they
respond to many natural and human-caused environ-
mental variables, and changes in the abundance or
distribution of this resource are likely to affect other
species that depend on eelgrass habitat (PSAT, 2002).
Living Resources
A variety of living resource indicators are used to
assess the health of Puget Sound. Population trends in
fish and wildlife can provide insight into the state of the
region's ecosystem. The extent of area open to shellfish
harvesting is an indicator of the amount of contamina-
tion in the Sound. In addition, the PSAT examines the
levels of several chemicals in the tissue of mussels and
harbor seals to determine how these contaminants are
behaving in the food chain. In general, the levels of
pollutants in Puget Sound vary regionally, with higher
levels found in marine life near urban areas. The effects
of contaminants on the health of the area's wildlife is
assessed by monitoring the occurrence of liver lesions in
English sole (PSAT, 2002).
The PSAT uses the population trends and spawning
potential of several key fish and wildlife species as indi-
cators of estuary health. In 2000 and 2001, coho
salmon appeared to be returning to Puget Sound in
small but increased numbers compared with returns in
the late 1990s. Rockfish, which can live for 80 to 100
years, are declining at an alarming rate, and the
spawning potential for rockfish measured in 2000 was
only 7% to 12% of the levels recorded in the late 1970s
(PSAT, 2002; 2005b). Scientists believe that this
decline, coupled with the decline of many other marine
fish species, may point to significant problems with the
entire Puget Sound ecosystem. A number of marine
bird species have declined by 50% or more in the past
20 years. Populations of scoters, which are large black
diving ducks with orange bills, have declined by 57% in
the past 20 years. During the same period, 13 out of 18
other marine diving birds in Puget Sound have shown
significant population declines. Some bird species, such
as the marbled murrelets, have experienced population
declines of more than 90% (PSAT, 2002).
Washington is among the top shellfish-producing
states in the nation, and the health of shellfish beds and
the suitability of shellfish for consumption closely
reflect conditions of the state's shellfish-growing envi-
ronment. The Washington Department of Health
(WDOH) classifies shellfish-growing areas to provide
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Puget Sound Action Team
information about the extent to which contamination
restricts the ability to harvest shellfish, and changes in
the classification of these areas can reflect problems
related to how land is used and cared for in the nearby
watersheds. Since 1980, nearly one-quarter of the
approximately 140,000 acres available for direct
commercial shellfish harvesting has been downgraded in
classification because of bacterial contamination.
During 2000-2001, the WDOH downgraded 849
acres and upgraded 1,540 acres. These areas were rela-
tively small when compared to the approximately
33,000 acres that were downgraded in the 1980s;
however, the net upgrade of 691 acres in 2000 and
2001 indicates that pollution-control efforts appear to
be balancing increasing water quality threats (PSAT,
2002).
Mussels filter large quantities of water and can accu-
mulate any toxic contaminants that are present in the
water or adsorbed on phytoplankton. The NOAA
National Mussel Watch Program data collected through
1998 demonstrated that multiple Puget Sound locations
experienced long-term declining trends in the concen-
trations of banned pesticides (e.g., chlordane, DDT)
and several metals (e.g., lead, mercury) in mussel tissue.
However, it also appeared that PCB levels in mussels
were no longer decreasing and possibly increasing
during the mid- to late 1990s. NOAA scientists have
used newly available data from 1999—2001 to construct
a 16-year record of PCB levels and to identify three
important patterns. First, concentrations of PCB in
mussels have generally been declining during the two
decades following the ban on most PCB uses in the
1970s. Second, the highest concentrations were consis-
tently found in mussels from central Puget Sound sites,
such as Four Mile Rock (north Elliott Bay) and adjacent
areas, confirming that this urban area is a long-term
source for PCBs. Finally, the long-term downward trend
was interrupted in the mid-1990s by increases in PCB
levels at many locations. Between 1999 and 2000, PCB
concentrations in mussels began to decrease again.
These patterns indicate that it is uncertain whether
PCBs will continue to decline at the rates seen from the
1970s to early 1990s (PSAT, 2002).
Harbor seals feed relatively high in the food chain
and accumulate contaminants from their food
(primarily fish) in their fatty tissue. As a result of the
widespread restrictions placed on PCB and DDT use in
the early 1970s, there was a sharp decline in measured
levels of these contaminants in Puget Sound harbor
seals through the 1970s and afterwards. These declines
have leveled off since the mid-1980s as contaminated
land and sediments continue to release PCBs into the
marine food chain (PSAT, 2002).
Scientists who routinely monitor English sole at six
Puget Sound locations have found significantly elevated
occurrences of liver lesions at two urban sites and one
near-urban site (O'Neill et al., 2001). PAH concentra-
tions in sediments were also elevated at these three sites.
These results indicate that the health of bottom-
dwelling fish in Puget Sound is worse in areas where
sediments are contaminated (Figure 6-18). The risk of
developing liver disease increased in English sole
sampled along the Seattle waterfront between 1989 and
1998, but decreased in 1999 and remained low in
2000; no increasing or decreasing trends were evident at
the other sites. The lower occurrence of liver lesions in
English sole during 1999 and 2000 may have resulted
from the numerous sediment-capping projects that have
been completed to the north and south, as well as in the
immediate vicinity of the Seattle waterfront, since 1989.
Collectively, these projects may have lowered the PAH
concentrations in sediments and reduced exposures to
English sole feeding in this area (PSAT, 2002).
Hood Canal
Strait of Georgia
Sinclair Inlet
Point Gardner
Commencement Bay
Seattle Waterfront
2 4 6 8 10
Risk of Liver Lesions
Source: Washington Department of Fish and Wildlife
Figure 6-18. Risk of liver disease in English sole based on
geographical location (PSAT 2002).
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Puget Sound Action Team
Environmental Stressors
Shoreline modifications, such as bulkheads or
seawalls, tend to harm habitat through the conversion
of tidelands to uplands. Modification also indirectly
affects habitat by altering nearshore processes. The
amount of modified shoreline in an area can be a useful
indicator of the effect people have on the nearshore
environment. In 2000, scientists with the Nearshore
Habitat Program at the WDNR completed a statewide
inventory to assess the extent of modification along salt-
water shorelines (Berry et al., 2001). Approximately
one-third of all saltwater shorelines in Washington have
some kind of shoreline modification structure. In the
PSAT study area, Snohomish and King counties have
the most extensively modified shorelines (PSAT, 2002).
Current Projects,
Accomplishments, and Future
Goals
Protecting and restoring Puget Sound is a long-term
commitment that requires continuing efforts by govern-
ment, tribes, private industry, environmental and citizen
groups, and individual residents throughout the region.
Although progress has been made on many fronts, new
challenges have emerged, and many existing problems
persist as the region's population grows and the area of
developed lands expands within the basin. The PSAT's
partnership prepared the Puget Sound Water Quality
Work Plan: 2003-2005 (PSAT, 2003b) as the fourth
biennial effort to specify and articulate actions to
continue implementing the 2000 Puget Sound Water
Quality Management Plan (PSAT, 2000). The work plan
outlines a 2-year strategy to achieve measurable progress
in protecting Puget Sound. More specifically, the plan
identifies ongoing issues (that require more than 2 years
to address), as well as associated priorities and recom-
mended actions to pursue during the biennium. These
issues for the 2003—2005 work plan include the
following:
• Declines in marine species (e.g., salmon, ground-
fish, and orcas)
• Freshwater and marine habitat loss and alteration
• Water quality problems that continue to threaten
the safe harvest of shellfish
• Stormwater runoff impacts on water quality,
streams and wetlands, and biological resources
• Bacterial contamination from on-site sewage
systems
• Non-native aquatic species that threaten the biodi-
versity, ecological stability, and commercial, agri-
cultural, or recreational activities that depend on
the Sound.
Conclusion
The overall view of the health of Puget Sound is
clearly complex, with different indicators demonstrating
different environmental quality results and trends over
time. Encouraging signs have been noted for about half
of the indicators measured by the NCA survey, as well
as for the PSAT's shellfish harvesting, swimming,
Spartina infestation, and salmon population indicators.
Mixed or discouraging signals for the other NCA indi-
cators and for a variety of fish, wildlife, and persistent
toxic contamination indicators were observed by both
EPA and the PSAT. PCB contamination remains a
major concern, and several other chemicals are being
closely watched to determine potential human health
and ecological risks. Based on data from the NCA
estuarine survey, the overall condition of Puget Sound is
rated fair.
The Puget Sound provides invaluable habitat for orca whales (Captain
Budd Christman, NOAA Corps).
332 National Estuary Program Coastal Condition Report
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
lower Columbia River Estuary Partnership
Lower Columbia River Estuary Partnership
Columbia
River Estuary
Partnership
www.lcrep.org
Background
The 4,300-mi2 Lower Columbia River Estuary
extends downstream from the Bonneville Dam at river
mile 146 to the mouth of the Columbia River and into
the Pacific Ocean to the 3-mile limit, which represents
the point where coastal waters are no longer influenced
by the plume of fresh water flowing into the ocean.
This estuarine system contains a wide variety of habitats
associated with marine, estuarine, and freshwater influ-
ences. These habitats range from open water to bottom
sediments, tidal flats, and the riparian zone. The Lower
Columbia River Basin drains approximately 18,000 mi2,
about 7% of the entire Columbia River Basin (LCREP,
1999).
The Lower Columbia River Estuary Partnership's
(LCREP's) Comprehensive Conservation and
Management Plan, Volume 1 (LCREP, 1999) identifies
many actions that can be conducted in the study area to
improve water quality and habitat in the Lower
Columbia River Estuary. The LCREP recognizes that
many impacts in the study area are the result of prob-
lems or sources elsewhere in the Columbia River basin;
therefore, efforts in the study area will be less effective if
changes in the entire basin do not occur. For this
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
lower Columbia River Estuary Partnership
reason, it is important not to separate the Lower
Columbia River Estuary from the larger watershed.
Although the LCREP's CCMP includes many actions
that specifically address the study area, it also considers
the impacts from the larger watershed and incorporates
actions to address these impacts, where needed.
Environmental Concerns
The LCREP completed its CCMP for the Lower
Columbia River Estuary in June 1999. The CCMP
contains 43 specific actions to address 7 priority issues:
biological integrity, impacts of human activity and
growth, habitat loss and modification, conventional
pollutants, toxic contaminants, institutional constraints,
and public awareness and stewardship. As part of the
planning process, a comparative risk assessment process
helped prioritize the LCREP's activities and identified
loss of habitat as the greatest risk to the health of the
Estuary. Based on this assessment, the LCREP has
chosen to direct much of its energy toward the protec-
tion and restoration of habitat.
Population Pressures
The population of the 11 NOAA-designated coastal
counties coincident with the LCREP study area
increased by 78.4% during a 40-year period, from
0.9 million people in 1960 to 1.6 million people in
2000 (Figure 6-19) (U.S. Census Bureau, 1991; 2001).
This rate of population growth was one of the lowest
for the West Coast NEPs and was much lower than the
population growth rate of 100.3% for the collective
2.0
•2 1.5
1.0
2 0.5
0.0
I960
2000
Figure 6-19. Population of NOAA-designated coastal counties
of the LCREP study area, 1960-2000 (U.S. Census Bureau, 1991;
2001).
NEP-coincident counties of the West Coast region. In
addition, the LCREP study area's population density of
138 persons/mi was the third-lowest density of the
West Coast NEPs (U.S. Census Bureau, 2001). This
estuary is not surrounded by the large metropolitan
areas that are characteristic of some other West Coast
NEPs, such as Puget Sound or the San Francisco
Estuary.
NCA Indices of Estuarine
Condition—Lower Columbia
River Estuary
The overall condition of the Lower Columbia River
Estuary is rated fair based on three of the indices of
estuarine condition used by the NCA (Figure 6-20).
The water quality and sediment quality indices are rated
fair, and the fish tissue contaminants index is rated
poor. Although data on the condition of the benthic
community were collected for this estuary, the Lower
Columbia River Estuary could not be rated using an
index based on deviations from the expected species
richness. Figure 6-21 provides a summary of the
percentage of estuarine area rated good, fair, poor, or
missing for each parameter considered. This assessment
is based on data collected by ODEQ and the WSDE
from 79 stations sampled in the LCREP estuarine area
in 1999 and 2000. Please refer to Tables 1-24, 1-25,
and 1-26 (Chapter 1) for a summary of the criteria used
to develop the rating for each index and component
indicator.
Overall Condition
Lower Columbia
River Estuary
(2.33)
Water Quality Index (3)
Sediment Quality Index (3)
Benthic Index (missing)
Fish Tissue Contaminants
Index (I)
Figure 6-20. The
overall condition of the
LCREP estuarine area
is fair (U.S. EPA/NCA).
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
[ower Columbia River Estuary Partnership
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80
Percent NEP Estuarine Area
100
Missing
Figure 6-21. Percentage of NEP estuanne area achieving each
ranking for all indices and component indicators — Lower
Columbia River Estuary (U.S. EPA/NCA).
Water Quality Index
Based on NCA survey results, the water quality index
for the Lower Columbia River Estuary is rated fair
(Figure 6-22). This index was developed using NCA
data on five component indicators: DIN, DIP, chloro-
phyll a, water clarity, and dissolved oxygen. Water
quality was rated fair in 60% of the estuarine area due
to limited water clarity and moderate DIP concentra-
tions.
Dissolved Nitrogen and Phosphorus I The
Lower Columbia River Estuary is rated good for DIN
concentrations and fair for DIP concentrations. One-
hundred percent of the estuarine area was rated good
for DIN concentrations, and 70% of the estuarine area
was rated fair for DIP concentrations.
Water Quality Index - Lower Columbia River
Estuary
Site Criteria: Number of component indicators in poor
or fair condition
• Good = No more than I is fair
OFair = I is poor, or 2 or more are fair
• Poor = 2 or more are poor
O Missing
Figure 6-22. Water quality index data for the Lower Columbia
River Estuary 1999 -2000 (U.S. EPA/NCA).
Coho salmon are found in the Lower Columbia River Estuary
(Oregon Department of Fish and Wildlife).
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
tower Columbia River Estuary Partnership
Chlorophyll a Chlorophyll a concentrations in
the Lower Columbia River Estuary are rated good.
Approximately 29% of the estuarine area was rated fair
for this component indicator, with the remaining 71%
of the area rated good. None of the LCREP's estuarine
area was rated poor for chlorophyll a concentrations.
Water Clarity I Water clarity in the Lower
Columbia River Estuary is rated poor. Approximately
35% of the estuarine area was rated poor for water
clarity, and an additional 31 % of the area was rated fair.
Dissolved Oxygen I Dissolved oxygen conditions
in the Lower Columbia River Estuary are rated good,
with 99% of the estuarine area rated good for this
component indicator. Although conditions in the
Estuary appear to be good for dissolved oxygen,
measured values reflect daytime conditions, and some
areas of the Estuary may still experience hypoxic
conditions at night.
Sediment Quality Index
The sediment quality index for the Lower Columbia
River Estuary is rated fair, with 11 % of the estuarine
area exceeding thresholds for one or more of the three
component indicators: sediment toxicity, sediment
contaminants, or sediment TOC (Figure 6-23).
Sediment Toxicity I The Lower Columbia River
Estuary is rated poor for sediment toxicity, with 10% of
the estuarine area rated poor for this component indi-
cator.
Sediment Contaminants I The Lower Columbia
River Estuary is rated good for sediment contaminant
concentrations, with only 1% of the estuarine area rated
poor for this component indicator and none of the area
rated fair.
Total Organic Carbon The Lower Columbia
River Estuary is rated good for sediment TOC. Ninety-
five percent of the estuarine area was rated good for this
component indicator, and 5% of the area was rated fair.
None of the LCREP's estuarine area was rated poor for
sediment TOC concentrations.
Sediment Quality Index - Lower Columbia River
Estuary
Site Criteria: Number and condition of component indicators
• Good = None are poor, and sediment contaminants is good
OFair = None are poor, and sediment contaminants is fair
9 Poor = I or more are poor
O Missing
Figure 6-23. Sediment quality index data for the Lower
Columbia River Estuary, 1999-2000 (U.S. EPA/NCA).
Benthic Index
The condition of the benthic invertebrate commu-
nity in the Lower Columbia River Estuary currently
cannot be rated using an index based on deviations
from the expected species richness. This conclusion was
based on 75 benthic samples taken in the LCREP estu-
arine area, of which 29 samples were collected in the
side embayments in 1999 and 46 were taken in the
main stem of the Columbia River in 2000. The NCA
approach requires a significant regression between
salinity and the log of species richness; however, this
relationship was not significant in the Lower Columbia
River Estuary (r" = 0.03, p > 0.10). The lack of a signif-
icant regression was not due to an inadequate range in
salinity because salinity for the Estuary ranged from
0.04 to 31.3 ppt. Species richness was low in the
Estuary, averaging only 6.0 species per sample over all
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
tower Columbia River Estuary Partnership
the samples and 4.4 species per sample in the samples
collected along the main stem of the Columbia River. It
is possible that stressors (e.g., dredging of the channel)
or naturally low diversity in the Estuary obscured any
simple relationship between salinity and species rich-
ness; however, when samples collected within 99 feet of
the shipping channel were removed from the regression
analysis, the regression relationship improved, but was
still not significant due to the wide range of species
richness values at freshwater sites. EPA was unable to
provide a relative benthic index assessment for the
Lower Columbia River Estuary using the NCA survey
data, and additional data analysis will be required to
find an alternate approach for the Estuary.
Fish Tissue Contaminants Index - Lower Columbia
River Estuary
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
OFair = Falls within Guidance range
• Poor = Exceeds Guidance range
Fish Tissue Contaminants Index
The fish tissue contaminants index for the Lower
Columbia River Estuary is rated poor. Forty-six percent
of all stations sampled where fish were caught exceeded
the EPA Advisory Guidance values using whole-fish
contaminant concentrations and were rated poor
(Figure 6-24). For populations that consume whole fish,
these risk calculations are appropriate. The contami-
nants found in fish tissues at elevated concentrations in
the Lower Columbia River Estuary most often included
total PCBs, DDT, DDD, DDE, and mercury.
Figure 6-24. Fish tissue contaminants index data for the Lower
Columbia River Estuary, 1999-2000 (U.S. EPA/NCA).
Astoria Bridge (LCREP).
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Lower Columbia River Estuary Partnership
Habitat Protection and Restoration
in the Lower Columbia
The floodplain of the Lower Columbia River Estuary
historically contained extensive and diverse wetland and
riparian habitats critical to fish and wildlife; however,
the impacts of development over the past 150 years
have significantly altered this complex system. Although
the Estuary still provides essential habitat for a great
number of freshwater and saltwater fish, numerous
shellfish, a variety of marine and water-dependent land
mammals, and over 175 species of birds, it is a very
different area from the one explored by Lewis and Clark
(ANEP, 200 la; LCREP, 2006). Loss of wetland habitat
is one of the greatest problems being addressed by the
LCREP. Evidence indicates that more than one-half of
the wetland areas in the Estuary have been lost since
1870 as a result of diking, draining, filling, dredging,
and flow regulation. Forested marshes in the lower 46
miles of the Lower Columbia River have decreased as
much as 75%, whereas barren lands and open water
areas have increased substantially (ODEQ, 2000).
The LCREP has made habitat restoration and
protection a top priority. The Partnership's CCMP
(LCREP, 1999) presents six actions specifically directed
toward habitat protection and restoration, and several
other actions involve a habitat element. The LCREP is
working to establish a coordination structure to ensure
that projects are developed using the best available
scientific information and prioritized according to the
life-cycle needs of endangered species, such as salmon
and other native organisms.
Since 1999, the LCREP's habitat restoration
program has funded 22 projects, resulting in the protec-
tion of more than 1,200 acres and the restoration of
more than 850 acres. The program has also spent $2.7
million to leverage nearly $9 million in restoration
funding with over 50 partners throughout Oregon and
Washington, resulting in 4,600 total acres protected or
restored in the Lower Columbia River Estuary (LCREP,
2005b). Some examples of these restoration projects are
discussed in the following sections.
Reconnecting historic floodplains to regular tidal wetting, such as seen on this 80-acre parcel, is one of the habitat restoration techniques
used by partners of the LCREP (Columbia Land Trust).
338 National Estuary Program Coastal Condition Report
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Lower Columbia River Estuary Partnership
Scappoose Bay Conservation Plan and
Restoration Projects
The LCREP worked with The Wetlands
Conservancy to conduct an inventory of naturally valu-
able habitat within the 8,960 acres of the Scappoose
Bay Bottomlands. Partnering with the Scappoose Bay
Watershed Council, the LCREP allocated grant funding
to remove multiple fish barriers, install fish-friendly
bridges, and fence stream riparian areas. The planning
area for these activities covers 200 acres of cattle farm-
land (The Wetlands Conservancy, 2004).
Grays Bay Area
Conservation/Restoration Projects
Partnering with the Columbia Land Trust, the
LCREP funded a multi-level restoration effort with
grant funding from the EPA Watershed Initiative and
the Bonneville Power Administration. At 5 different
sites, the project resulted in the conservation of 880
acres of floodplain, the reconnection of 500 acres of
historic floodplain, the restoration of 300 acres of
salmon habitat, and the enhancement of 3 miles of
riparian habitat (CREST, 2006).
Strategic Prioritization for Habitat
Restoration
As a next step in the Partnership's habitat restoration
program, the LCREP has initiated an effort with part-
ners and interested parties to develop a focused Strategic
Habitat Restoration Plan, which will detail the most
ecologically beneficial locations for restoration and
describe the most appropriate types of restoration strate-
gies to undertake in those areas. Beginning in 2006, the
LCREP will employ this tool in the restoration project
selection process, which will identify project value based
on its significance to the Columbia River ecosystem.
Ultimately, projects selected through this framework
will provide greater cumulative benefits to the entire
system, while adaptive management and effectiveness
monitoring of these projects will ensure continued
progress and improvements to the system's health over
the long term (Evans et al., 2006).
I
Replacing undersized, non-performing culverts, such as the one seen here on Honeyman Creek, allows for full fish passage and tidal influ-
ence in tributary streams. The photo on the left is a pre-restoration representation, whereas the photo on the right is after restoration
(Scappoose Bay Watershed Council [left] and the LCREP [right]).
National Estuary Program Coastal Condition Report 339
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Lower Columbia River Estuary Partnership
Lower Columbia River Estuary
Partnership Indicators of
Estuarine Condition
The LCREP has developed a set of six environmental
indicators that attempt to provide accessible informa-
tion about the health of the Lower Columbia River
Estuary. These indicators are considered key measures of
the Estuary's ecological integrity and are meant to be a
step in the process of relaying important information
about the estuarine system to policy makers and the
public. The LCREP's environmental indicators are the
following:
• Habitat (loss, opportunity, protection and conserva-
tion, restoration, net change)
• Biotic integrity (native species assessment)
• Land use (land-use changes, riparian integrity)
• Water quality (concentrations of toxic contaminants
and convention pollutants, temperature, and
dissolved oxygen)
• Stewardship (children's educational and field
programs, volunteer monitoring, and restoration)
• Appreciation (park visitors, recreational and shellfish
permits, membership in environmental non-govern-
mental organizations).
The LCREP's indicators were carefully chosen based
on a number of factors. Each indicator had to be a
measurable and quantifiable value, be understandable to
the public, have sufficient historical records to show
trends, relate to the overall condition of the Estuary,
allow for an assessment of present conditions and a
prediction of future trends, provide sufficient facts to
support goal-setting and program management, and
provide targets and endpoints for the restoration of the
Estuary.
Water and Sediment Quality
In 2004 and 2005, the LCREP partnered with
USGS and the ODEQ to monitor water quality at
three fixed stations along the Lower Columbia River
and the Willamette River. Selected water samples were
analyzed for a variety of parameters, including nutrients,
chlorophyll a, suspended sediment, total coliforms,
trace elements, and a variety of chemical contaminants
(LCREP, 2006). Water quality sampling using semiper-
meable membrane devices (SPMDs) was also conducted
in the Lower Columbia River and its tributaries during
2003 and 2004. SPMDs are used to mimic the accu-
mulation of contaminants in the fatty tissues of fish.
During this study, concentrations of dieldrin and PCBs
commonly exceeded human health criteria; DDT
compound concentrations exceeded the criteria less
frequently; and PAH concentrations were below the
criteria (Johnson and Norton, 2005). Additional SPMD
samples were collected in 2005. More information
about the LCREP's water quality monitoring efforts is
available at http://www.lcrep.org.
Water temperatures and dissolved oxygen concentra-
tions are also monitored in the Lower Columbia River
Estuary. Cool (68 degrees Fahrenheit or less) water
temperatures in the Estuary are essential for native
aquatic species, which experience stress as temperatures
rise. Average and maximum summer water temperatures
have increased by approximately 4 degrees since 1938.
In 2002, measured dissolved oxygen concentrations in
the Estuary were above Washington's and Oregon's state
standard of 8 mg/L (LCREP, 2005a).
Habitat Quality
Habitats in the LCREP study area have been
changing over time, and the acreage of developed land
and open water in the Lower Columbia River Estuary
has increased substantially since the 1880s. At the same
time, the areal extents of the Estuary's tidal swamps and
marsh habitat have decreased by 77% and 57%, respec-
tively. Although the average tree cover in most of the
study area (the region near Longview, WA, was excluded
from this analysis) decreased from 46% to 24%
between 1972 and 2000, the amount of area with thick,
dense canopy tree cover has increased since 1986
(LCREP, 2005a).
The LCREP and its partners have undertaken several
measures to monitor, assess, and map habitats in the
Estuary. The Partnership's habitat status monitoring
program was established to create a long-term data set
used to assess the status and trends of the Estuary's
aquatic habitats (LCREP, 2006). The Lower Columbia
River and Estuary Ecosystem Classification System is
under development by the LCREP, USGS, and the
University of Washington to delineate the Estuary's
340 National Estuary Program Coastal Condition Report
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Lower Columbia River Estuary Partnership
different landscape structures and guide habitat moni-
toring efforts (Simenstad et al., 2005). Field work has
also been combined with satellite images, digital aerial
photos, bathymetry, Light Detection And Ranging
(LIDAR), and high-resolution hyperspectral images to
develop detailed and comprehensive habitat maps and
habitat data layers (LCREP, 2006).
Living Resources
Approximately 24 threatened and endangered species
of plants, fish, animals, and birds can be found in the
Lower Columbia River Estuary. Although populations
of some of these species (e.g., bald eagles) are slowly
recovering, others (e.g., chinook salmon) are not. The
number of occupied bald eagle nests along the
Columbia River has been increasing slowly since 1978;
however, the productivity of those nests located below
river mile 60 remains low due to significant contami-
nant concentrations (e.g., DDE, PCBs, and dioxins)
found in the egg shells collected from this portion of
the Estuary. During the past 100 years, the number of
chinook salmon returning to spawn in the Estuary has
decreased from a range of 450,000-550,000 fish to an
average of 100,000 salmon. Although a variety of
factors (e.g., hydropower operations, harvest, ocean
conditions) contributed to this population decline,
habitat loss and degradation is cited as the leading
cause. Since reaching a low of 25,000 returning fish in
1999, chinook salmon returns have improved slightly
(LCREP, 2005a).
At least 81 invasive species (e.g., American shad,
purple loosestrife, Chinese mystery snail, Eastern snap-
ping turtle, nutria) have been introduced to the Lower
Columbia River Estuary since the mid-1880s. The
majority of these species originated in North America,
and domestic shipping is most likely an important
vector for the introduction of new species to the
Estuary. The rate at which new species are discovered
has increased from one every 5 years between the 1880s
and the 1970s to one every five months since 1994.
Although this rate of increase can be attributed to more
new species being introduced to the Estuary, an
increasing number of improved surveys to monitor
invasive species has also contributed to the growing
number of species detected. For example, an invasive
species survey conducted at 134 stations in the LCREP
study area during 2002 and 2003 identified 269 aquatic
species. Twenty-one percent of these were invasive
species, and the origins of another 45% of the identified
species were unknown (Sytsma et al., 2004; LCREP,
2005a).
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Lower Columbia River Estuary Partnership
Toxic contaminants have been detected in the fatty
tissues of fish and wildlife living in the Lower Columbia
River Estuary, and interim health advisories have been
issued for dioxins, PCBs, and pesticides in the fatty
tissue of all fish in the Estuary (LCREP, 2005a; U.S.
EPA, 2005a). Starting in 2005, the LCREP and NOAA
began testing juvenile salmon tissue and stomach
contents for concentrations of chemical contaminants.
The resulting data will be used to assess the effects of
toxic contaminants on the survival and productivity of
the Estuary's juvenile salmon and to assist with the
development of three models designed to identify cont-
aminant sources; describe potential modes and routes of
transport, exposure, and uptake; and analyze the
possible effects on survival and productivity of listed
salmon species (LCREP, 2006).
Environmental Stressors
The LCREP uses the percentage of the study area's
impervious surface and the number of innovative
stormwater management projects implemented as indi-
cators of estuarine condition. Between 2000 and 2005,
the amount of impervious cover in the LCREP study
area has increased significantly. Innovative stormwater
management projects have been implemented in the
study area, especially in the Portland and Vancouver
areas (LCREP, 2005a). These projects are highlighted in
the LCREP's Lower Columbia River Field Guide to
Water Quality Friendly Development, which provides
local examples of different stormwater management
techniques and is available online at http://www.krep.
org/fieldguide.
Current Projects,
Accomplishments, and Future
Goals
Monitoring the Estuary to track its condition over
time and to develop a better understanding of the
highly complex ecosystem is another critical element of
the LCREP. During the development of its CCMP, the
LCREP and a highly dedicated group of monitoring
organizations spent almost 2 years developing the Lower
Columbia River Estuary Plan, Volume 2: Aquatic
Ecosystem Monitoring Strategy for the Loiver Columbia
River-Information Management Strategy (LCREP, 1998).
The Monitoring Strategy of this report lays out a
phased-in approach to implementing a comprehensive
monitoring plan for the Lower Columbia River Estuary.
Special projects have been initiated to enhance under-
standing of the Estuary, with attention paid to
addressing the monitoring needs of salmon restoration.
Data management is another focus of the LCREP's
current efforts. Currently, there is no single place where
one can go to find all the existing information about
the Lower Columbia River Estuary. The Information
Management Strategy of this report (LCREP, 1998) lays
out a multi-phase approach for improving access to and
management of data. An example of progress is the
availability of technical data regarding the condition of
the Estuary, including data from the Bi-State Water
Quality Study, is available online at http://www.lcrep.org.
The LCREP has also focused its resources on devel-
oping educational programs for the area's students and
volunteer opportunities for residents. Since 2000, the
Partnership has developed more than 50 different field-
based Columbia River education curricula for more
than 32 school districts and assisted with classroom
programs, field trips, and on-river trips tor more than
45,000 students. The Partnership has also provided over
8,000 volunteers the opportunity to help plant more
than 11,000 native trees and shrubs at 18 habitat
restoration sites (LCREP, 2005a).
Conclusion
Based on data from the NCA estuarine survey, the
overall condition of the Lower Columbia River Estuary
is rated fair. The LCREP has been working collabora-
tively with many other organizations to monitor the
ecosystem; educate the public; and assess, protect, and
restore the extensive and diverse habitats that comprise
the Lower Columbia River Estuary. These efforts have
had positive effects in several areas of estuarine health
(e.g., bald eagle population increases, acreage of restored
habitat); however, other areas (e.g., water temperature
increases, toxic contaminant concentrations in fish
tissue) remain a concern.
342 National Estuary Program Coastal Condition Report
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tillamook Estuaries Partnership
Tillamook Estuaries Partnership
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Background
Although it is Oregon's second-largest estuary,
Tillamook Bay is relatively small (approximately 13 mi2)
and shallow (average depth of 6 feet) compared to other
NEP estuaries. Located on Oregon's northern coast,
Tillamook Bay is part of a coastal, temperate rainforest
ecosystem. Annual precipitation averages 90 inches in
the lower basin and close to 200 inches in the uplands.
This rainfall supplies fresh water to the basin's five major
rivers (Tillamook, Trask, Wilson, Kilchis, and Miami),
which drain a 597-mi watershed that includes some of
North America's richest timber and dairy lands
(TBNEP, 1999). Known as the "land of cheese, trees,
and ocean breeze," Tillamook County boasts a greater
population of cows than people and is dominated by
federal, state, and private forest land, which comprises
almost 90% of the county (TBNEP, 1998). Tillamook
Bay supports an oyster aquaculture industry, a commer-
cial/recreational port, and a recreational salmon fishery
(TBNEP, 1999).
Historically dependent on resource-extraction indus-
tries, the local economy of Tillamook County increas-
ingly relies on tourism and transfer payments to provide
for the county's 25,000 citizens (TBNEP, 1999). The
National Estuary Program Coastal Condition Report 343
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tillamook Estuaries Partnership
county's median household income is well below the
state avetage and was only 80% of the national average
in 2002 (U.S. Census Bureau, 2006). Although the
service sector is expanding because of tourism and a
growing population of retirees, dairy farming, logging,
and fishing still define the cultural landscape of the area
(TBNEP, 1999).
By the early 1990s, local citizens began to voice
concerns about the basin's declining natural resources.
Loss of spawning and rearing habitat had reduced
salmon runs, and decreasing water quality regularly
violated federal water quality standards and led to
closures of commercial shellfish beds. Erosion and sedi-
ment deposition, combined with development in the
floodplain, exacerbated water quality issues and habitat
degradation while increasing the magnitude and
frequency of flood events. To reverse these trends, the
Tillamook Estuaries Partnership (TEP) undertook
5 years of research, public outreach, and policy analysis,
resulting in completion of the "Restoring the Balance":
Comprehensive Conservation and Management Plan for
Tillamook Bay, Oregon in 1999 (TBNEP, 1999). The
TEP implements its CCMP under three program areas:
habitat enhancement, education, and research and
monitoring. The TEP also supports partner-led projects
through its Local Grant Program.
Environmental Concerns
The most significant environmental problems in the
Tillamook Bay watershed are habitat loss and simplifica-
tion, water quality, erosion and sedimentation, and
flooding, and the TEP researched and characterized
these problems during its CCMP development. The
Tillamook Bay basin has lost almost 85% of its histor-
ical intertidal wetlands to agricultural and urban devel-
opment (TBNEP, 1999). In addition, populations of
four of the five anadromous salmonid species (coho and
chum salmon, steelhead and cutthroat trout) have
dramatically decreased from historical levels. Loss of
spawning and rearing habitats are the major contribu-
tors to the declining populations. None of Tillamook
County's major watersheds meets the Clean Water Act
standards established by EPA and ODEQ, and bacterial
contamination and elevated water temperatures are the
two parameters of highest priority. The flood of 1996,
as well as the many floods that came before it, displaced
residents and caused major environmental degradation
and millions of dollars in property dam age. Loss of
floodplain function and stream complexity are the key
contributors to increased flooding and are a focus of the
TEP's enhancement efforts (TBNEP, 1999).
Population Pressures
The population of the NOAA-designated coastal
county (Tillamook) coincident with the TEP study area
increased by only 28% during a 40-year period, from
18,955 people in I960 to 24,262 people in 2000
(Figure 6-25) (U.S. Census Bureau, 1991; 2001). This
rate of population growth for the TEP study area was
one of the lowest rates of population growth for the
West Coast NEPs, and only one-fourth the population
growth rate of 100.3% for the collective NEP-coinci-
dent coastal counties of the West Coast region.
Tillamook County also had the lowest population
density (22 persons/mi2) of any of the West Coast
NEPs (U.S. Census Bureau, 2001). This estuary is not
surrounded by the large metropolitan areas that are
characteristic of some West Coast NEP estuaries, such
as Puget Sound or the San Francisco Estuary.
.030
.025 -
.020 -
.015 -
rt .010 -
2000
Figure 6-25. Population of NOAA-designated coastal county of
the TEP study area, 1960-2000 (U.S. Census Bureau, 199 I; 2001).
344 National Estuary Program Coastal Condition Report
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Jillamook Estuaries Partnership
NCA Indices of Estuarine
Condition—Tillamook Bay
The overall condition of Tillamook Bay is rated good
based on the four indices of estuarine condition used by
the NCA (Figure 6-26). The water quality index is rated
fair, and the sediment quality, benthic, and fish tissue
contaminants indices are rated good. Figure 6-27
Overall Condition
Tillamook Bay
(4.5)
Water Quality Index (3)
Sediment Quality Index (5)
Benthic Index (5)
Fish Tissue Contaminants
Index (5)
Figure 6-26. The
overall condition of the
TEP estuarine area is
good (U.S. EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80
Percent NEP Estuarine Area
100
Figure 6-27. Percentage of NEP estuarine area achieving each
ranking for all indices and component indicators —Tillamook Bay
(U.S. EPA/NCA).
provides a summary of the percentage of estuarine area
rated good, fair, poor, or missing for each parameter
considered. This assessment is based on data collected
by ODEQfrom 29 stations sampled in 1999. Please
refer to Tables 1-24, 1-25, and 1-26 (Chapter 1) for a
summary of the criteria used to develop the rating for
each index and component indicator.
Water Quality Index
Based on NCA survey results, the water quality index
for Tillamook Bay is rated fair. This index was devel-
oped using NCA data on five component indicators:
DIN, DIP, chlorophyll a, water clarity, and dissolved
oxygen. Most (69%) of the estuarine area was rated fair
because of limited water clarity and moderate levels of
DIP (Figure 6-28).
Water Quality Index -Tillamook Bay
Site Criteria: Number of component indicators in poor
or fair condition
• Good = No more than I is fair
O Fair = I is poor, or 2 or more are fair
• Poor = 2 or more are poor
O Missing
Figure 6-28. Water quality index data forTillamook Bay, 1999
(U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 345
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tillamook Estuaries Partnership
Dissolved Nitrogen and Phosphorus I
Tillamook Bay is rated good for DIN concentrations
and fair for DIP concentrations. Concentrations of
DIN were rated good in 100% of the estuarine area,
and DIP concentrations were rated fair in 97% of the
area.
Chlorophyll a Chlorophyll a concentrations in
Tillamook Bay are rated good. Three percent of the
estuarine area was rated fair for this component indi-
cator, with the remainder of the area (97%) rated good.
None of the TEP estuarine area was rated poor for
chlorophyll a concentrations.
Water Clarity Water clarity in Tillamook Bay is
rated poor. Approximately 43% of estuarine area was
rated poor for this component indicator, and 25% of
the area was rated fair.
Dissolved Oxygen Dissolved oxygen conditions
in Tillamook Bay are rated good, with 100% of the
estuarine area rated good for this component indicator.
Although conditions in Tillamook Bay appear to be
generally good for dissolved oxygen, measured values
reflect daytime conditions, and some areas of the Bay
may still experience hypoxic conditions at night.
Sediment Quality Index
The sediment quality index for Tillamook Bay is
rated good (Figure 6-29). This index was developed
using NCA data on three component indicators: sedi-
ment toxicity, sediment contaminants, and sediment
TOC. No area of the Bay exceeded thresholds for any
of these component indicators.
Sediment Toxicity I Sediment toxicity for
Tillamook Bay is rated good, with none of the estuarine
area rated poor for this component indicator.
Sediment Contaminants I Tillamook Bay is rated
good for sediment contaminant concentrations, with
100% of the estuarine area rated good for this compo-
nent indicator.
Total Organic Carbon I Tillamook Bay is rated
good for TOC concentrations, with 100% of the
estuarine area rated good for this component indicator.
Sediment Quality Index -Tillamook Bay
Site Criteria: Number and condition of component indicators
• Good = None are poor, and sediment contaminants is good
OFair = None are poor, and sediment contaminants is fair
®Poor = I or more are poor
O Missing
Fishing for Chinook salmon is popular in Tillamook Bay (TEP).
Figure 6-29. Sediment quality index data for Tillamook Bay,
1999 (U.S. EPA/NCA)
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tillamook Estuaries Partnership
&
Benthic Index
-*n
Fish Tissue Contaminants Index
The condition of the benthic invertebrate communi-
ties in Tillamook Bay is rated good based on deviations
from the expected species richness (Figure 6-30). This
analysis was based on 28 benthic samples collected
during 1999. A significant linear regression between log
species richness and salinity was found in Tillamook
Bay, although it was not strong (r2 = 0.31, p < 0.01).
One site, representing about 3% of the estuarine area,
was rated poor based on a lower-than-predicted species
richness. The cause for the less-than-expected species
richness at this site is not readily apparent because no
sediment ERMs were exceeded, only three ERLs were
exceeded, and TOG concentrations were within the
range found in the Bay. Another three sites, representing
11% of the estuarine area, were rated fair, and 24 sites,
representing 86% of the area, were rated good.
Benthic Index -Tillamook Bay
Site Criteria: Compared to
expected diversity
• Good = > 90%
OFair = 75% - 90%
• Poor = < 75%
O Missing
This fish tissue contaminants index for Tillamook
Bay is rated good (Figure 6-31), with only 8% of all
stations sampled where fish were caught exceeding EPA
Advisory Guidance values for whole-fish contaminant
concentrations. These risk calculations are appropriate
for populations that consume whole fish. The contami-
nant found most often in fish tissues from Tillamook
Bay was total PCBs.
Sediment Contaminant Criteria (Long et al., 1995)
ERM (Effects Range Median)—Determined for each
chemical as the 50th percentile (median) in a database of
ascending concentrations associated with adverse biological
effects.
ERL (Effects Range Low)—Determined for each
chemical as the I Oth percentile in a database of ascending
concentrations associated with adverse biological effects.
Fish Tissue Contaminants Index -Tillamook Bay
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
OFair = Falls within Guidance range
• Poor = Exceeds Guidance range
Figure 6-30. Benthic index data forTillamook Bay, 1999 (U.S.
EPA/NCA).
Figure 6-31. Fish tissue contaminants index data forTillamook
Bay, 1999 (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 347
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tillamook Estuaries Partnership
Addressing Bacterial
Contamination in Tillamook Bay
The driving force behind Tillamook Bay's nomina-
tion to the NEP was bacterial contamination. Inputs of
fecal coliform bacteria have resulted in frequent water
quality standard exceedences in the Bay's tributaries and
periodic closures of the Bay's oyster shellfishing industry
(Sullivan et al., 2005). To combat this problem, the
TEP has initiated an innovative monitoring strategy to
answer three key questions relating to bacteria in the
Bay and its watershed:
1. Is bacteria loading to the lower reaches of the Bay's
tributary rivers increasing or decreasing over
timescales of years to decades?
2. Where, how often, and for what length of time does
each of the Bay's five major tributary rivers violate
state water quality standards for bacteria?
3. What are the sources of the contamination, and how
much pollution do they contribute?
The TEP has instituted two complementary moni-
toring approaches to try and answer these questions: the
Storm-Based Monitoring Program and the Volunteer
Monitoring Program. In addition, the TEP has part-
nered with Oregon State University to embark on a
complementary 3-year Genetic Marker Study.
The Storm-Based Monitoring Program measured
fecal coliform bacteria concentrations and loads (as well
as other water quality parameters) to the Bay during
storm events. Between 1996 and 2002, the program
monitored approximately 28 separate storms on the
Bay's five tributary rivers. Results of this effort included
the following insights: (1) fall storm events exhibited
the highest levels of bacterial loading to the Bay; (2)
bacteria concentrations increased dramatically during
storm events, but varied greatly among the Bay's five
rivers; (3) bacteria concentrations measured in the rivers
appeared to be strongly influenced by precipitation
patterns prior to a storm and by rainfall intensity during
the storm; and (4) drier conditions prior to a storm and
greater rainfall during a storm generally resulted in
higher bacteria concentrations in the rivers (Sullivan et
al., 2002).
In addition to the initial set of storm-sampling sites,
the Storm-Based Monitoring Program also conducted
an intensive storm-monitoring effort during a 2-year
period on two river reaches identified as major bacteria-
contributing areas. Potential bacteria sources were docu-
mented and mapped using photos, global positioning
systems (GPSs), and field surveys to attempt to link
bacteria concentration spikes to likely sources. Results
of this effort are being used to identify those source
areas that appear to be the largest bacteria contributors
to the rivers and to prioritize the areas for corrective
action (Sullivan et al., 2002).
Since 1995, participants in TEP's Volunteer
Monitoring Program have braved wind, rain, sleet, and
occasional sun to collect water samples from 37 sites
across all 5 of the major tributaries entering Tillamook
Bay. Monitoring results from this effort are entered into
a long-term database that is shared with both local and
state partners (TEP, 2006b). This information assisted
in the development of a bacteria TMDL (ODEQ,
2001) for the watershed and has guided the TEP's
process to prioritize sites for enhancement. Results of
the Volunteer Monitoring Program revealed the
following insights: all five of Tillamook Bay's main trib-
utary rivers routinely violate Oregon's bacteria water
quality standard for water contact recreation; bacteria
concentrations peak during the summer low-water
period and during some fall, winter, and spring storms;
and the Tillamook River routinely has the highest
bacteria concentrations of the five rivers (ODEQ,
2001).
Because bacterial contamination is largely a problem
resulting from non-point source pollution, researchers
are searching for new methods to differentiate among
potential sources, such as manure from pastures, failing
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Jillamook Estuaries Partnership
septic systems, and STP overflows. A joint study by
Oregon State University and the TEP seeks to identify
bacteria sources by detecting genetic marker sequences
that are specific to the host species that produced the
feces. The intent of the study is to enable researchers to
discriminate among human, cow, domestic pet, water-
fowl, and other wildlife bacteria sources. Preliminary
results indicate that ruminants (e.g., cows, elk) are a
source of widespread bacterial contamination and that
human contributions to the contamination in some
river segments are also significant (TEP, 2006b).
The results of these efforts have led the TEP to
undertake several priority projects to reduce bacterial
contamination in the Bay. In collaboration with the
Tillamook County On-Site Sanitation Division, private
septic systems in the watershed will be inspected and
repaired as needed. The City of Tillamook has recently
completed a Stormwater Management Plan that will
identify measures to reduce bacterial loading and other
contaminants. In addition, a buffer-strip effectiveness
study is testing an experimental demonstration buffer
strip to determine its effectiveness in removing bacteria
from pasture runoff and help select BMPs for manure
management. Finally, a pilot project has begun to
develop and implement performance-based policies for
agriculture to meet or exceed water quality standards in
the lower Tillamook Bay basin (TEP, 2006b).
A volunteer collects a plankton sample inTillamock Bay (TEP).
National Estuary Program Coastal Condition Report 349
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tillamook Estuaries Partnership
Tillamook Estuaries Partnership
Indices of Estuarine Condition
The TEP has developed a set of environmental indi-
cators to assess water quality, habitat extent, and the
status of living resources in Tillamook Bay. Each of the
draft indicators is tied to objectives/goals from the
TEP's CCMP and seek to answer one of the TEP's
focus questions. For example, the number of stream
miles opened through fish passage enhancement
projects measures progress towards the CCMP goal of
enhancing 100 miles of upland instream habitat by
2010 and determines whether more freshwater habitat
is becoming available to native salmon and trout (TEP,
2004).
Water and Sediment Quality
Although not part of the NCA's water quality index,
bacterial contamination is the priority water quality
issue in Tillamook Bay and its tributaries (TBNEP,
1999). Sewer outfalls, leaking or malfunctioning septic
tanks, and runoff from the watershed's dairy farms
contribute fecal coliform bacteria to the Bay. Although
bacterial loading has increased historically as farming
and development in the area increased, recent moni-
toring has shown improving trends in some river
reaches (TEP, 2006a). This is likely due to the imple-
mentation of the TEP's CCMP. The TEP indicators for
water quality include ongoing monitoring in the Bay
and tributaries to continue tracking changes in fecal
coliform bacteria concentrations (TEP, 2004).
Dissolved oxygen concentrations and rises in stream
temperatures are also major water quality concerns in
the TEP study area (TEP, 2006a). Eutrophication and
low dissolved oxygen concentrations have not been a
problem in Tillamook Bay proper; however, low
dissolved oxygen levels have been observed in some of
the Bay's lowland sloughs and tributaries (TBNEP,
1999). Although the NCA data noted good dissolved
oxygen concentrations throughout the Bay, the NCA
sampling sites were primarily located in the main
portion of the Bay. The TEP is working with ODEQ to
further evaluate the extent and impact of low dissolved
oxygen levels in Tillamook Bay sloughs. Low water
temperatures in the Bay's streams are important for
maintaining the area's salmon habitat; however, water
temperatures in the Wilson, Trask, and Tillamook rivers
Dairy herds are a prominent agricultural use of land in Tillamook County (TEP).
350 National Estuary Program Coastal Condition Report
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CHAPTER 6 1 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tillamook Estuaries Partnership
have exceeded water quality standards for temperature
(TBNEP, 1999). The TEP's indicators include moni-
toring water temperature in streams and dissolved
oxygen levels in sloughs (TEP, 2004).
Habitat Quality
Maintaining and improving the habitats necessary to
support this estuary's declining salmonid populations is
an important priority for the TEP. Healthy freshwater
and riparian habitats are important for maintaining low
water temperatures and for providing spawning grounds
for salmonids, whose young need salt marshes, tidal
channels, and eelgrass beds for food and protection
(TEP, 2006a). The TEP has developed several draft
indicators for assessing habitat quality and quantity in
Tillamook Bay, including changes in the distribution
and type of riparian vegetation along the Bay's tributary
rivers, the number of stream miles affected by fish
passage enhancement projects, the areal extent of
wetlands and open water restored through the removal
of tidal restrictions, and changes in the extent of
seagrass beds (TEP, 2004).
The amount of historical information available for
the TEP indicators varies. For example, historic and
recent data indicate that Tillamook Bay has lost roughly
85% of its intertidal wetlands to agricultural and resi-
dential development. To address these losses, the
CCMP establishes a goal of restoring 750 acres of these
habitats (TBNEP 1999), and the Partnership will have
restored approximately 400 acres by the summer of
2007. In cases where the TEP knows little about
historic habitats, indicators characterize the status of the
resource and track change from the present. For
example, the TEP monitors the change in eelgrass
distribution from its current coverage of 897 acres
(TEP, 2005).
Living Resources
The TEP has been implementing projects aimed at
evaluating the status and trends of the abundance and
distribution of aquatic species. Examples of these
projects include an exotic species detection effort, a
rapid bioassessment, and a study on fish use of the
estuary. In addition, the TEP's living resource indicators
of estuarine condition include the annual number of
coho salmon adults returning to the study area for
spawning, as well as the annual number of coho, chum,
Chinook, steelhead, and cutthroat smolts migrating
downstream from the Little North Fork Wilson River
and Little South Fork Kilchis River (TEP, 2004).
The Exotic Species Project, which is being pursued
for the LCREP, TEP, and PSAT, is seeking to develop a
consistent approach for monitoring aquatic nuisance
species. Together, these three NEPs and other partners
in these basins will develop a regionally coordinated
approach for monitoring aquatic nuisance species in the
Pacific Northwest using models developed and tested in
the San Francisco Estuary watershed (TEP, 2006b). As
an initial step for this project, the TEP has developed
An Exotic Species Detection Plan for Tillamook Bay
(Cohen, 2004).
The TEP's Tillamook Bay Rapid Bio-Assessment is
designed to quantify the abundance and distribution of
four species of juvenile salmonids throughout the Bay's
watershed. The full basin view of each species' distribu-
tion and their spatial shifts in abundance will provide
valuable information for the development of a restora-
tion strategy based on passage barriers, peak spawning
and rearing reaches, temperature-limiting habitats, and
upstream-migration behaviors. The 3-year inventory
began in 2005 and is encompassing approximately 350
stream miles. In 2005, the inventory found that the
number of coho salmon returning to the Bay's streams
for spawning was insufficient to adequately seed the
watershed's available habitat (Bio-Surveys, L.L.C., 2005;
TEP, 2006b).
The primary objectives of the Fish Use of the
Estuary study were to develop baseline information on
fish use of the Tillamook Bay estuary and to test and
evaluate a sampling approach for long-term monitoring
of fish abundance and distribution across major habitat
types within the estuary. The sampling design for the
long-term monitoring program was structured to allow
the testing of hypotheses regarding the use of three
regions of the estuary (lower, middle, and upper), rwo
major substrate types (fine-grained and coarse-grained),
and the effect-sampling time (months, within months,
and years) for relatively abundant anadromous salmonid
and non-salmonid species. Monitoring data from 1999
through 2001 indicated that fish species composition in
the estuary has been relatively stable since the mid-1970s
(Ellis, 2002; TEP, 2006b).
National Estuary Program Coastal Condition Report 351
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Tillamook Estuaries Partnership
Current Projects,
Accomplishments, and Future
Goals
The TEP's primary goals are to enhance water
quality to meet state and federal standards, restore
native salmonid populations, reduce the frequency and
impacts of catastrophic flooding, and encourage stew-
ardship among residents and visitors. To attain these
goals, the TEP and its many partners are implementing
targeted resource-enhancement projects, characterizing
the estuary and its watersheds, and educating citizens
and visitors about the Bay's natural resources and the
importance of stewardship. The TEP plans to continue
pursuing these activities through three programs: the
Habitat Enhancement Program (developing and imple-
menting on-the-ground projects aimed at improving the
production and function of natural systems); the
Research and Monitoring Program (characterizing the
interactions of human and natural systems, tracking
system-wide trends, and evaluating the effectiveness of
CCMP implementation); and the Education Program
(working to facilitate a stewardship ethic among visitors
and residents of Tillamook County through hands-on
learning and outreach activities).
The TEP's annual workplan details the projects that
the Partnership undertakes within each of these
programs. One of the tools the TEP is using to track
CCMP implementation is an innovative Web site
known as the Performance Indicators Visualization and
Outreach Tool (PIVOT), which is available at
http://gisweb.co.tillamook.or.us/mapping/pivot/tillamoo
k.htm. The TEP is also currently developing a compre-
hensive monitoring program to more fully characterize
long-term, system-wide trends and the impact of
CCMP implementation (TEP, 2005).
To implement the CCMP s actions aimed at recon-
necting intertidal wetlands and enhancing tidal marshes,
the TEP raised more than $1.3 million to acquire three
properties that form a 375-acre peninsula at the conflu-
ence of the Wilson and Trask rivers. Currently
underway, this project is expected to result in the
protection and restoration of a natural, functioning
ecosystem on approximately 200 acres within the
formerly-diked tidelands and forested wetlands at the
Bay's southern end. The remaining 175 acres will be
restored under a "muted tidal connection" to ensure
flood mitigation. Primarily, the fully reconnected areas
will be restored to intertidal habitats consisting of high
salt marsh, brackish marsh, and forested wetlands.
Existing remnant floodplain forests will be permanently
protected and managed to maintain their natural values
(USAGE, 2004a).
In 2003, the TEP initiated its Backyard Planting
Program (BYPP) to help landowners on high-priority
streams restore degraded riparian zones. The BYPP
coordinator collaborates with interested landowners to
develop an enhancement plan for their property. The
BYPP provides free removal of invasive vegetation,
plants native trees and shrubs, and maintains the site for
3 years. By the end of its third year, the BYPP will have
enrolled more than 80 landowners and restored 15
miles and 75 acres of high-priority riparian habitat
(TEP, 2006b).
Conclusion
Tillamook Bay is representative of many small Pacific
Northwest estuaries. Dominated by rugged mountains
with narrow coastal plains, it presents a challenging
combination of environmental concerns. Elevated
bacteria levels have closed oyster beds to shellfishing,
and loss of habitat and increasing stream temperatures
have impacted local salmonid populations. Based on the
results of the NCA survey, the overall condition of
Tillamook Bay is rated good. Although fair and poor
conditions were noted for several indicators, this was
the highest rating received by any of the six West Coast
NEP estuaries monitored. The TEP is finding ways to
protect both the area's natural resources and its natural
resource-dependent economy. The TEP has focused on
reducing bacteria contamination in the Bay and its trib-
utaries and improving the area's habitat quality for
salmonid populations.
352 National Estuary Program Coastal Condition Report
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
San Francisco Estuary Project
San Francisco Estuary Project
Oan
Francisco
Estuary
Project
Central Bay
South Boy
lower South Boy
sfep.abag.ca.gov
Background
The San Francisco Estuary is one of the largest estu-
aries on the West Coast, encompassing about 460 mi2
of open water. The Estuary is shallow, and approxi-
mately one-third of the total water area has a depth of
less than six feet. The Sacramento and San Joaquin
rivers supply approximately 90% of the Estuary's fresh-
water input and drain about 40% of California's land
area. These rivers enter the Estuary through the
Sacramento-San Joaquin River Delta, a large area of
diked and drained swampland in the northern portion
of the Estuary (SFEP, 1999). Major embayments within
the San Francisco Estuary include the Suisun, San Pablo,
Central, South, and Lower South bays.
The San Francisco Estuary and its associated tribu-
taries encompass roughly 1,600 mi2, provide drinking
water to 23 million Californians (two-thirds of the states
population), and irrigate 4.5 million acres of farmland.
The Estuary also enables the residents of the nation's
fifth-largest metropolitan region to pursue diverse activi-
ties, including shipping, fishing, recreation, and
commerce. Finally, the Estuary hosts a rich diversity of
flora and fauna, with nearly half of the birds that migrate
along the Pacific Flyway and about two-thirds of the
state's salmon passing through the Estuary (SFEP, 2004).
National Estuary Program Coastal Condition Report 353
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Son Francisco Estuary Project
Environmental Concerns
Freshwater management is an environmental concern
in the San Francisco Estuary region. Each day, millions
of people, industries, and municipalities around the
Estuary use river water for an array of activities, then
collect, recycle, treat, and discharge their wastewater
into the Estuary. In rural areas, farmers irrigate crops
and water their livestock. Maintaining river flows under
the pressure of exporting water to southern California is
a major environmental concern in the Estuary, and
during droughts and heavy rain years, this pressure
makes managing the system even trickier. Add to these
needs other issues, such as pesticides and other pollu-
tants that get washed into the creeks, rivers, and bays,
and water quality management for the Estuary becomes
even more challenging.
Population Pressures
The population of the 12 NOAA-designated coastal
counties coincident with the San Francisco Estuary
Project (SFEP) study area increased by 96.1% during a
40-year period, from 4.5 million people in I960 to
8.7 million people in 2000 (Figure 6-32) (U.S. Census
Bureau 1991; 2001). This rate of population growth
for the SFEP study area was slightly lower than the
population growth rate of 100.3% for the collective
NEP-coincident coastal counties of the West Coast
region. However, the coastal counties surrounding
the SFEP had the highest population density (844
persons/mi2) of any of the West Coast NEP study areas
10
o 4
I960
2000
Figure 6-32. Population of NOAA-designated coastal counties
of the SFEP study area, 1960-2000 (U.S. Census Bureau, 1991;
2001).
(U.S. Census Bureau, 2001). The San Francisco Estuary
is surrounded by major metropolitan areas that serve as
large centers for international commerce and industrial
and recreational activities.
NCA Indices of Estuarine
Condition—San Francisco
Estuary
The overall condition of the San Francisco Estuary is
rated fair based on the four indices of estuarine condi-
tion used by the NCA (Figure 6-33). The water quality
index is rated fair to poor, the sediment quality index is
rated fair, the benthic index is rated good, and the fish
tissue contaminants index is rated poor. Figure 6-34
provides a summary of the percentage of estuarine area
rated good, fair, poor, or missing for each parameter
considered. This assessment is based on data collected
by the NS&T Program and Moss Landing Marine
Laboratories, under contract to the Southern California
Water Resources Research Project (SCWRRP), from 50
stations sampled in the San Francisco Estuary in 2000.
Please refer to Tables 1-24, 1-25, and 1-26 (Chapter 1)
for a summary of the criteria used to develop the rating
for each index and component indicator.
Overall Condition
San Francisco Estuary
(2.75)
Water Quality Index (2)
Sediment Quality Index (3)
Benthic Index (5)
Fish Tissue Contaminants
Index (I)
Figure 6-33. The
overall condition of the
SFEP estuarine area is
fair (U.S. EPA/NCA).
354 National Estuary Program Coastal Condition Report
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Son Francisco Estuary Project
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80
Percent NEP Estuarine Area
Missing
Figure 6-34. Percentage of NEP estuarine area achieving each
ranking for all indices and component indicators San Francisco
Estuary (U.S. EPA/NCA).
Water Quality Index
Based on NCA survey results, the water quality index
for the San Francisco Estuary is rated fair to poor
(Figure 6-35). This index was developed using NCA
data on five component indicators: DIN, DIP, chloro-
phyll a, water clarity, and dissolved oxygen. Some 20%
of the estuarine area was rated poor for water quality,
and 73% of the area was rated fair. Diminished water
quality in the Estuary was primarily due to limited
water clarity and to elevated levels of DIN and DIP.
Water Quality Index - San Francisco Estuary
Site Criteria: Number of component indicators in
poor or fair condition
• Good = No more than I is fair
OFair = f is poor, or 2 or more are fair
• Poor = 2 or more are poor
O Mis sing
Good
7% Poor
(5
Fair
73%
Figure 6-35. Water quality index data for the San Francisco
Estuary, 2000 (U.S. EPA/NCA).
The dominant marsh vegetation in this area of the
San Bruno Marsh is an invasive, non-native Sport/no,
which is a hybrid of an introduced and a native
species (San Francisco Estuary Invasive Spartina
Project).
National Estuary Program Coastal Condition Report 355
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CHAPTER 6 ' WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
San Francisco Estuary Project
Dissolved Nitrogen and Phosphorus I The San
Francisco Estuary is rated fair for DIN concentrations
and poor for DIP concentrations. Concentrations of
DIN were rated fair in 68% of the estuarine area, and
DIP concentrations were rated poor in 74% of the area.
In addition to natural inputs of nutrients from offshore
coastal upwelling, high levels of urban and agricultural
runoff into the Sacramento Pviver may also be major
contributors to the elevated nutrient levels found in the
San Francisco Estuary.
Chlorophyll a Chlorophyll a concentrations in
the San Francisco Estuary are rated good. Ten percent
of the estuarine area was rated fair for this component
indicator, and the remaining 90% was rated good.
Water Clarity Water clarity in the San Francisco
Estuary is rated poor. Approximately 36% of the estu-
arine area was rated poor for this component indicator,
and 31% of the area was rated fair.
Dissolved Oxygen I Dissolved oxygen conditions
in the San Francisco Estuary are rated good, with 99%
of the estuarine area rated good for this component
indicator. Although conditions in the San Francisco
Estuary appear to be generally good for dissolved
oxygen, measured values reflect daytime conditions, and
some areas of the Estuary may still experience hypoxic
conditions at night.
Sediment Quality Index
The sediment quality index for the San Francisco
Estuary is rated fair (Figure 6-36). This index was devel-
oped using NCA data on three component indicators:
sediment toxicity, sediment contaminants, and sediment
TOC. Four percent of the estuarine area was rated poor
for sediment quality, exceeding thresholds for at least
one of these component indicators, and 73% of the area
was rated fair, primarily as a result of sediment contami-
nant levels.
Sediment Toxicity \ Sediment toxicity in the San
Francisco Estuary is rated good, with 100% of the estu-
arine area rated good for this component indicator.
Sediment Contaminants The San Francisco
Estuary is rated good for sediment contaminant concen-
trations, with 4% of the estuarine area rated poor for
this component indicator and 73% of the area rated
fair.
Total Organic Carbon I The San Francisco
Estuary is rated good for sediment TOC. TOC concen-
trations were rated good in 96% of the estuarine area
and fair for the remaining 4% of the area.
Sediment Quality Index - San Francisco Estuary
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
OFair = None are poor,and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
\
Figure 6-36. Sediment quality index data for the San Francisco
Estuary, 2000 (U.S. EPA/NCA).
356 National Estuary Program Coastal Condition Report
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CHAPTER 6 ! WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
San Francisco Estuary Project
&
Benthic Index
•^H
Fish Tissue Contaminants Index
The condition of the benthic invertebrate communi-
ties in the San Francisco Estuary is considered good
based on deviations from the expected species richness
(Figure 6-37). A significant linear regression between
log species richness and salinity that was moderately
strong (r2 = 0.54, p < 0.01) was found in the Estuary.
Six percent of the estuarine area was rated poor based
on a lower-than-predicted species richness, and 16% of
the area was rated fair. The remaining 78% of the estu-
arine area was rated good for benthic condition. It is
possible that sediment contamination contributed to
the lower species richness in several of the areas rated
poor and fair because 6 ERLs were exceeded at 6 of the
11 sampling sites in these areas. However, the reduced
species richness is not simply related to sediment conta-
mination because 21 of the 39 sites rated good for the
benthic index had an equivalent or greater number of
contaminants exceeding their ERLs.
Benthic Index - San Francisco Estuary
Site Criteria: Compared to
expected diversity
• Good = > 90%
OFair = 75% - 90%
• Poor = <7S%
O Missing
Good
78%
Figure 6-37. Benthic index data for the San Francisco Estuary,
2000 (U.S. EPA/NCA).
The fish tissue contaminants index for the San
Francisco Estuary is rated poor. Fifty-eight percent of all
stations sampled where fish were caught exceeded EPA
Advisory Guidance values using whole-fish contaminant
concentrations (Figure 6-38). These risk calculations are
appropriate for populations that consume whole fish.
The contaminants found in the fish tissues sampled
included total PCBs and, occasionally, mercury.
Sediment Contaminant Criteria (Long et al., 1995)
ERM (Effects Range Median)—Determined for each
chemical as the 50th percentile (median) in a database of
ascending concentrations associated with adverse biological
effects.
ERL (Effects Range Low)—Determined for each
chemical as the I Oth percentile in a database of ascending
concentrations associated with adverse biological effects.
Fish Tissue Contaminants Index - San Francisco
Estuary
Site Criteria: EPA Guidance concentration
• Good = Below Guidance range
OFair = Falls within Guidance range
• Poor = Exceeds Guidance range
Figure 6-38. Fish tissue contaminants index data for the
San Francisco Estuary, 2000 (U.S. EPA/MCA).
National Estuary Program Coastal Condition Report 357
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
San Francisco Estuary Project
Ecosystem Indicators for the San
Francisco Estuary
The San Francisco Estuary is considered one of the
best-studied ecosystems in the world; however, the
myriad of disparate data-collection efforts for the
Estuary has not resulted in a coherent performance-
measurement system. Currently, no single, objective,
and comprehensive assessment of the health of the San
Francisco Estuary and its watersheds is widely recog-
nized as valid by ecosystem managers and policy
makers. Such an assessment would identify problems
early, direct agency efforts towards real priorities, and
measure the impacts that collective actions are having
on the systems health so that the SFEP can continue to
adapt and improve its management strategies. The
assessment would be conducted using a variety of envi-
ronmental indicators, which are the vital signs derived
from the chemical, biological, and physical measure-
ments that mark the improvement or deterioration of
the ecosystem. A recently released U.S. Government
Accountability Office (GAO) report (U.S. GAO, 2004)
recommends that leadership at the highest levels of
government mesh the disparate efforts of multiple agen-
cies and organizations into a coherent, science-based
environmental management system for the Estuary.
Although no program in the San Francisco Estuary
area is currently charged with integrating measurements
and indicators into an assessment of ecosystem condi-
tion, identifying attributes that define ecosystem condi-
tion, or pinpointing gaps in that knowledge, progress is
being made towards these goals. In 2004, The Bay
Institute (TBI) and its partners made the first attempt
to assess the ecological condition of the Estuary and
reported the results using language accessible to the
general public in its Ecological Scorecard (TBI, 2003).
Additional partnerships between organizations studying
the Estuary have been created to develop a consensus set
of indicators for use by all stakeholders. These partner-
ships recently completed a report (Thompson and
Gunther, 2004) documenting 47 separate recom-
mended environmental indicators and have organized
indicator workshops. These efforts build on previous
indicator identification efforts and existing Bay-region
monitoring programs, including the Inneragency
Monitoring Program and the USGS Regional
Monitoring Program.
The Ecological Scorecard was a collaborative project
between the San Francisco Estuary Institute (SFEI), the
Center for Ecosystem Management, and TBI. Assisted
by a grant from the SFEP, this project evolved over a
3-year period, with input from a wide-range of local
scientists and a panel of nationally recognized experts.
The Scorecards Bay Index uses science-based indicators
to grade the condition of die San Francisco Bay region,
the first of a series of four major ecological regions of
the Estuary (i.e., San Francisco Bay, San Francisco
Delta, San Joaquin River, and Sacramento River) to be
assessed. The Scorecards indicators are combined into
eight indices that track the Estuary's environment (e.g.,
habitat, freshwater inflow, water quality); its fish and
wildlife (e.g., food web, shellfish, fish); and the manage-
ment of its resources (e.g., fishable, swimmable, drink-
able). The grading system compares current conditions
in the Bay and its watershed to historical conditions,
environmental and public health standards, and restora-
tion goals. Grades in the 2005 Scorecard (see figure)
range from B to F, reflecting the long-term decline in
the Bay's ecological health; however, there are some
small but noticeable short-term improvements in the
area's habitat and shellfish populations (TBI, 2003;
2005).
Another effort to develop environmental indicators is
being led by the SFEP and its partner, SFEI. These
agencies have formed a Bay Area Indicator Consortium
to provide direction in strategizing the development of
ecosystem indicators for the San Francisco Estuary. The
Consortium recommends that the same indicators
developed for the Ecological Scorecard be expanded and
used as the starting point for the ecosystem indicators.
In May 2004, the SFEP partnered with the SFEI and
358 National Estuary Program Coastal Condition Report
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CHAPTER 6 ' WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Son Francisco Estuary Project
the Consortium to produce the report
Development of Environmental Indicators of
the Condition of San Francisco Estuary: A
Report to the San Francisco Estuary Project,
which was submitted to EPA
Headquarters in September 2004
(Thompson and Gunther, 2004).
With support from EPA, the
Consortium organized an Indicators
Workshop in January 2005. Workshop
participants explored new state and federal
initiatives highlighting the need for
"performance-based environmental
management," as well as recent successes
by the SEEP to develop a meaningful
environmental indicator system. The
workshop's purpose was to build consensus
on the importance of and the need for
scientifically valid, leading environmental
indicators; to develop a framework for
interagency cooperation and collaboration
on the development, refinement, and use
of environmental indicators; and to attract
commitments of ongoing financial and
programmatic support. Workshop atten-
dees included approximately 40 partici-
pants representing the agencies developing
and entities using the data (SEEP, 2006).
m
D+
Score = 31
C+
Score = 58
Score = 65
F
Score = 10
B
Score = 73
C-
Score = 45
C-
Score = 38
C-
Score = 46
Habitat
Bay habitat loss is slowly being
reversed, but pace of restoration
unchanged since 2003 - at current rate,
more than 150 years to reach tidal marsh
restoration goal.
Freshwater Inflow
Reduced inflows still degrade the Bay
ecosystem - inflow improved in 2004,
but overall conditions since 2000 are
worse than two previous decades.
Water Quality
Open waters are cleaner than in 2003,
but not all standards are met in parts of
the Bay. Toxic sediments, stormwater
runoff are major problems. South and
San Pablo Bays are most polluted.
Food Web
Plankton levels in Suisun Bay are still
critically low, reducing food resources
for fish and birds. Phytoplankton
levels in all other parts of the Bay are
improving.
Shellfish
Crab and shrimp numbers rise in Central
and South Bays, but not in the upper
Bay. Estuarine species lose ground to
marine shellfish.
Fish
Recent upward trend reverses, fish
populations return to critically low
levels. Estuarine species of the upper
Bay are hardest hit.
Fishable-Swimmable-Drinkable
More fish were caught but most are still
unsafe to eat. Beach closures continue
to rise, drinking water violations hold
steady.
Stewardship
Little progress towards conserving
more water, reducing pesticide use, and
restoring freshwater inflows, but some
efforts to issue pollution limits move
forward.
Grades are for the 2002-2005 period
A = Excellent
B = Good
C = Fair
D = Poor
F = Critical
Short-term = trend over
last 5 years
Long-term = trend over last
25 years or more
= improving
= declining
= stable
San Francisco Bay Index 2005 Scorecard (TBI, 2005).
National Estuary Program Coastal Condition Report 359
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CHAPTER 6
WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Son Francisco Estuary Project
San Francisco Estuary Project
Indicators of Estuarine Condition
The San Francisco Estuary has had the benefit of
several long-term monitoring programs, including the
Regional Monitoring Program for Trace Substances
(RMP), sampling and analysis by USGS, and the
Interagency Ecological Project (IEP). The RMP has
investigated chemical contamination in the water, sedi-
ments, and biota of the Estuary since 1993 and
provides data on spatial patterns and long-term trends
for use in management of the Estuary (SFEI, 2003).
The USGS has more than 35 years of water quality data
on various parameters, such as chlorophyll, nutrients
(phosphorus and nitrogen), suspended sediments,
salinity, and dissolved oxygen. The USGS data provide
a record of biological and chemical changes in the
Estuary. These data have been used to show improve-
ments in dissolved oxygen concentrations in the South
Bay and changes in phytoplankton production in
Suisun Bay (USGS, 2006b). The IEP has monitored
fisheries and the effects of freshwater diversions on the
biota of the San Francisco Bay proper and the
Sacramento-San Joaquin Delta since 1971 (IEP, 2006).
Recent IEP data have shown drastic declines in impor-
tant delta fish species, such as striped bass, delta smelt,
and longfin smelt (Hieb et al., 2005). Other local, state,
and national programs, such as the Bay Protection and
Toxic Cleanup Program, Coastal Intensive Sites
Network (CISNet), EMAP, and NOAA's NS&T
Program, have also provided data on the water, sedi-
ments, and biota of the San Francisco Estuary. It is
beyond the scope of this writeup to comprehensively
discuss all of these indicators; however, several indicators
of particular interest are discussed in the following
sections. Additional information about the San
Francisco Estuary is available from http://sfep.abag.
ca.gov or http://www.sfei.org.
Water and Sediment Quality
Current and historical activities in California have
contributed PCBs, pesticides, and mercury and other
heavy metals (e.g., silver and copper) to the sediments
of the San Francisco Estuary. Urban runoff in area
watersheds is a significant, contemporary source of
various contaminants, including mercuiy and PCBs,
which are currently the topic of TMDLs proposing
large reductions in urban runoff (CRWQCB, 2004).
Although many of these contaminants have been
banned, they are persistent in the environment, biomag-
nify through the food web, and bioaccumulate in fish
and wildlife. The issue of sediment contamination in
the Estuary is exacerbated by the waterbody's current
levels of turbidity. Hydraulic gold mining in the Sierra
Nevada foothills during the Gold Rush washed
hundreds of millions of metric tons of sediment into
the Estuary (Wright and Schoellhamer, 2004), which
was enough sediment to decrease water depths by as
much as five to ten feet (CRWQCB, 2004). Sediments
within the shallow Estuary continue to be resuspended
by daily tidal actions and winds. Resuspension of conta-
minated sediments introduces biologically available
contaminants into the water column. The turbidity that
is caused by this resuspension also controls the depth to
which natural light can penetrate in the water column,
limiting photosynthesis and affecting the food web.
The highest concentrations of contaminants in the
sediments are most often found at the urbanized edges
of the Estuary, and the distribution of these contami-
nants is primarily driven by two factors: inputs from
industrial and military sources near San Jose, southern
San Francisco, and Oakland, as well as the East Bay
shoreline; and the distribution of the fine particles to
which these contaminants are sorbed. Many of the areas
with high concentrations of PCBs, DDT, and/or chlor-
dane in sediment correspond to the areas of the Estuary
(e.g., South San Francisco Bay, San Pablo Bay, and
along the East Bay shoreline) with high percentages of
fine sediments (Connor et al., 2004).
PCB contamination remains one of the greatest
water quality concerns in the Estuary, and PCB clean-
up is a primary focus of the San Francisco Regional
Water Quality Control Board (SFRWQCB). PCB cont-
amination is greatest in the South Bay; all samples from
the South Bay exceeded the PCB water quality objec-
tive, with maximum concentrations measured at the
southern end of the South Bay. The few samples that
did not exceed the objective were from the northern
portion of the San Francisco Estuary (CRWQCB,
2004). In another study, the California Toxic Rule
(CTR) water quality criteria for PCBs were exceeded in
90% of RMP water samples collected from the Estuary
from 1993 to 2003, and regression analyses have shown
360 National Estuary Program Coastal Condition Report
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CHAPTER 6 WEST COAST NA1IONAL ESTUARY PROGRAM COASTAL CONDITION
Son Francisco Estuary Project
exponential declines in PCB concentrations in mussels
at most transplant locations from 1980 to 2003 (Davis
et al., in prep).
Although concentrations of legacy pesticides (i.e.,
pesticides that have been banned, including DDTs,
chlordane, and dieldrin) in the Estuary continue to be
an issue, there are some indications that water quality
has improved over time. Legacy pesticide concentrations
exceeded CTR water quality criteria in 5% to 20% of
water samples collected during 1993-2001 (Connor et
al., 2004); however, declining concentrations of legacy
pesticides have been observed in transplanted mussels
from the Estuary (Davis et al., in prep).
Mercury contamination in the Estuary dates back to
19th-century mining practices, and sediment cores from
the South Bay reflect the historic changes in concentra-
tions over time (SFEI, 2004). Pre-mining concentra-
tions were about four to five times lower than today's
concentrations (Conaway et al., 2003). The legacy of
mercury mining in the South Bay has created a reservoir
of high mercury concentrations within the Bay's water
and sediments (Figure 6-39). Old mines are also a
©
Sediment: Mercury
Range: 0.04 - 0.42 (mg/Kg)
Q Below TMDL (0.20)
0 0.21 -0.26
0.27-0.30
0.31 -0.32
0.33 -0.42
f} Random
(•) Historic
0 8 10 20 Miles
Iti i I i i i I
continuing source of mercury, which can be mobilized
from land and transported to the Estuary during rainfall
events. In 2002, the concentration of total mercury
exceeded the water quality objective in 32% of samples
and was above the sediment target concentration in
84% of the samples (SEFI, 2004).
Other contaminants, such as copper, have demon-
strated declines in the San Francisco Estuary. Copper
concentrations in water, clams, and sediments collected
from the South Bay declined from 1979 to 2003. RMP
water data show statistically significant declines in
copper concentrations at all historical South Bay
stations, and USGS data show corresponding declines
in copper concentrations measured in the clam Macoma
baltbica and in sediments from the South Bay. Declines
of copper in Macoma have been correlated with declines
in copper in effluents from the Palo Alto WWTP,
located in the South Bay (SFEI, 2004).
Primary production of phytoplankton in the San
Francisco Estuary has historically been light-limited
because of the waterbody's turbidity (SFEI, 2004).
In recent years, chlorophyll levels in the Estuary have
©
o
©
°
o
Water: Total Mercury
Range: 0.00 1 3 - 0.0762 (|jg/L)
O 0.0013-0.0050
O 0.005 1 - 0.0074
0.0075-0.0094
0.0095 - 0.0250
Below guideline
10.0.251 -0.0752
Above guideline
Random
Historic
O
0 5 10
l i i i t
20 Miles
Figure 6-39. Maps of mercury concentrations in water and sediment of the San Francisco Estuary (SEFI, 2004).
National Estuary Program Coastal Condition Report 361
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
San Francisco Estuary Project
increased, while turbidity in the Bay has declined (SFEI,
2006). A South Bay suspended-sediment model, devel-
oped by USGS, predicts that increases in wetland area
(as proposed under the South Bay Salt Pond Project)
could result in increased sediment deposition onto
wetlands and a subsequent decrease in suspended sedi-
ments in the water column (Shellenbarger et al., 2004).
The resulting increase in light penetration could cause
higher phytoplankton productivity. In the northern
reaches of the Estuary, chlorophyll concentrations have
dramatically decreased in Suisun Bay sites since the
invasion of the freshwater clam Potamocorbula in 1986.
The high abundance of this filter-feeding clam has
resulted in declines in chlorophyll in this Bay, from an
average of 9.8 mg/L (pre-invasion) to 2.1 mg/L (post-
invasion) (SFEI, 2003).
Habitat Quality
Wetlands serve several important functions in the
San Francisco Estuary, including acting as natural filters,
trapping sediment, and providing habitat for a variety
of fish, shellfish, waterfowl, and other wildlife. It is esti-
mated that the Estuary has lost more than 500,000
acres of tidal wetlands since 1850 (SFEP, 1999). The
acquisition and restoration of the region's wetlands is a
top implementation priority of the SFEP's Comprehen-
sive Conservation and Management Plan (SFEP, 1993),
and the SFEP has focused on tracking this issue as an
indicator of the health of the Estuary. Since 2001,
15,000 acres of Cargill salt ponds and related lands have
been acquired in the South Bay, and 1,400 acres have
been acquired in the North Bay (SFEP, 2004).
Habitat in the Estuary has been affected by the intro-
duction of invasive species. For example, giant reed
(Arundo donax) was originally introduced into
California by the Spanish in the late 1800s for erosion
control along drainage canals. Since then, this species
has become a significant problem along riparian areas
around the Estuary because it spreads easily, requires
large amounts of water, can smother native riparian
vegetation, and is highly flammable. The reed has been
found from Sacramento River tributaries to small urban
streams throughout the Estuary. Eradication and educa-
tion programs for this invasive species are currently
underway in areas of the Estuary (SFEP, 2000).
Living Resources
Public attention has focused on invasive species in
the Estuary since the 1990s, when the first comprehen-
sive study was pursued (Cohen and Carlton, 1998).
Some of the many invasive species present in the San
Francisco Estuary include the green crab, shimofuri
goby, Spartina alterniflora and its hybrids, Asiatic clams,
and Asiatic zooplankton. For example, the green crab
(Carcinus maenas), native to the Atlantic coast of
Europe, was first found in the southern portion of the
San Francisco Estuary in the early 1990s and has spread
north at least as far as the Carquinez Strait. Researchers
have found that, in contrast to their slow growth rates
in Europe, green crabs grow rapidly and reach sexual
maturity during their first year in the Estuary. During
the course of a 9-year study, the green crab significantly
reduced the abundance of 20 invertebrate species, and
within just 3 years of being introduced, reduced densi-
ties of native clams and native shore crabs by 5% to
10% (SFEP, 2000). Studies are still underway to deter-
mine the full impacts of these recent invaders on the
estuarine ecosystem.
Chemical contaminant levels in fish and wildlife are
a concern in the San Francisco Estuary. For example,
25 years after the ban on the use of PCBs in California,
concentrations in some Estuary sport fish remain
10 times higher than human health consumption guide-
lines (Davis et al., in prep). An interim human health
consumption advisory issued by the California Office of
Environmental Health Hazard Assessment (OEHHA),
in response to elevated levels of mercury, PCBs, and
other contaminants, has been in place since 1994
(SFEI, 2005). Between 1994 and 2003, 93% of all fish
sampled by the RMP exceeded the California OEHHA
screening value for PCBs; roughly 50% exceeded the
screening value for mercury; and 3.5% exceeded the
screening value for DDT. In addition, all leopard shark
samples and almost all striped bass samples exceeded the
mercury screening value (Greenfield et al., 2005). The
SFRWQCB has calculated that a 40% reduction in
mercury levels in striped bass would be necessary to
meet the TMDL target of 0.2 ppm (Looker and
Johnson, 2004). Over the long term, concentrations of
lipid-normalized DDTs in leopard shark, shiner, and
white croaker suggest statistically significant declines in
362 National Estuary Program Coastal Condition Report
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
San Francisco Estuary Project
concentrations from 1994 to 2003. Decreases in chlor-
dane concentrations in leopard sharks, striped bass, and
white croaker were also observed (Connor et al., 2004).
No long-term trends have been detected in lipid-
normalized PCB data. PCB levels in leopard shark,
white croaker, and striped bass were higher in 1994
compared to other years, but the interannual variation
since 1994 has fluctuated without a clear decline.
Mercury concentrations in striped bass have shown no
decline during the period from 1970 to 2003 (Green-
field et al., 2005).
Similarly, mercury levels in bird eggs remain a
concern for Estuary managers. Concentrations of
mercury in eggs from area terns and endangered
California clapper rails have been close to the wet-
o
o
o
o
o
o-
jO
o
0
p
o
o
r • o
V', °
0
.'O
'"JO
Benthic Impairment
of San Francisco Estuary
Benthic Assessment Categories
O No impact
O Slight impact
O Moderate impact
• Severely impacted
O
o
' o
o
"O'
Figure 6-40. Map of benthic impact based on assessment
of benthic assemblage. Data from from NOAA-EMAR RMR
Bay Protection and Toxic Cleanup Program, and CISNet (SFEI).
weight threshold-effects level target of 0.5 ppm
proposed in the draft TMDL for mercury (Schwarzbach
and Adelsbach, 2003). Recent RMP data show median
wet-weight concentrations of mercury in least tern eggs
to be 0.6 ppm (SFEI, 2006). A more conservative
threshold may be established to protect more sensitive
species, such as the endangered least tern.
Scientists from the RMP and the Southern
California Coastal Water Research Project (SCCWRP)
have developed a multi-metric approach for measuring
the effects of contaminants on benthic communities.
Benthic communities were assessed based on taxa diver-
sity, abundance of organisms per sample, number of
contaminant-tolerant organisms, and the proportion of
contaminant-sensitive benthic amphipods to sensitive
mollusks. Highly impacted sites were concentrated in
the lower-central and southern portions of the Estuary,
and the most severely impacted benthic sites were
located in sub-embayments, coves, and channels along
the margins of the Estuary (Figure 6-40). In particular,
all samples from San Leandro Bay were classified as
severely impacted, and samples from the deeper areas of
the Estuary indicated minimal impact. Combining this
method with other measures of contamination, such as
sediment toxicity and sediment chemistry, can help
support the link between contamination and benthic
impact (SWRCB, 2004).
Racing on the San Francisco Estuary (SFEP).
National Estuary Program Coastal Condition Report 363
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CHAPTER 6
WEST COAST NATIONAL ESTUARY PROGRAM C.OASTAL CONDITION
Son Francisco Estuary Project
Current Projects,
Accomplishments, and Future
Goals
Probably the biggest, most visible accomplishment of
the SFEP is the large number of environmental educa-
tion and outreach efforts taking place around the San
Francisco Estuary, as well as an incredible number of
watershed management planning activities. Almost
every city or town now has a "friends of" creek or river
group that has adopted the waterway running through
its midst, and parks, ponds, and marshes have likewise
been taken under someone's wing. Interest and a sense
of ownership in the Estuary—in part encouraged by the
improved public access offered by the San Francisco Bay
Trail—is on the rise. As the state's population increases
and open space and wildlife habitat continue to be lost
to housing and development, the Estuary becomes yet
an even more important resource to Bay-area residents.
This grassroots energy in turn feeds regulatory efforts to
protect and enhance the Estuary.
Water supply reliability and adequate inflows to
protect aquatic resources are priorities of the SFEP's
CCMP (SFEP, 1993). Cutoff of California's surplus
water supplies from the Colorado River by the U.S.
Department of Interior (DOI) provided the impetus for
a historic shift from an era of centralized state and
federal water planning to a more regionally and market-
driven approach. Working together several years ago,
water and environmental interests helped pass
Proposition 50, the largest water bond in California
history.
Data from the RMP and other programs have been
integral in the development of TMDL reports by the
SFRWQCB. TMDLs are action plans that set targets
for acceptable levels of the contaminants that threaten
the beneficial uses of the Estuary, such as sport fishing,
wildlife habitat, and the preservation of rare and endan-
gered species. The SFRWQCB plans to issue TMDLs
for mercury and PCBs within the next year; these cont-
aminants have exceeded thresholds of concern by factors
of almost 4 to 10 (SFEI, 2005). TMDLs for other cont-
aminants are also planned. Except for diazinon, which is
driven by aquatic toxicity, these TMDLs are mostly
driven by the impacts of the contaminants on human
and wildlife consumers of contaminated fish (Figure
6-41) (SFEI, 2005). Since many contaminants partition
to the sediments, the SFRWQCB is proposing sediment
targets as a means of reducing contaminant levels in fish
and wildlife to safe levels. Fish targets are also likely to
be included.
Stronger planning, improved regulations, and
increased acquisition and restoration are the main thrust
of 12 wetland management actions called for in the
SFEP's CCMP. One element, the setting of goals for the
types, locations, and quantities of wetlands desired to
maintain the ecosystem's health, will provide the biolog-
ical foundation for the regional wetlands management
plan.
Magnitude of Impairment
Threshold for Concern
.eopard Shark White Croaker Surf Scoter Crustacean (amphipod)
Figure 6-41. Summary of degree of Estuary impairment by
high-pnonty pollutants in various species (SFEi, 2005).
364 National Estuary Program Coastal Condition Report
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CHAPTER 6 ' WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITIOiXI
Son Francisco Estuary Project
Public support for wetlands and creek restoration has
been tremendous, as indicated by the large numbers of
volunteers who have adopted creeks and participated in
restoration activities. One SFEP Implementation
Committee member reported that, in his organization
alone, more than 12,000 people logged 36,000 volun-
teer hours. Planned restoration projects include about
19,000 acres in the North Bay (13,000 acres of tidal
marsh and 6,000 acres of non-tidal or mixed hydrology)
and 18,000 acres in the South Bay (SFEP, 2004).
Conclusion
The task confronting those working on assessing and
managing the San Francisco Estuary and its watershed
is complex because of the diversity and scale of the
human demands on the Estuary. Many potentially
competing needs must be carefully balanced by many
different agencies and stakeholder groups. Within this
context, there are a variety of monitoring and assess-
ment initiatives and concerns. Based on data from the
NCA, the overall condition of the San Francisco
Estuary is rated fair; however, data from the SFEP and
other sources indicate that chemical contaminants are
affecting the beneficial uses of the Estuary. Water
quality guidelines continue to be exceeded for PCBs
and legacy pesticides; chemical contaminant levels in
many popular sport fish continue to exceed human
health screening values; and evidence exists that benthic
communities are affected by high levels of contamina-
tion. The aquatic food web of the San Francisco Estuary
is continually exposed to multiple contaminants, and
these contaminant levels pose a threat to the fish and
wildlife in the Estuary, as well as to sport fish
consumers. Estuary managers, through the TMDL
process, are establishing target values for protection of
the Estuary's beneficial uses. Long-term monitoring is
crucial in illuminating changes in contaminant levels in
the waters, sediments, and wildlife of the Estuary.
Integrating this information into policy allows for a
scientifically sound basis for the management of the San
Francisco Estuary.
Alcatraz Island is located in the San Francisco Estuary (Jennifer Lloyd Blough).
National Estuary Program Coastal Condition Report 365
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Morro Bay National Estuary Program
Morro Bay National Estuary Program
www.mbnep.org
Background
Morro Bay is a 3.6-mi2, semi-enclosed body of water
located along the central California coast. This shallow
estuarine system includes a diverse array of wetland
habitats, including sub tidal and intertidal eelgrass beds,
mudflats, salt marsh, and brackish and freshwater
wetlands on the Bay fringe. The Morro Bay watershed
covers approximately 75 mi2 of San Luis Obispo
County. The predominant land use in the watershed is
rangeland for beef cattle, and other uses include irri-
gated agriculture, open space, and developed lands. The
area is seismically active, and several earthquake faults
are located within or near the watershed. Morro Rock, a
local landmark, is the most westerly visible in a chain of
extinct volcanic plugs that divide the two coastal valleys
that drain into the Bay (Morro Bay NEP, 2000).
Morro Bay is a major tourist attraction, with more
than 25,000 people living within the Bay's watershed
and an average of 1.5 million visitors per year. The area's
economy is dominated by tourism and visitor-serving
businesses, which generate 37% of all jobs and one-
third of the general fund revenues for the City of Morro
Bay. The Bay provides critical resources to fishing and
recreational boating industries, with more than
366 National Estuary Program Coastal Condition Report
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CHAPTER 6 ' WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Morro Bay National Estuary Progran
100 commercial vessels providing a value of roughly
$7 million to the local economy. Recreational fishing
takes place from shore, docks, piers, and a variety of
boats, and catches include a diversity of species, such as
Pacific halibut, shark, jacksmelt, black surfperch, and
starry flounder. More than 270 acres of the estuary are
leased for commercial shellfish operations focused on
the Pacific oyster. The estuary and surrounding habitats
are an important stop-over area on the Pacific Flyway
for migratory birds and are home to 16 federally threat-
ened or endangered species, some of which are found
nowhere else in the world (Morro Bay NEP, 2000).
In 1995, the Morro Bay National Estuary Program
(Morro Bay NEP) was established to address the envi-
ronmental concerns facing this nationally significant
estuary, and the program's Morro Bay Comprehensive
Conservation & Management Plan was finalized in 2000
(Morro Bay NEP, 2000). The Morro Bay NEP study
area includes Morro Bay, its watershed, and to some
extent, Estero Bay from Point Buchon in the south to
Point Estero in the north.
Environmental Concerns
Erosion in the watershed and the resulting sedimen-
tation of the estuary is one of the most severe threats
facing Morro Bay. Sediment delivery has increased over
time due to changes in land use, as well as to the alter-
ation and loss of streams and flood plains. The Bay has
lost more than a quarter of its tidal volume in the past
century, and left unchecked, sedimentation will
continue to degrade and destroy subtidal and intertidal
habitats. In addition to sedimentation, development,
and other land-use changes, changes in drainage
patterns, erosion, and growth of invasive species such as
Arundo donax (giant reed) in riparian corridors and
veldt grass in the coastal dunes have contributed to the
loss of natural habitat in the study area. Some obvious
effects of habitat loss in Morro Bay include the likely
extinction of the Morro Bay kangaroo rat and decreases
in populations of steelhead trout, a federal endangered
species (Morro Bay NEP, 2000).
Population Pressures
The population of the NOAA-designated coastal
county (San Luis Obispo) coincident with the Morro
Bay NEP estuarine study area increased by 204.4%
during a 40-year period, from 0.08 million people in
1960 to 0.25 million people in 2000 (Figure 6-42)
(U.S. Census Bureau, 1991; 2001). This rate of popula-
tion growth for the Morro Bay NEP was the highest
rate observed for any of the six West Coast NEPs and
was more than double the average growth rate of
100.3% for the collective NEP-coincident coastal coun-
ties of the West Coast region. In contrast, San Luis
Obispo County had the second-lowest population
density (75 persons/mi2) of any of the West Coast
NEPs (U.S. Census Bureau, 2001). This estuary is not
surrounded by a large metropolitan area, but is a major
recreational area and agricultural center for the local
coastal community.
<3 O.I
I960
1970
1990
2000
1980
Year
Figure 6-42. Population of the NOAA-designated coastal
county of the Morro Bay NEP study area, 1960-2000 (U.S.
Census Bureau, 1991:2001)
National Estuary Program Coastal Condition Report 367
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Morro Bay National Estuary Program
NCA Indices of Estuarine
Condition—Morro Bay
The overall condition of Morro Bay is rated good
based on three of the indices of estuarine condition
used by the NCA (Figure 6-43). The water quality and
fish tissue contaminants indices are rated good, and the
sediment quality index is rated fair. Although data on
the condition of the benthic community were collected
for this estuary, Morro Bay could not be rated using an
Overall Condition
Morro Bay
(4.33)
Water Quality Index (5)
Sediment Quality Index (3)
Benthic Index (missing)
Fish Tissue Contaminants
Index (5)
Figure 6-43. The
overall condition of the
Morro Bay NEP estu-
arine area is good (U.S.
EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80 100
Percent NEP Estuarine Area
Missing
Figure 6-44. Percentage of NEP estuarine area achieving each
ranking for all indices and component indicators — Morro Bay
(U.S. EPA/NCA).
index based on deviations from the expected species rich-
ness. Figure 6-44 provides a summary of the percentage
of estuarine area rated good, fair, poor, or missing for
each parameter considered. This assessment is based on
data collected by the Moss Landing Marine Laboratories,
under contract to the SCWRRP, from 30 sites sampled
in the Morro Bay NEP estuarine area in 2003. Please
refer to Tables 1-24, 1-25, and 1-26 (Chapter 1) for a
summary of the criteria used to develop the rating for
each index and component indicator.
Water Quality Index
Based on NCA survey results, the water quality index
for Morro Bay is rated good (Figure 6-45). This index
was developed using NCA data on five component
indicators: DIN, DIP, chlorophyll a, water clarity, and
dissolved oxygen. Seventeen percent of the estuarine area
was rated fair for water quality, and 83% of the area was
rated good. Diminished water quality was primarily due
to limited water clarity and elevated levels of DIP.
Water Quality Index - Morro Bay
Site Criteria: Number of component indicators in
poor or fair condition
• Good = No more than I is fair
OFair = I is poor, or 2 or more are fair
• Poor = 2 or more are poor
O Missing
Figure 6-45. Water quality index data for Morro Bay, 2003
(U.S. EPA/NCA).
368 National Estuary Program Coastal Condition Report
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CHAPTER 6 ; WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Morro Bay National Estuary Program
Dissolved Nitrogen and Phosphorus I DIN
concentrations in Morro Bay are rated good, but DIP
concentrations are rated fair. Concentrations of DIN
were rated good in 100% of the estuarine area, whereas
fair DIP concentrations occurred in 100% of the area.
In addition to natural inputs of nutrients from offshore
coastal upwelling, high levels of urban and agricultural
runoff may also be major contributors to the elevated
nutrient levels found in Morro Bay.
Chlorophyll ft Chlorophyll a concentrations in
Morro Bay are rated good, with 100% of the estuarine
area rated good for this component indicator.
Water Clarity Water clarity in Morro Bay is rated
good. Approximately 8% of the estuarine area was rated
poor for this component indicator, and 11 % was rated
fair.
Dissolved Oxygen Dissolved oxygen conditions
in Morro Bay are rated good, with 77% of the estuarine
area rated good and 22% of the area rated fair. Only
1 % of the estuarine area was rated poor for this compo-
nent indicator; however, these measured values reflect
daytime conditions, and some areas of the Bay may still
experience hypoxic conditions at night.
Sediment Quality Index
The sediment quality index for Morro Bay is rated
fair (Figure 6-46). This index was developed using NCA
data on three component indicators: sediment toxicity,
sediment contaminants, and sediment TOC. Ten
percent of the estuarine area was rated poor for sedi-
ment quality, and 7% of the area was rated fair,
primarily as a result of sediment toxicity.
Sediment Toxicity I Sediment toxicity for Morro
Bay is rated poor, with 10% of the estuarine area rated
poor for this component indicator.
Sediment Contaminants I Morro Bay is rated
good for sediment contaminant concentrations because
none of the estuarine area was rated poor for this
component indicator and 7% of the area was rated fair.
Total Organic Carbon Morro Bay is rated good
for sediment TOC because 67% of the estuarine area
Sediment Quality Index - Morro Bay
Site Criteria: Number and condition of
component indicators
• Good = None are poor, and sediment
contaminants is good
OFair = None are poor, and sediment
contaminants is fair
• Poor = lor more are poor
O Missing
Figure 6-46. Sediment quality index data for Morro Bay, 2003
(U.S. EPA/NCA).
was rated good for TOC concentrations and the
remaining 33% of the area was rated fair.
Benthic Index
Currently, the condition of the benthic invertebrate
communities in Morro Bay cannot be rated using an
index based on deviations from the expected species
richness because this approach requires a significant
regression between salinity and the log of species rich-
ness. This relationship was not significant in the Morro
Bay data collected during the 2003 NCA survey. The
lack of a significant regression was probably due to an
inadequate range in salinity because the Bay's salinity
ranged only from 33.9 to 35.1 psu (or salinity values
indicative of ocean water). Species richness in the Bay
ranged between 2 and 19 species per sample.
National Estuary Program Coastal Condition Report 369
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CHAPTER 6 WEST COAST NATIONAL ESTJARY PROGRAM COASTAL CONDITION
Morro Bay National Estuary Program
Fish Tissue Contaminants Index
The fish tissue contaminants index is rated good for
Morro Bay, although this rating should be interpreted
cautiously because of the small number of sample
stations where fish tissues were obtained (7 of 30
stations). Figure 6-47 shows that fish tissue at 71% of
stations (5 of 7) where fish were caught had tissue cont-
aminant levels below EPA Advisory Guidance values
using whole-fish contaminant concentrations. These
risk calculations are appropriate for populations that
consume whole fish. Samples from two Morro Bay
stations were rated fair based on concentrations of
mercury and DDT.
Fish Tissue Contaminants Index - Morro Bay
Site Criteria: EPA Guidance concentration
• Good — Below Guidance range
O Fair = Falls within Guidance range
• Poor = Exceeds Guidance range
Figure 6-47. Fish tissue contaminants index data for Morro Bay,
2003 (U.S. EPA/NCA).
©
A great egret lazily takes flight across Morro Bay (Morro Bay NEP).
370 National Estuary Program Coastal Condition Report
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CHAPTER 6 I WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Morro Bay National Estuary Progran
Kids' Beach Cleanup Event and
Aerial Art a Success
Two hundred second-grade students traveled from
the Central Valley to Cayucos State Beach, CA, on May
13, 2005, for the Kids' Beach Clean-up Event. In an
effort to protect marine resources, the students volun-
teered to collect trash and other debris from the beach
to keep these materials from entering the ocean. The
participating students were from Strathmore and Seville,
CA, two small towns in the Central Valley county of
Tulare. This was the first visit to the seashore for many
of the students. A week before the field trip, Morro Bay
NEP staff member Cheryl Lesinski gave a classroom
presentation to students that focused on the impacts
that marine debris and pollution can have on beach
resources. This project was funded by the California
Coastal Commission's Whaletail License Plate program.
As part of the beach cleanup event, the entire group
took part in an aerial art formation (see photo). Stand-
ing together in lines, the children spelled out the word
"PROTECT" as a reminder to all Californians that the
ocean is a valuable resource that needs our help (Morro
Bay NEP, 2005).
California students involved in beach cleanup event (Morro Bay NEP).
National Estuary Program Coastal Condition Report 371
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Morro Bay National Estuary Program
Morro Bay National Estuary
Program Indicators of Estuarine
Condition
The Morro Bay NEP and its partners employ a
variety of monitoring methods and use a suite of
indicators to track changes in water quality, suitable
habitat areas, and the health of living resources in the
Morro Bay estuary. The following section discusses
selected key indicators that are used by the Morro Bay
NEP to evaluate the health of the estuary and its
watershed. Additional information is available at
http://www.mbnep.org.
Water and Sediment Quality
The Morro Bay NEP's Volunteer Monitoring
Program (VMP) is the main program conducting water
quality monitoring in the study area. The Morro Bay
VMP monitors monthly for total coliform and E, coli,
nutrients, dissolved oxygen levels, pH, salinity, flow,
temperature, and HABs (Kitajima, 2003). In accor-
dance with EPA's recommendations, the Morro Bay
VMP has begun using Enterococci as the main pathogen
indicator for marine waters (Morro Bay NEP, 2006b).
Ongoing monitoring indicates that bacterial contam-
ination and nutrient over-enrichment are key water
quality concerns in the estuary and watershed. From
2002 to 2004, bacteria sampling results indicated that
the majority of the creek sites sampled were unsafe for
human contact in at least 30% of the samples collected
and that three of the seven sites in the estuary were
unsafe in 10% to 20% of the samples collected (Morro
Bay NEP, 2006a). High fecal bacteria levels are of
concern for shellfish beds, as well as for human health
impacts from recreational contact with creek and Bay
waters. Two of the three commercial shellfish lease areas
in Morro Bay are partially closed because of elevated
bacteria levels, and all harvesting areas are closed
following storm events (Morro Bay NEP, 2000; 2006a).
High levels of nitrates and phosphates are present in
portions of the Chorro and Los Osos drainages. These
increased levels of nutrients are mostly attributed to-
agricultural runoff, WWTP effluent, grazing lands, and
poorly functioning septic systems (Morro Bay NEP,
2000).
Habitat Quality
One of the key indicator measures used to evaluate
habitat changes in Morro Bay is the acres and/or linear
miles of habitat protected and restored. Since 2001,
more than 3,000 acres of valuable wildlife habitat have
been permanently protected in the Morro Bay water-
shed, and 4.5 miles of stream habitat have been restored
(Morro Bay NEP, 2006a).
The monitoring of changes in the areal extent of
different estuarine habitat areas (e.g., eelgrass, mudflats,
salt marsh) is also useful. In particular, the Morro Bay
NEP has found that the number of acres of eelgrass in
Morro Bay is a good indicator of the health of living
resources in the watershed. In 2003, the estuary
contained approximately 330 acres of subtidal and
intertidal eelgrass, 380 acres of salt marsh, 1,200 acres
of intertidal mud flats, and 175 acres of subtidal habitat
(USAGE, 2003). The Morro Bay eelgrass beds are some
of the largest and healthiest in central and southern
California and support the highest diversity of inverte-
brates of any habitat in the estuary (Morro Bay NEP,
2000).
Sediment deposition is being tracked carefully to
observe its impact on habitat conditions in the Morro
Bay estuary because modeling of future sedimentation
has suggested that the area suitable for eelgrass could be
reduced by 48% during the next 50 years if sedimenta-
tion rates are not slowed (USAGE, 2003). One specific
goal of the Morro Bay NEP is a 15% reduction in
average annual sediment loads in stream and estuary
waters by 2010 (Morro Bay NEP, 2000). The recently
adopted sediment TMDL calls for a 50% reduction in
average annual sediment load during the next 50 years
(CCRWQCB, 2002a). Monitoring stations to track
deposition rates in the estuary were recently established,
and detailed bathymetric surveys of the Bay will provide
ongoing information about overall sedimentation rates
(Morro Bay NEP, 2006a).
The number of invasive species in Morro Bay is
another potentially useful indicator that is still under
development by the Morro Bay NEP, but which may
become a useful measure for habitat quality and the
health of living resources over time. Portions of the
estuary's various habitat have been impacted by invasive
plant species. During a habitat survey conducted in
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CHAPTER 6 I WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Morro Bay National Estuary Program
1998, the invasive species cape ivy was a dominant
plant in the herb layer of Chorro Creek and was also
present along the lower reaches of Los Osos ("reek
(Morro Bay NEP, 2000).
Living Resources
Measurements of macroinvertebrate populations and
diversities are also used to indicate the health of living
resources in Morro Bay. Benthic infauna have been
monitored annually at a number of creek sites in the
Morro Bay watershed. Water quality monitoring
provides a snapshot of conditions at that time, whereas
macroinvertebrate analysis reflects stream health over a
longer time period because long-term water quality
affects which species ultimately establish themselves or
thrive in the estuary watershed (Kitajima, 2003). The
abundance of macroinvertebrar.es and the ease of
sampling also make benthic infauna good environ-
mental indicators.
Central Coast steelhead trout have been listed as a
federal threatened species by the NMFS because of
declining habitat quality throughout the species range.
By 2000, the steelhead population in Morro Bay had
decreased to less than 1% of the 1950 population size.
Anadromous (migratory) fish are good indicators of
resource health because they depend on the entire
ecosystem, from the upper watershed to the coastal
ocean, for their life cycle (Morro Bay NEP, 2000). Local
population size and availability of habitat for this species
are two of the indicators used to evaluate living
resources in Morro Bay.
Morro Bay is also increasingly being recognized as an
area that is critical in supporting resident and migratory
bird species. Black brant and other migratory waterfowl
utilize the Bay as an overwintering site and as a feeding
and resting site during their migration along the Pacific
Flyway. Surveys of the black brant population are used
to study the density, age composition, and habitat delin-
eation of this species. Average mid-winter, single-day
counts of the brant have declined from about 7,000 in
the 1930s to roughly 3,000 in 2000 (Roser, 2003). The
Morro Bay NEP coordinates biannual surveys of shore-
bird abundance and diversity, which have shown rela-
tively stable trends since the mid-1990s (Morro Bay
NEP, 2006a). The Audubon Society consistently rates
Morro Bay as among the top 5 areas (out of 963 sites
nationwide) for diversity of winter bird species, with
around 200 species and more than 50,000 individual
birds counted in a single day in December (Morro Bay
NEP, 2000).
Schools of top smelt are common in Morro Bay (Morro Bay NEP).
National Estuary Program Coastal Condition Report 373
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Morro Bay Notional Estuary Program
Current Projects,
Accomplishments, and Future
Goals
Some of the recent environmental success stories and
restoration efforts in Morro Bay include the following:
• Project Clearwater (formerly the Morro Bay
Watershed Enhancement Project) has helped
farmers and ranchers improve land management
practices. These efforts have resulted in the imple-
mentation of more than 235 BMPs and helped
prevent more than 172,000 tons of soil erosion
(CSLRCD, 2006).
• The 1,860-acre Maino Ranch Conservation
Easement has been purchased to protect the
natural resources, rural character, and working
landscape of the Maino Ranch in the Morro Bay
watershed. The easement greatly restricts the
subdivision and development potential of the
ranch (Morro Bay NEP, 2000).
• A 580-acre property spreading below Hollister
Peak and across Chorro Creek has become one of
California's newest ecological reserves. The Chorro
Creek Ecological Reserve, once slated for a golf
course and resort, includes approximately two
miles of Chorro and San Luisito creeks, as well as
large swaths of restorable flood plain near scenic
Highway 1. The Morro Bay NEP is working with
the California Department of Fish and Game to
restore the natural floodplain and freshwater
wetlands on this property (Morro Bay NEP,
2006a).
• The Morro Bay NEP's efforts to reduce bacterial
pollution include working with the boating
community, limiting cattle access to watershed
creeks, and encouraging the implementation of a
centralized WWTP for the bayside community of
Los Osos, which is currently on individual septic
systems (Morro Bay NEP, 2000).
• The Central Coast Regional Water Quality
Control Board (CCRWQCB) has declared Morro
Bay and its creeks as impaired waters for a
number of pollutants and has adopted TMDLs
covering the estuary and creeks for pathogens,
sedimentation, nutrients, and dissolved oxygen
(CCRWQCB, 2002a; 2002b; 2004a; 2004b;
2004c; 2005). The Morro Bay NEP is a key
component of the implementation and moni-
toring for these efforts to improve water quality.
Specific actions taken to control nutrient inputs to
the Bay include implementing nitrogen-control
measures for wastewater effluent, improving
wastewater treatment in Los Osos, and assisting
farmers and ranchers with BMPs (Morro Bay
NEP, 2000; 2004).
Conclusion
Based on data from the NCA survey, the overall
condition of Morro Bay is rated good. The Morro Bay
NEP considers the primary threats facing the estuary
and its watershed to be erosion and sedimentation,
bacterial contamination, low freshwater flows to the
Bay, elevated levels of heavy metals and other toxics in
Bay sediments, nutrient over-enrichment, loss of
wildlife habitat, and the decline of the local steelhead
trout population. The Morro Bay NEP is a collaborative
effort that brings local citizens, local government, non-
profit agencies, and landowners together to protect and
restore the physical, biological, economic, and recre-
ational values of the Morro Bay estuary. The primary
goals of the NEP are to slow the process of Bay sedi-
mentation; protect and enhance steelhead trout popula-
tions and habitat; protect and restore the integrity of
the diverse habitats in the watershed and the wildlife
that depend on them; promote public awareness and
involvement in estuarine management through
outreach, education, and volunteering; and ensure that
estuary and creek waters are clean and fully support
healthy eelgrass beds, safe recreational uses, and thriving
fish and shellfish populations.
374 National Estuary Program Coastal Condition Report
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Santa Monica Bay Restoration Commission
Santa Monica Bay Restoration Commission
www.santamonicabay.org
Pacific
Ocean
Polos Verdes
Peninsula
Background
Santa Monica Bay is a 306-mi" estuary located west
of Los Angeles on the Pacific Coast of California and
bordered on the north by the Santa Monica mountains.
The Bay reaches depths of up to 1,640 feet and has a
total volume of about 6.8 trillion gallons. The Santa
Monica Bay watershed encompasses more than 400 mi2
and includes a large number of highly populated
communities, including Beverly Hills, Calabasas, Culver
City, El Segunclo, Malibu, Redondo Beach, Santa
Monica, West Hollywood, and part of Los Angeles.
More than 3 million people live within the watershed,
and between 50 to 60 million visits are made to Santa
Monica Bay each year. The Bay receives freshwater
inputs from 28 stream drainage basins, with the largest
flows coming from Malibu Creek and Ballona Creek
(Martin et al., 1996).
The Santa Monica region features a range of habitat
types, including coastal scrub, wetland and rocky inter-
tidal zones, kelp beds, open water, and both hard- and
soft-bottom areas (Martin et al., 1996). The Bay serves
as home to more than 5,000 species of birds, fish,
mammals, plants, and other wildlife. The Bays 50 miles
of coastline provide recreational opportunities for an
National Estuary Program Coastal Condition Report 375
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Santo Monica Bay Restoration Commission
estimated 500,000 visitors a day at the height of the
summer season (ANEP, 200Id). Sport fisheries are a
booming industry, and the Bay is home to chub mack-
erel, barred sand bass, kelp bass, and California spiny
lobster, among other species (Martin et al., 1996).
Human development has replaced more than 95% of
the Bay's historic coastal wetlands and degraded the
remaining 5%, putting some species in danger of local
extinction (ANEP, 200Id). Only a few thousand acres
of wetlands (e.g., riparian zones, lakes, ponds, coastal
marshes, and lagoons) remain in the watershed (Martin
et al., 1996).
The State of California and EPA established the
Santa Monica Bay Restoration Project (SMBRP) as an
NEP in December 1988. The project was formed to
develop a plan that would ensure the long-term health
of the Bay and its watershed. In January 2003, the
SMBRP formally became an independent state organi-
zation and is now known as the Santa Monica Bay
Restoration Commission (SMBRC) (SMBRC, 2006).
Environmental Concerns
Research suggests that there are 19 pollutants of
immediate concern in Santa Monica Bay (SMBRC,
2006). Sources and pathways of contaminants include
industrial discharges, urban runoff into creeks and
storm drains, municipal WWTPs, boating and shipping
activities, dredging, and advection of pollutants from
other areas (Martin et al., 1996). About 645 million
gallons of treated wastewater are discharged to Santa
Monica Bay each day via 7 major point-source facilities
and more than 160 permitted smaller commercial and
industrial facilities (Martin et al., 1996; SMBRC,
2006). Urban and stormwater runoff carried through
the region's massive storm drain systems and few
remaining streams is a serious year-round concern. Each
year, an average of 30 billion gallons of storm water and
urban runoff are discharged through more than 200
outlets into Santa Monica Bay (Martin et al., 1996).
Population Pressures
The population of the 4 NOAA-designated coastal
counties (Los Angeles, Orange, San Bernardino, and
Ventura) coincident with the SMBRC study area
increased by 99.2% during a 40-year period, from 7.4
million people in 1960 to 14.8 million people in 2000
(Figure 6-48) (U.S. Census Bureau 1991; 2000). This
rate of population growth for the SMBRC study area
was slightly less than the average growth rate of 100.3%
observed for the collective NEP-coincident coastal
counties of the West Coast region; however, the
SMBRC-coincident coastal counties had the second-
highest population density in 2000 with 553
persons/mi2 (U.S. Census Bureau, 2001). This estuary
is surrounded by a large, sprawling metropolitan area
and is a major recreational area for the local coastal
community.
.o
'
3
a
o
a.
I960
2000
Figure 6-48. Population of NOAA-designated coastal counties
of the SMBRC study area, 1960-2000 (U.S. Census Bureau, 1991;
2001).
NCA Indices of Estuarine
Condition—Santa Monica Bay
The overall condition of Santa Monica Bay is rated
fair based on three of the indices of estuarine condition
used by the NCA (Figure 6-49). The water quality
index is rated good, and the sediment quality and fish
tissue contaminants indices are rated poor. Although
data on the condition of the benthic community were
collected for this estuary, Santa Monica Bay could not
be rated using an index based on deviations from the
expected species richness. Figure 6-50 provides a
summary of the percentage of estuarine area rated good,
fair, poor, or missing for each parameter considered.
This assessment is based on data collected by the Moss
Landing Marine Laboratories, under contract to the
SCWRRP, from 47 sites sampled the SMBRC estuarine
area in 2003. Please refer to Tables 1-24, 1-25, and 1-26
(Chapter 1) for a summary of the criteria used to develop
the rating for each index and component indicator.
376 National Estuary Program Coastal Condition Report
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CHAPTER 6 i WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Santa Monica Bay Restoration Commission
Overall Condition
Santa Monica Bay
(2.33)
Water Quality Index (5)
Sediment Quality Index (I)
Benthic Index (missing)
Fish Tissue Contaminants
Index (I)
Figure 6-49. The
overall condiLion of Lhe
SMBR.C estuarine area
is fair (U.S. EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus(DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminants Index
20 40 60 80
Percent NEP Estuarine Area
Missing
Figure 6-50. Percentage of NEP esLuarine area achieving each
ranking for all indices and component indicators --• Santa Monica
Bay (U.S. EPA/NCA).
Water Quality Index
Based on NCA survey results, the water quality index
for Santa Monica Bay is rated good. This index was
developed using NCA data on five component indica-
tors: DIN, DIP, chlorophyll a, water clarity, and
dissolved oxygen. Fourteen percent of the estuarine area
was rated fair for water quality, and 86% of the area was
rated good (Figure 6-51).
Dissolved Nitrogen and Phosphorus I DIN
and DIP concentrations in Santa Monica Bay are rated
good. All of the estuarine area was rated good for DIN
concentrations, whereas 29% of the area was rated fair
for DIP concentrations. In addition to natural inputs of
nutrients from offshore coastal upwelling, high levels of
urban and agricultural runoff may also be major
contributors to the nutrient levels found in Santa
Monica Bay.
Water Quality Index - Santa Monica Bay
Site Criteria: Number of component
indicators in poor or fair condition
• Good = No more than I is fair
O Fair = I is poor, or 2 or more
are fair
• Poor = 2 or more are poor
O Missing
Good
86%
Figure 6-51. Water quality index data for Santa Monica
2003 (U.S. EPA/NCA).
National Estuary Program Coastal Condition Report 377
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Santa Monica Bay Restoration Commission
Chlorophyll a \ Chlorophyll a concentrations in
Santa Monica Bay are rated good, with 100% of the
estuarine area rated good for this component indicator.
Clarity I Water clarity in Santa Monica Bay-
is rated good. Approximately 5% of the estuarine area
was rated poor for this component indicator, and 5% of
the area was rated fair.
Dissolved Oxygen I Dissolved oxygen conditions
in Santa Monica Bay are rated good, with 1 00% of the
estuarine area rated good for this component indicator.
It should be noted that these measured values reflect
daytime dissolved oxygen conditions, and some areas of
the Bay may still experience hypoxic conditions at
night.
Sediment Quality Index
The sediment quality index for Santa Monica Bay is
rated poor. This index was developed using NCA data
on three component indicators: sediment toxicity, sedi-
ment contaminants, and sediment TOG. Fifty-nine
percent of the estuarine area exceeded thresholds for at
least one of these component indicators and was rated
poor, and 41% of the estuarine area was rated good
(Figure 6-52).
••*
Plover (Brad Ashbaugh).
Sediment Toxicity I Sediment toxicity for Santa
Monica Bay is rated poor, with 21 % of the estuarine
area rated poor for this component indicator.
Sediment Contaminants I Santa Monica Bay is
rated poor for sediment contaminant concentrations,
with 59% of the estuarine area rated poor for this
component indicator.
Total Organic Carbon I Sediment TOG for
Santa Monica Bay is rated good, with 89% of the
estuarine area rated good for this component indicator.
Sediment Quality Index - Santa Monica Bay
Site Criteria: Number and condition
of component indicators
•Good = None are poor, and
sediment contaminants
is good
OFair = None are poor, and sediment
contaminants is fair
• Poor = I or more are poor
O Missing
Figure 6-52. Sediment quality index data for Santa Monica Bay,
2003 (U.S. EPA/NCA).
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Santa Monica Bay Restoration Commission
Benthic Index
Presently, the condition of the benthic invertebrate
communities in Santa Monica Bay can not be rated
using an index based on deviations from the expected
species richness because this approach requires a signifi-
cant regression between salinity and the log of species
richness. This relationship was not significant in the
Santa Monica Bay data collected during the 2003 NCA
survey.
Fish Tissue Contaminants Index
The fish tissue contaminants index for Santa Monica
Bay is rated poor because 50% of the stations where fish
were caught were rated poor (Figure 6-53). However,
this rating should be interpreted cautiously because of
the small number of Bay stations (8) where fish tissues
were collected.
Fish Tissue Contaminants Index -
Santa Monica Bay
Site Criteria: EPA Guidance
concentration
• Good = Below Guidance range
OFair = Falls within
Guidance range
• Poor = Exceeds Guidance range
Figure 6-53. Fish tissue contaminants index data for Santa
Monica Bay, 2003 (U.S. EPA/NCA).
Santa Monica Bay Restoration
Commission Indicators of
Estuarine Condition
The SMBRC is using or developing several indica-
tors to evaluate water and sediment quality, habitat
conditions, and stressors for the SMBRC estuarine area.
Indicators are typically ranked with regard to availability
of data for reporting on the state of the Bay; some of
the indicators of higher quality are described below.
Water and Sediment Quality
Indicators used by the SMBRC for water and sedi-
ment quality include the following:
• Concentrations of five heavy metals: cadmium,
copper, lead, silver, and zinc
• Concentrations of fecal and total coliform bacteria
and Enterococd (pathogen indicators)
• Beach Report Card grades (summer and winter)
based on measurement of bacterial indicators
• Number and effectiveness of pathogen-reduction
projects along the Bay's beaches (SMBRC, 2004).
Since the early 1970s, the loading of seven heavy
metals from the two largest WWTPs has decreased by
67% to 99%, and the loading of total suspended solids
has decreased by more than 80%. As a result, impaired
estuary bottom habitats near discharge outfalls have
shown signs of recovery (SMBRC, 2006).
Monitoring of bacterial indicators on beaches is
usually conducted on a daily basis (Heal the Bay, 2004).
In general, the number of days per year during which at
least one beach is closed due to sewage spills has greatly
decreased (ANEP, 200Id). The environmental group
Heal the Bay compiles grades for a Beach Report Card
system based on bacterial indicator measurements. The
2003-2004 Annual Beach Report Card (Heal the Bay,
2004) shows that most beaches had very good water
quality, with 268 of 373 (72%) locations receiving A
grades for the year during dry weather. In addition,
other grade ratings included 44 B grades (12%), 27 C
grades (7%), 15 D grades (4%), and 19 F grades (5%).
The monitored beach with the poorest dry weather
water quality during 2003 and 2004 was Surfrider
Beach (Heal the Bay, 2004).
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Santo Monica Boy Restoration Commission
Santa Monica Bay Stormwater
Projects
The SMBRC is taking many different approaches to
address the issue of pollutants found in stormwater
runoff (see table). Since 1992, the SMBRC has secured
more than $30 million in state and local bond funding
for more than 30 pollution-control projects, including
dry-weather runoff diversions from storm drain outlets
along Santa Monica Bay beaches, a state-of-the-art
urban runoff treatment and reclamation facility in Santa
Monica, and many devices to capture trash, oil, grease,
and sediments in storm drains throughout the water-
shed (SMBRC, 2006).
Many of the SMBRC projects funded to date have
been in the Ballona Creek watershed. Before its exten-
sive settlement and urbanization, Ballona Creek was a
meandering perennial stream that was lined with dense
vegetation and met the Pacific Ocean in a broad
expanse of tidal lagoons, salt marshes, and wetlands.
Today, Ballona Creek is a nine-mile long flood-protec-
tion channel that drains the Los Angeles basin,
including all or parts Beverly Hills, Culver City,
Inglewood, Los Angeles, Santa Monica, West
Hollywood, and unincorporated Los Angeles County.
To address impairments to waterbodies in the Ballona
Creek watershed, the SMBRC, in partnership with the
Los Angeles County Department of Public Works, the
City of Los Angeles, and the Ballona Creek
Renaissance, led the efforts of the Ballona Creek Task
Force and developed a comprehensive watershed
management plan for Ballona Creek. This work is
essential towards efforts to restore the water quality and
ecology of Santa Monica Bay and its watershed
(SMBRC, 2006).
Examples of Approaches to Managing
Stormwater Runoff
• Structural BMPs, such as dry-weather runoff diver-
sion, installation of in-stream trash capture devices
and catchbasin retrofits, and installation of filtration
devices along roadways or in parking; lots
• Public education and outreach
• Elimination of illicit connections and illegal
discharges to the storm drains via enhanced storm
drain inspections and improved ordinances
• Non-structural BMPs, such as catchbasin stenciling,
enhanced catchbasin/trash can cleanings, and street
sweeping
• New land-use practices to increase on-site stormwater
infiltration and reduce erosion
• Promotion and enforced implementation of BMPs at
industrial facilities and construction sites (SMBRC,
2006).
380 National Estuary Program Coastal Condition Report
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CHAPTER 6 | WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Santa Monica Bay Restoration Commission
Recent Stormwater Pollution-Prevention Projects (SMBRC, 2006)
Project
Ballona Creek Litter
Collection Project
Jurisdiction
County of
Los Angeles
Cost Treatment Device(s)
$600,000 200 catchbasin debris-
excluder devices and several
vortex separation systems
Purpose
Capture, analyze, and
characterize trash from
eight different land-use types
Ballona Creek
Water Quality
Improvement Project
City of Culver City $ 168,500
Continuous deflective
separation (CDS) device
Reduce total suspended
solids, hydrocarbons, oil,
grease, and trash
Pollutant Removal
Devices in Storm
Drain System
City of Los Angeles $ 1,336,000
Urban Stormwater devices in
Ballona Creek watershed.
Trash collection devices will
be installed at four locations
in south central Los Angeles
and a gravity system will be
installed in an industrial land-
use area of Manchester
Remove sediment, metals,
oil, and grease
Pollutant Removal
Devices in Storm
Drain System
City of
Santa Monica
$500,000 Two-stage filter system to
remove pollutants from a
catchment discharging to
Ballona Creek
Remove gross solids and
floatables (Stage I) and
additional trash, sediment,
and soluble compounds
(Stage 2)
Pollutant Removal
Devices in Storm
Drain System
City of
Manhattan Beach
$215,000 CDS devices
Reduce total suspended
solids, hydrocarbons, oil,
grease,and trash
Catchbasin Debris
Excluder Devices
City of
West Hollywood
$30,000 20 catchbasin debris-
excluder devices
Reduce the amount of litter
and debris
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Santa Monica Bay Restoration Commission
Habitat Quality
A variety of indicator measures are being evaluated
by the SMBRC to help monitor the range and condi-
tion of habitats that exist in this estuary system.
Examples of the indicator measures being considered for
habitat loss or change over time are the following:
• Acres of wetlands gained or lost and the number of
acres of riparian habitat (e.g., wetlands and open
habitat areas)
• Size of kelp canopy and abundance of kelp beds
along the Palos Verdes Shelf and Malibu coast
• Concentration of metals in Bay sediments and
condition of benthic community (benthic habitat)
(SMBRC, 2004).
Measurements of the size and abundance of kelp
beds in this estuary system are considered to be good
indicators for evaluating this important habitat and
resource. From the mid-1970s to 1997, improved
wastewater treatment processes resulted in an 80%
reduction in discharge of total suspended solids from
the White Point outfall. This reduction, along with kelp
replanting efforts in the 1970s, resulted in a remarkable
increase in kelp canopy, from a low of 5 acres in 1974
to a peak of more than 1,100 acres in 1989 (SMBRC,
2006).
Concentrations of heavy metals (e.g., lead, copper,
zinc, mercury) in Bay sediments are considered an
important indicator for evaluating the condition of
benthic habitats. The City of Los Angeles'
Environmental Monitoring Division has data from
1974—2003 and has indicated that soft-bottom habitats
have been one of the most highly impacted habitats in
this estuary, primarily due to discharges from STPs. The
Marina Del Rey Harbor, the Palos Verdes Shelf, and the
Ballona Creek Entrance Channel have typically been
some of the hot spots for concentrations of DDT,
PCBs, copper, zinc, or other contaminants in sediment
(SMBRC, 2006).
Living Resources
One of the key indicators used by the SMBRC for
evaluating living resources is the CPUE of select resi-
dent species in Santa Monica Bay. Species that can serve
as indicators include rockfish, surf perches, kelp bass,
sand bass, sheepshead, and halibut. Species that could
be potential indicators, but for which no current data
exist, include red sea urchins and spiny lobsters
(SMBRC, 2006).
Changes in the abundance of target species (e.g.,
rockfish, sea stars, mussels) and in species diversity
within intertidal zones are considered two good quality
indicators, but adequate data are not yet available. The
The SMBRC evaluates the size and abundance of kelp beds in Santa Monica Bay (NOAA).
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CHAPTER 6 WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Santa Monica Bay Restoration Commission
condition of runs for the amazing grunion fish popula-
tion is also an indicator being considered (SMBRC,
2004). Evidence suggests that many rockfish species
have been experiencing significant population declines
due to overfishing along the West Coast, including
species in Santa Monica Bay. According to federal
assessments, bocaccio (one type of rockfish) has
declined to about 5% of its historic abundance
(SMBRC, 2006). Another source of concern is the
rapid decline of black abalone, a rocky intertidal species.
Although the cause of the decline of this species is not
completely understood, researchers have speculated that
a combination of over-harvesting, predation, competi-
tion, environmental changes, and disease may be
responsible (SMBRC, 2006).
One of the major environmental concerns facing the
SMBRC is improving the status of threatened and
endangered species in Santa Monica Bay, while mini-
mizing and/or eliminating the varied effects of invasive
species. The measurement of the number of acres of
invasive plant species and the number of invasive preda-
tors are indicators under development to assess the
threats to the ecosystems and living resources in Santa
Monica Bay. Invasive plants and animals (e.g., the giant
reed, castor bean, wild tree tobacco, crayfish, bullfrog,
mosquito fish, and largemouth bass) have decreased the
biological diversity of native ecosystems by out-
competing or displacing native species. They also reduce
habitat availability and water quality for native species
in Santa Monica Bay (SMBRC, 2006).
Data on levels of DDT and PCBs in white croaker
and kelp bass tissue are reported by the Los Angeles
County Sanitation Districts, EPA, and the Montrosc
Settlements Restoration Program. These indicators are
considered to be the most useful for evaluating health
risks associated with seafood consumption (SMBRC,
2004). Average concentrations of DDT and PCBs in
most seafood species have fallen to near or below levels
of concern for human consumption, but remain high in
white croaker collected on the Palos Verdes shelf
(ANEP, 200Id; U.S. EPA, 2006e). Fish consumption
advisories have been posted in the Bay area since 1985
(U.S. EPA, 2005a).
Environmental Stressors
Information collected on the amount of trash in Bay
waterways shows that more than 4,000 tons of trash are
collected from Santa Monica Bay beaches each year
(Martin et al., 1996). Additionally, a 1994 survey found
that 25% of bottom sediments sampled in Santa
Monica Bay contained man-made materials of some
kind (SMBRC, 2006).
Pelicans following a fishing boat into the harbor (William B. Folsom,
NMFS).
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CHAPTER 6 I WEST COAST NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Santa Monica Bay Restoration Commission
Current Projects,
Accomplishments, and Future
Goals
Some of the environmental accomplishments and
restoration efforts in the Santa Monica Bay area include
the following:
• Development of a comprehensive Bay-wide moni-
toring program and funding for an in-depth study
to assess the loading of toxic air pollutants to the
watershed (ANEP, 200Id).
• Completion of upgrades to full secondary treat-
ment by the Los Angeles Hyperion Wastewater
Treatment Plant and Wastewater Pollution
Control Plant operated by the Los Angeles
County Sanitation District, which greatly reduces
the amount of direct waste discharge to the Bay.
• Approval of a Santa Monica ordinance to reduce
the amount of urban runoff pollution that reaches
Santa Monica Bay, requiring a 0.75" reduction in
rainfall leaving impermeable surfaces of newly
developed parcels in the city (City of Santa
Monica, 2006).
• An EPA-conducted pilot program to cap contami-
nated sediments with clean sediment in
DDT/PCB-contaminated areas of the Palos
Verdes shelf.
• Provision of more than $450,000 by the SMBRC
to community groups, local governments, and
schools to educate and inspire people of all ages to
take care of Santa Monica Bay (ANEP, 200Id).
• Acquisition by the State of California of 483 acres
of the Ballona wetlands, the largest remaining
coastal wetland in the Santa Monica Bay
ecosystem (The Trust for Public Land, 2003).
• Restoration of the Zuma Lagoon and wetland, the
first coastal freshwater wetland project in the area
(ANEP, 2001).
Conclusion
Santa Monica Bay faces a series of environmental
challenges. Sediment quality in the Bay is still threat-
ened by levels of DDT, PCBs, copper, and zinc. Most
recreational beaches in the estuary have very good water
quality, as evidenced by the local Beach Report Card
system, but the amount of trash and debris entering the
Bay is still a significant concern. The monitoring of
certain target species of fish and wildlife (e.g., rockfish,
black abalone) and other threatened resources in this
estuary is important to control population declines. In
addition, invasive species still have an impact on the
natural plant and animal populations in the watershed
because they crowd out native biota and damage func-
tioning ecosystems. Habitat conditions in the Santa
Monica Bay estuary are being continually monitored by
the SMBRC and its partners to prevent declines in the
size and quality of wetlands, riparian habitat, kelp beds,
and intertidal habitats. In addition, the SMBRC is faced
with educating Los Angeles' diverse audiences about the
importance of pollution prevention and environmental
restoration, as well as implementing a comprehensive
monitoring program to more effectively assess the
condition across the Bay. Based on data from the NCA
estuarine survey, the overall condition of Santa Monica
Bay is rated fair.
Seagulls rest on a sand bar (John H. McShane).
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CHAPTER 7
PUERTO RICO NATIONAL ESTUARY PROGRAM COASTAL
CONDITION
*xl
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CHAPTER 7 PUERTO RICO NATIONAL ESTUARY PROGRAM COASTAL CONDITION
San Juan Bay Estuary Partnership
San Juan Bay Estuary Partnership
de la Bahia de San Juan
www.estuario.org
Background
Located on the northern coast of the island territory
of Puerto Rico, the San Juan Bay Estuary (Estuario de
la Bahia de San Juan) is semi-enclosed by the
surrounding mainland, mangroves, and wetlands and is
linked to the Atlantic Ocean via a series of intercon-
nected bays, channels, and lagoons. This estuarine
system includes San Juan Bay; the Martin Pena, San
Antonio, and Suarez channels; and the Condado, Los
Corozos, San Jose, Torrecilla, and Pinones lagoons.
Multiple tributaries flow into the San Juan Bay Estuary,
the largest being the Puerto Nuevo River. Salt water
enters the Estuary from the Atlantic Ocean through the
Boca del Morro to San Juan Bay, through El Boqueron
to Condado Lagoon, and through Boca de Cangrejos to
Torrecilla Lagoon. The limited flushing capacity and
low tidal range of this estuarine system make the San
Juan Bay Estuary susceptible to the retention of toxic
pollutants (Martin et al., 1996).
For centuries, the San Juan Bay Estuary has provided
a number of invaluable resources for the residents of
Puerto Rico, including commercial port facilities,
beaches, recreational parks, and natural and historic
areas; however, the societal needs associated with the
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CHAPTER 7 PUERTO RICO NATIONAL ESTUARY PROGRAM COASTAL CONDITION
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growth of the surrounding population have resulted in
the degradation of the natural resources of this system.
Recognizing the constant threats to the Estuary, the
Governor of Puerto Rico nominated San Juan Bay
Estuary for inclusion into EPA's NEP in 1992, leading
to the official creation of the San Juan Bay Estuary
Partnership (SJBEP).
Environmental Concerns
One of the SJBEP's first tasks was to identify the
priority problems of the San Juan Bay Estuary. To carry
out this task, the SJBEP considered information from
different scientific studies, expert scientific opinion,
and public meetings and workshops. Based on these
combined inputs, the SJBEP is addressing the
following problems (listed in order of importance):
• Poor water circulation
• Illegal sanitary discharges
• Contamination by toxic substances and nutrients
• Lack of an ecosystem management plan
• Lack of community participation.
Population Pressures
The SJBEP study area is coincident with eight urban
municipalities on the northeast coast of Puerto Rico.
The population of these coastal municipalities
(Bayamon, Carolina, Cantano, Guaynabo, Loiza, San
Juan, Toa Baja, and Trujillo Alto) was almost 1.18
million people in 2000 (Figure 7-1), and the population
density was 5,055 persons/mi2 (U.S. Census Bureau,
2001). This represents the highest population density
observed for any of the 28 NEPs—more than 60%
higher than the population density of the counties coin-
cident with the HEP study area. Development and
population pressures are especially strong surrounding
the San Juan Bay Estuary, which has long served as a
center of commerce and shipping in the Caribbean and
is currently a center for commercial and recreational
fisheries and recreational activities for the area's highly
urbanized island community.
1.4
^ 1.2
O
= 1.0
E
c 0.8
0 0.6
Q.
£ 0.2
0.0
NA
NA
NA
NA
I960
1970
1980
Year
1990 2000
Figure 7-1. Population of the coastal municipalities coincident
with the SJBEP study area, 1960-2000 (U.S. Census Bureau, 199 I;
2001).
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CHAPTER 7 ' PUERTO RICO NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Son Juan Bay Estuary Partnership
The following sections of this report discuss
two different approaches for characterizing
estuarine condition.
Approach I -The NCA provides unbiased,
quality-assured data that can be used to make
consistent "snapshot" comparisons among the
nation's estuaries.These comparisons are
expressed in terms of the percent of estuarine
area in good, fair, or poor condition.
Approach 2 - Each individual NEP collects
site-specific estuarine data in support of local
problem-solving efforts. These data are difficult
to compare among NEPs, within regions or
nationally, because the sampling and evaluation
procedures used by the NEPs are often unique
to their individual estuaries. However, these
assessments are important because NEP-
collected data can evaluate spatial and temporal
changes in estuarine condition on a more
in-depth scale than can be achieved by the
NCA snapshot approach.
NCA Indices of Estuarine
Condition—San Juan Bay Estuary
In the winter of 2002, EPA's Region 2 conducted a
survey in the San Juan Bay Estuary that focused on
generating a comprehensive biological and chemical
assessment of sediment throughout the Estuary (U.S.
EPA, 2002b). In partnership with the NCA, a survey
design and data-collection strategy that was compatible
with EPA's NEP assessment effort was employed. Thirty-
four sites were visited during this survey for the SJBEP
assessment. Additionally, Region 2 conducted an inde-
pendent fish tissue contaminants survey in San Jose
Lagoon—a coastal lagoon within the San Juan Bay
Estuary system—and the data from this survey contrib-
uted to the fish tissue contaminants evaluation for this
Estuary.
Based on the data collected during the Region 2
survey efforts, the overall condition of the San Juan Bay
Estuary is rated poor (Figure 7-2). The water quality
index for the Estuaiy is rated fair, and the sediment
quality, benthic, and fish tissue contaminants indices are
rated poor. Figure 7-3 shows the percent of estuarine area
rated good, fair, poor, and missing for each parameter
considered. Please refer to Tables 1-24, 1-25, and 1-26
(Chapter 1) for a summary of the criteria used to develop
the rating for each index and component indicator.
Overall Condition
San Juan Bay
Estuary
(1.5)
Water Quality Index (3)
Sediment Quality Index (I)
Benthic Index (I)
Fish Tissue Contaminants
Index (I)
Figure 7-2. The
overall condition of the
SJBEP estuarine area is
poor (U.S. EPA/NCA).
Water Quality Index
Nitrogen (DIN)
Phosphorus (DIP)
Chlorophyll a
Water Clarity
Dissolved Oxygen
Sediment Quality Index
Sediment Toxicity
Sediment Contaminants
Total Organic Carbon (TOC)
Benthic Index
Fish Tissue
Contaminant Index
20 40 60 80
Percent NEP Estuarine Area
100
I [ I Missing
Figure 7-3. Percentage of NEP estuarine area achieving each
ranking for all indices and component indicators — San Juan Bay
Estuary.
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San Juan Bay Estuary Partnership
Water Quality Index
The water quality index for San Juan Bay Estuary is
rated fair because 74% of the estuarine area was rated
fair or poor for water quality (Figure 7-4). This index
was developed using NCA data on five component indi-
cators: DIN, DIP, chlorophyll a, water clarity, and
dissolved oxygen. Threshold values used to determine
the condition of individual water quality parameters
were based on those used by the NCA for assessing
tropical waters (see Chapter 1 for additional details),
and all water quality component indicators were rated
fair.
Water Quality Index - San Juan Bay Estuary
Site Criteria: Number of component
indicators in poor or fair condition
• Good = No more than I is fair
OFair = I is poor, or 2 or more are fair
• Poor = 2 or more are poor
O Missing
Figure 7-4. Water quality index data for San Juan Bay Estuary,
2002 (U.S. EPA/NCA).
Dissoh'ed Nitrogen and Phosphorus I The San
Juan Bay Estuary is rated fair for both DIN and DIP
concentrations. With respect to DIN concentrations,
45% of the estuarine area was rated good, 10% was
rated fair, and 23% was rated poor. Poor DIP levels
occurred in 19% of the estuarine area, with 2% of the
area rated fair and only 1% of the area rated good;
however, NCA data on DIP concentrations were
unavailable for 78% of the SJBEP estuarine area.
Chlorophyll il Chlorophyll a concentrations in
the San Juan Bay Estuary are rated fair. The NCA
survey results showed good chlorophyll a conditions for
73% of the estuarine area, with 9% of the area rated
fair and 11 % of the area rated poor. NCA data on
chlorophyll a concentrations were unavailable for 7% of
the SJBEP estuarine area.
Water Clarity I Water clarity for the San Juan Bay
Estuary is rated fair. For tropical waters, a range of 20%
to 40% expected light penetration at 1 meter is consid-
ered fair. Measurements above this range are considered
good, and those below are considered poor. In the San
Juan Bay Estuary, only Secchi depth measurements
were available to assess water clarity. A light extinction
coefficient was calculated for each Secchi depth reading
and compared to the light extinction coefficient of the
expected or reference value (at 1 meter) appropriate for
the region (Smith et al., 2006). These evaluations show
that 54% of the estuarine area was rated good for water
clarity, 12% was rated fair, and 17% was rated poor.
Water clarity data were unavailable for 17% of the
SJBEP estuarine area.
Dissolved Oxygen I The San Juan Bay Estuary is
rated fair for dissolved oxygen concentrations. Estimates
show that 57% of the estuarine area was rated fair, 36%
of the area was rated good, and none of the area was
rated poor. NCA data on dissolved oxygen concentra-
tions were unavailable for 7% of the SJBEP estuarine
area.
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CHAPTER 7 PUERTO RICO NATIONAL ESTUARY PROGRAM COASTAL CONDITION
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Sediment Quality Index
The sediment quality index for San Juan Bay
Estuary is rated poor (Figure 7-5). This index was
developed using NCA data on three component indi-
cators: sediment toxicity, sediment contaminants, and
sediment TOG. About one-third (33%) of the estu-
arine area was rated poor for sediment quality, and
another 4% was rated fair. NCA data on sediment
quality were unavailable for 15% of the SJBEP
estuarine area.
Sediment Toxicity The San Juan Bay Estuary is
rated poor for sediment toxicity. Twenty-nine percent
of the estuarine area was rated poor for this component
indicator, and 56% of the area was rated good. NCA
data on sediment toxicity were unavailable for 15% of
the SJBEP estuarine area.
Sediment Quality Index - San Juan Bay Estuary
Site Criteria: Number and condition of
component indicators
• Good= None are poor, and sediment
contaminants is good
OFair = None are poor, and sediment
contaminants ts fair
• Poor = I or more are poor
O Missing
Figure 7-5. Sediment quality index data for San Juan Bay
Estuary, 2002 (U.S. EPA/NCA).
Sediment Contaminants I The San Juan Bay
Estuary is rated fair for sediment contaminant concen-
trations. Five percent of the estuarine area was rated
poor for sediment contaminants, and 18% of the area
was rated fair. NCA data on sediment contaminant
concentrations were unavailable for 15% of the SJBEP
estuarine area.
Total Organic Carbon TOC concentrations in
the sediments of the San Juan Bay Estuary are rated
good, with 65% of the estuarine area rated good for
this component indicator. TOC concentrations were
rated fair and poor in 13% and 7% of the estuarine
area, respectively and NCA data on this component
indicator were unavailable for 15% of the SJBEP
estuarine area.
Benthic Index
A benthic index has not been developed for Puerto
Rico. As a surrogate for benthic condition, benthic
samples from the San Juan Bay Estuary were examined
using ecological community indicators that contribute
to all of the benthic indices developed by the NCA for
the Northeast Coast, Southeast Coast, and Gulf Coast
regions, and benthic diversity was used directly to eval-
uate benthic condition. If benthic diversity was less
than 75% of the observed mean diversity for all loca-
tions sampled in Puerto Rico during the NCA surveys,
the site was rated poor.
The benthic index for the San Juan Bay Estuary is
rated poor because 65%) of estuarine area had low
benthic diversity and was rated poor (Figure 7-6).
Benthic diversity data were unavailable for the
remaining 35% of the estuarine area. When the areas
that were rated poor for benthic condition were
compared with the areas rated poor for water and
sediment quality, it was determined that all of the
SJBEP areas with low benthic diversity were also rated
poor for at least one other index. Eighty-three percent
of the area with low benthic diversity co-occurred with
both poor sediment and water quality condition; 10%
co-occurred with only poor sediment quality condi-
tions; and 7% occurred with only poor water quality
conditions.
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Benthic Index - San Juan Bay Estuary
Site Criteria: Compared to
expected diversity
• Good=>90%
OFair = 75% - 90%
• Poor =<75%
OMissing
Poor
65%
Figure 7-6. Benthic index data for San Juan Bay Estuary, 2002
(U.S. EPA/NCA).
Fish Tissue Contaminants Index
The results from a separate survey conducted in the
San Jose Lagoon, one of the larger coastal lagoons
within the San Juan Bay Estuary were used as a surro-
gate for the NCA's fish tissue contaminants evaluation.
The goals of the San Jose Lagoon survey were to eval-
uate whether toxic compounds were present in edible
fish and shellfish tissues and to develop risk-based
human health consumption advisories for the Lagoon.
The survey design partitioned the Lagoon into four
quadrants that were as equal in size as geographically
possible. Trawls were conducted in each of these quad-
rants to collect tissue samples from four target species:
blue crab (Callinectes sapidus), yellowfin mojarra
(Eugerres cinereus), striped mojarra (Eugerres brasilianus),
and snook (Centropomus sp.}. Five individuals of each
species were culled for contaminant analysis. Finfish
fillets (with skin) and separate crab tissue and
hepatopancreas samples were used for analysis (U.S.
EPA, 2000d).
Based on the concentrations of contaminants found
in fish and crustacean tissues during the San Jose
Lagoon survey, the fish tissue contaminants index for
the San Juan Bay Estuary is rated poor because 40% of
all samples analyzed for contaminants exceeded EPA
Advisory Guidance values (Figure 7-7).
Fish Tissue Contaminants Index - San Juan Bay
Estuary
Site Criteria: EPA Guidance concentration
• Good= Below Guidance range
O Fair = Falls within Guidance range
• Poor = Exceeds Guidance range
San Jose
Lagoon
Poor
40%
Figure 7-7. Fish tissue contaminants index data for San Juan Bay
Estuary, 2002 (U.S. EPA/NCA).
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CHAPTER 7 PUERTO RICO NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Son Juan Bay Estuary Partnership
Getting the Message to the
People—The San Juan Bay Estuary
Partnership Educational Outreach
Efforts
The SJBEP has been working very hard in the area
of educational outreach. Several projects have been
implemented to increase public awareness of the
Estuary and its ecological importance.
Bay Day Festival of the Estuary
The SJBEP held its first Bay Day Festival of the
Estuary: Two Windows, Land and Sea (Festival del
Estuario: Dos Ventanas, Tierra y Mar) in May 2003. A
large number of people participated in the festival,
which included more than 30 environmental art exhibi-
tions and presentations; diving and kayaking lessons;
and environmental arts and crafts workshops, as well as
a number of activities specifically designed for children.
Numerous local artists participated in the festival, which
received significant coverage from various media,
including television, radio, and newspaper. The event
also provided the setting for the expansion and continu-
ation of cooperative efforts and collaborations between
federal and local government agencies, community
groups, and the SJBEP.
Teacher Training Workshops
Workshops developed and presented on environ-
mental topics train local teachers about the effective use
of San Juan Bay Estuary environmental education
curriculum and related educational materials. In
October 2004, one workshop for private school science
teachers drew more than 100 participants. These one-
day workshops take place periodically and have the
support of the Department of Education, which sent
out an official announcement to the schools located
around San Juan Bay Estuary. The workshops provide a
session on the use and application of the curriculum
and feature information on the ecological values of the
San Juan Bay Estuary system, environmental threats to
die Estuary, and proposed solutions. Workshops also
include environmental games and presentations by
representatives from the Puerto Rico Department of
Natural and Environmental Resources, Environmental
Quality Board, Solid Waste Management Authority
Agency, Highway and Transportation Agency, and the
group working on restoration of the Cucharillas marsh.
This fish and wildlife exhibit shows species that are in danger
of extinction (Susan Rivera, SJBEP).
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School Day for the San Juan Bay
Estuary
The School Day for the San Juan Bay Estuary
encourages students to complete a project related to the
Estuary. Students from the municipalities coincident
with the SJBEP study area are invited to participate and
submit abstracts of possible projects. The participating
schools then plan an environmental activity that focuses
on conservation efforts for the Estuary, and these activi-
ties are normally completed in April as part of the Earth
Day celebration. Past student projects have involved a
variety of activities, including beach cleanups, recycling,
theater plays, monologues, and poster- and wall-
painting contests. These activities create awareness
about the importance of protecting, restoring, and
conserving the San Juan Bay Estuary.
Volunteer Program
Long-term public support and participation in
Estuary protection and restoration activities is necessary
and critical for the successful implementation of the
SJBEP's Comprehensive Conservation and Management
Plan for the San Juan Bay Estuary (SJBEP, 2001). A
volunteer program was created to encourage and facili-
tate active involvement by citizens in the Estuary's
restoration process. University students participating in
this program are encouraged to work with the SJBEP,
using the SBJEP's objectives as potential subjects for
developing their own research. These environmental
volunteers will provide the resources needed to
complete many of die SJBEP's proposed projects.
Outdoor activities accomplished during the 2005 Teacher Training Workshop included teachers kayaking or paddling
to several areas of the Estuary, providing a first-hand, unforgettable experience for most of the participants (SJBEP).
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CHAPTER 7 PUERTO RICO NATIONAL ESTUARY PROGRAM COASTAL CONDITION
Son Juan Bay Estuary Partnership
San Juan Bay Estuary Partnership
Indicators of Estuarine Condition
A Long-Term Environmental Indicator Program
(LTEIP) has been proposed for the San Juan Bay
Estuary to help assess the effectiveness of the area's
conservation and restoration efforts. The indicators
monitored by the LTEIP will be divided into four
groups: Water-Sediment Quality, Biological Productivity
and Respiration, Biota Distribution, and Biota-Pollutant
Interactions. An important component of the LTEIP
will be the preparation and dissemination of educational
material as part of the SJBEP's outreach component.
Other monitoring efforts have been proposed in the
SJBEP's CCMP (SJBER 2001) to focus on the conse-
quences of such events as petroleum spills, discharges
from boats and ships, and high-temperature cooling
water releases from thermoelectric plants. These events
reduce the capacity of the Estuary's waters to retain
oxygen.
Water and Sediment Quality
The SJBEP uses both chemical and bacteriological
indicators to evaluate point and non-point sources of
contamination. The most common indicators reported
in the SJBEP CCMP are concentrations of nitrogen and
phosphorus, dissolved oxygen, fecal coliform bacteria,
and toxic substances (e.g., mercury, lead, arsenic, PCBs).
Although the SJBEP does not monitor for these indica-
tors directly, the indicators have been monitored for
previous studies conducted by independent consultants,
EPA, and the Puerto Rico Environmental Quality
Board (EQB), as well as for previous studies supported
by the SJBER Some of these indicators are currently
evaluated for the Puerto Rican Water Quality Standards
to define designated uses for different waterbodies.
The most common and widespread impairments to
the Estuary's waters are nutrient enrichment/eutrophica-
tion and fecal contamination caused primarily by sewage
discharges through non-point sources. Malfunctioning
on-site septic systems, illegal connections to storm
sewers, and direct discharges from unsewered areas are
some of the current non-point sources of nutrients and
fecal contamination related to sewage discharges into
the San Juan Bay Estuary and its tributaries.
Nutrient and dissolved oxygen concentrations have
been used to assess water quality in the San Juan Bay
Estuary. No evidence of use impairments due to
nitrogen and phosphorus loads have been reported in
most of the San Juan Bay Estuary since point-source
discharges from the Puerto Nuevo STP outfall into the
Estuary were eliminated in 1985 (TetraTech, Inc.,
1992). Dissolved oxygen levels in the Estuary's
eutrophic waters vary widely depending on the time of
day. This variation in dissolved oxygen concentrations
is typically found in the San Jose and Los Corozos
lagoons; however, the control of oxygen-consuming
substances from industrial point-source discharges has
gradually improved the dissolved oxygen levels in some
areas of the Estuary (Webb and Gomez-Gomez, 1998).
Fecal coliform concentrations in most areas of the
Estuary remain above the levels required to meet water
quality standards (SJBEP, 2001), and as a result, the
SJBEP sponsored a study to determine the public
health risks from direct and indirect contact activities
(e.g., bathing, fishing) in areas where fecal coliform
concentrations were measured. These concentrations
were measured in single samples collected at 16 sites in
the Estuary. Although the fecal coliform concentrations
measured in samples from six of the sites exceeded
water quality standards, the study concluded that risk
levels associated with water contact activities were
within acceptable levels. The study also interviewed
area residents about their fish-consumption habits and
found that, although more than 40% of the people
interviewed consumed food from Estuary waters, none
reported any illnesses as a result of this consumption
(Seguinot-Barbosa & Vazquez, 1999).
The San Juan Bay Estuary is also affected by other
types of pollutants (e.g., metals, oils, and other
substances) that gain access to the Estuary through
storm sewers or runoff. The total volume of runoff can
be much greater than the volume from other sources,
causing significant contribution of contaminants
(Horsley & Witten, Inc., 1995). Furthermore, the
urbanization of drainage basins, removal of in-stream
and bank vegetation, and alteration of streams and
rivers due to channelization contribute to erosion and
sedimentation rates in the area, as well as to the degra-
dation of water quality in the Estuary and its tribu-
taries. In the upper part of the watershed, erosion
394 National Estuary Program Coastal Condition Report
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CHAPTER 7 PUERTO RICO NATIONAL ESTUARY PROGRAM COASTAL CONDITION
San Juan Bay Estuary Partnership
accounts for an average loss of 4 inches of soil per year,
much of which enters the Estuary (Webb and Gomez-
Gomez, 1998).
PCBs, the pesticide DDT (and its metabolites DDD
and DDE), the common elasticizing agent bis(2-ethyl-
hexl)phthalate, lead, and mercury are the most abun-
dant contaminants in the sediments of the SJBEP
system. Figures 7-8 and 7-9 show the trends in the sedi-
ment contaminant concentrations from 1925 through
1995 (SJBEP, 2001). Although the occurrence of these
contaminants in San Juan Bay Estuary sediments is
expected to decrease with time, toxic pollutants in the
surface bottom sediments of some areas may persist at
relatively high concentrations for some time. The
average sediment deposition rate for the San Juan Bay
Estuary (excluding Martin Pefia Channel) is about two
MPN500 CRZ400 SJS300 TRC200
EXPLANATION
•• 1925-49
Drainage basin boundary
1950-74
SJN600 Station name
Figure 7-8. Sediment concentrations (ug/kg) of PCB, dieldnn, and DDT and its metabolites at different locations in the San Juan Bay
Estuary and during different time periods (SJBEP, 2001).
National Estuary Program Coastal Condition Report 395
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CHAPTER 7 PUERTO RICO NATIONAL ESTUARY PROGRAM COASTAL CONDITION
San Juan Bay Estuary Partnership
Drainage basin boundary
EXPLANATION
^•1 1925-49
1950-74
^•1 1975-95
SJN600 Station name
Figure 7-9. Sediment concentrations (Mg/kg) of mercury, lead, and arsenic at different locations in the San Juan Bay istuary and
during different time periods (SJBER 2001).
inches per decade; therefore, contaminated sediments
will need significant time to be buried by incoming,
less-contaminated sediments (Webb & Gomez-Gomez,
1998). For these reasons, Webb & Gomez-Gomez
(1998) concluded that contaminated sediments in such
areas of the estuary as the Martin Pena Channel and the
San Jose and Los Corozos lagoons present a potential
threat to human health; however, EPA reviewed this
assessment and concluded that, based on the confined
nature of the contaminated sediments, there was no
threat to human health by direct contact (U.S. EPA,
1996). This determination certified that a CERCLA
removal action, consisting of identifying and remedi-
ating hazardous waste sites, was not warranted.
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CHAPTER 7 PUERTO RICO NATIONAL ESTUARY PROGRAM COASTAL CONDITION
San Juan Bay Estuary Partnership
Habitat Quality
Swamps, marshes, mangroves, aquatic vegetation,
coral reefs, and sandy beaches are some of the habitats
that are found in the San Juan Bay Estuary, which
harbors very rich and diverse aquatic communities.
Marshes and mangroves support a great variety of juve-
nile fish and invertebrates and provide food and nesting
habitat for many different bird species. Marshes also
play an important role in the cycle of nutrients and
filter contaminants that have been washed into the
Estuary from the upper parts of the basin by runoff.
The preservation of marsh and mangrove habitats is
clearly included as an objective in the SJBEP CCMP
(SJBEP, 2001).
Table 7-1 shows the area of marsh and mangrove
habitats, as well as the change in area between 1936 and
1995, in different locations within the Estuary. The area
between the Torrecilla and Pinones lagoons showed a
significant net increase based on an increase in the
mangrove area; however, this increase could be due to
the succession of one kind of mangrove habitat by
another, and not necessarily due to an improvement in
the original habitat. This was the only area around San
Juan Bay Estuary that exhibited a positive gain in total
marsh and mangrove acreage between 1936 and 1995
(SJBEP, 2001).
Puerto Rico has one of the most diverse ecosystems
of seagrass and SAV in the North Atlantic Ocean. Table
7-2 shows the areal coverage of these habitats, which are
very important in supporting biodiversity and a variety
of other ecological resources. For example, these habitats
provide nutrients and primary energy for different fish
species. The SJBEP places high emphasis on improving
the overall condition of these habitats by improving the
San Juan Bay Estuary's water quality (SJBEP, 2001).
Table 7-1. Trends in the Acreage of San Juan Bay Estuary Marsh and Mangrove Habitats Over Time
(SJBEP, 2001)
Location
Time Period
Mangrove Area
(Acres)
Marsh Area
(Acres)
Total Change
(Acres)
San Juan Bay and
Condado Lagoon
1936
1995
% change
458
329
-28%
1,327
566
-57%
1,785
895
-50%
Marti'n Pefia Channel
1936
1995
% change
1,029
327
-67%
578
197
-84%
1,607
524
-73%
San Jose Lagoon to
Suarez Channel
1936
1995
% change
704
327
-54%
68
197
+ 190%
772
524
-32%
Torrecilla and Pinones
areas
1936
1995
% change
2,790
4,561
+63%
1,904
1,101
-42%
4,694
5,662
+21%
Table 7-2. Areal Extent of Seagrass (acres) and Surface Water (mi2) in the San Juan Bay Estuary
(SJBEP, 2001)
Habitat
San Juan Bay
Condado
Lagoon
San Jose
Lagoon
Torrecilla
Lagoon
Surface water area (mi2)
4.56
0.15
2.11
0.95
Seagrass area (acres)
31
35
O.I
National Estuary Program Coastal Condition Report 397
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CHAPTER 7 PUERTO RICO NATIONAL ESTUARY PROGRAM COASTAL CONDITION
San Juan Bay Estuary Partnership
Living Resources
In 1998, the SJBEP supported a study to investigate
the levels of seven heavy metals in the tissue of mojarra,
blue crabs, and false mussels taken from the San Jose
and Corozos lagoons. This study found that the
concentrations of mercury and lead in some samples
were above the standards recommended by the FDA.
Although the average mercury concentration in mojarra
was below the FDA standard, two samples had concen-
trations that exceeded the FDA standard. In addition,
the average lead concentration in mojarra exceeded the
lead standard. None of the blue crab samples exceeded
the standard for mercury or lead; nevertheless, the
regular consumption of blue crabs, particularly the
hepatopancreas tissue, from these lagoons poses a poten-
tial public health problem resulting from elevated PCB
levels in the tissue. Concentrations in some samples of
false mussels exceeded the standard for lead, but not the
standard for mercury; however, false mussels are typi-
cally not consumed by humans (Delgado-Morales et al.,
1999).
Environmental Stressors
The discharge of nutrients and bacteria from septic
systems and illegal sewer connections impacts water
quality in the San Juan Bay Estuary; therefore, moni-
toring septic system performance and/or the number of
illegal sewer connections may provide insight into ways
of resolving the problem. At the present time, informa-
tion about the number of septic systems functioning
properly or malfunctioning, as well as how frequently
these on-site systems are maintained, is not available.
Illegal connections of sanitary sewers to storm sewers, as
well as direct discharges of sewage, have been reported
throughout the Estuary and its watershed; however, this
condition is most common in the communities closest
to the Estuary (Puerto Rico EQB, 1989; 1994; 1996).
In a study performed by the Puerto Rico EQB from
1986 to 1989, almost 40% of the structures surveyed in
the communities adjacent to the Martin Pena Channel
were found to discharge raw sewage into storm sewers
or directly into the Estuary or its tributaries (Puerto
Rico EQB, 1989). The SJBEP CCMP recommends the
construction of a sanitary sewer system that would
connect to the existing regional STPs for those commu-
nities bordering the Estuary (SJBEP, 2001). As shown
The green heron (Butondes wrescens) is a common resident of
the San Juan Bay Estuary. This small, gray-green waterbird forages
mostly in shallow waters, such as mangrove swamps, searching for
small fish and invertebrates (SJBEP).
by a similar effort undertaken in the Condado Lagoon
during the 1960s and 1970s (Rivera-Cabrera, 1990), a
sanitary sewer system is expected to be the most effec-
tive and efficient way of eliminating illegal storm sewer
connections and direct sewage discharges to the Estuary.
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CHAPTER 7 PUERTO RICO NATIONAL ESTUARY PROGRAM COASTAL CONDITION
San Juan Bay Estuary Partnership
Current Projects,
Accomplishments, and Future
Goals
The SJBEP has implemented 41 projects—10 new
projects financed by grants from past years, 14 new
projects financed in this fiscal year, and 17 projects that
were in progress and scheduled to be completed during
the 2004-2005 fiscal year. Simultaneously, the SJBEP
has been able to finalize 15 projects from past years,
complying with 11 actions proposed in the Partnership's
CCMP (SJBEP, 2005). The SJBEP will base its future
goals on goals already established in the CCMP, which
are divided into three areas of concern:
• Improve the water and sediment quality of San
Juan Bay Estuary to ensure suitability for
fishing and swimming and to promote other
compatible recreational and commercial activi-
ties - The SJBEP will accomplish part of this goal
through the LTEIP, which will provide the NEP
with data to inform the public about the health of
the Estuary and to take corresponding actions.
The SJBEP is also actively working as a new
member of the Ecological Corridor Commission
of San Juan, which was created as part of the Law
of the San Juan Ecological Corridor in 2003 (Law
206) to oversee the acquisition of parcels of land
and transform them into an ecological corridor of
approximately 1,000 acres.
• Enhance and maintain an ecosystem that
supports an optimum diversity of living
resources on a sustained basis - The SJBEP will
continue to implement 18 actions conceptualized
to fulfill this important goal through its Volunteer
Program. In 2006, the SJBEP will implement 6 of
the 18 actions and will build partnerships to rein-
force future conservation projects.
• Maximize public involvement in the implemen-
tation of the CCMP - Nine projects have been
approved by the SJBEP Board of Directors to
support 100% of the actions under this area of
concern, and the SJBEP Volunteer Program will
help to achieve this goal.
The following new activities were implemented during
2005 to enrich the SJBEP and its CCMP:
• Integrated Media and Communications
Program - In 2002, 84% of the Estuary's local
residents interviewed did not recognize the word
or concept of an "estuary" (Personal communica-
tion, Bauza-Ortega, 2006). In order to resolve this
challenge, the Partnership conducted a focus
group study in which a comprehensive media plan
was developed. The integrated media approach
outlined in the plan conveyed a message of
restoration and conservation for the Estuary using
multiple resources, including electronic media
(e.g., interactive Web page), traditional media
(e.g., newsletter, radio programs), and monthly
seminars.
• Christmas Card Competition - During this
project, Puerto Rico elementary school students
learned about San Juan Bay Estuary and helped
promote the SJBEP's mission through the devel-
opment of a Christmas card exhibit. One card
design, selected by a jury, was printed and deliv-
ered to all members of the SJBEP mailing list and
contacts.
• Collaboration with the Enlace del Cano Martin
Pena Project - This project is responsible for
dredging the Martin Pena Channel, relocating
people affected by dredging activities, constructing
new homes, and developing and implementing
the complex educational strategy that requires
relocating people who have lived in a particular
community for decades. The SJBEP collaborates
with the Enlace Project in the educational phase
and has completed several important activities
through the years, such as theater workshops,
community concerts, contests, publications, and
technical support and environmental consulting
through the staff scientist.
• Annual Audubon Society Bird Census - For the
past 9 years, the annual Audubon Society Bird
Census has helped identify bird species density in
the SJBEP study area. Local species data are
updated through this annual census.
National Estuary Program Coastal Condition Report 399
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CHAPTER 7 I PUERTO RICO NATIONAL ESTUARY PROGRAM COASTAL CONDITION
San Juan Boy Estuary Partnership
Conclusion
Based on data from the NCA estuarine survey, the
overall condition of the San Juan Bay Estuary is rated
poor. Although the Estuary's water quality index is rated
fair, the sediment quality, benthic, and fish tissue conta-
minant indices are rated poor. The data used by the
SJBEP to assess water quality in the Estuary indicate
that bacterial contamination caused by the discharge of
sewage from non-point sources is a concern in the area
and has negatively affected water quality. A variety of
toxic chemicals have been detected in Estuary sediments
and may persist at relatively high concentrations for
some time. The development of a maritime and air
transportation infrastructure, as well as of residential
and industrial areas, have caused significant modifica-
tion and loss of important habitats in the Estuary. Most
of these modifications have occurred in the western half
of the Estuary basin, where the pressures of urban
growth and development on the San Juan Bay Estuary
are greatest. The SfBEP is focusing its attention on
developing a strong outreach program to inform the
local population about conditions in the Estuary.
L **
». *
The green iguana (Iguana iguana), locally known as "gallina de palo", is an invasive species that was introduced into
Puerto Rico from Central and South America by the pet trade in the 1970s.The SJBEP plans to study the ecology of
the green iguana and evaluate its potential for negative impact to the local biodiversity (SJBEP).
400 National Estuary Program Coastal Condition Report
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APPENDIXA
PROCEDURES FOR CALCULATING TOTAL POPULATION,
POPULATION GROWTH RATE, AND POPULATION DENSITY
FOR VARIOUS GEOGRAPHIC AREAS
••••1
.
-------
APPENDIXA
PROCEDURES FOR CALCULATING TOTAL POPULATION,
POPULATION GROWTH RATE, AND POPULATION DENSITY
FOR VARIOUS GEOGRAPHIC AREAS
Introduction
Human population pressures can be evaluated using
several measures. For the U.S. Environmental Protect-
ion Agency's (EPA's) National Estuary Program Coastal
Condition Report (NEP CCR), three measures were
used to evaluate the impact of human population
pressures on the 28 NEP estuaries of the United States:
total population, population growth rate over a speci-
fied time interval, and population density (persons/mi2
of land area). These population pressures were measured
for each individual NEP estuary and compared to those
calculated for other NEP estuaries, all coastal areas, all
non-coastal areas, and the conterminous United States
to assess the relative impacts of human populations on
estuarine condition.
The National Oceanic & Atmospheric Administra-
tion (NOAA) recently published the report Population
Trends along the Coastal United States: 1980-2008
(Crossett et al., 2004), which presents an overview of
coastal population trends from 1980 through 2003,
projected changes in coastal populations through 2008,
and the definition of a NOAA-designated coastal
county. The NOAA Special Projects office designates a
county as a coastal county if one of the following
criteria is met:
• At a minimum, 15% of the county's total land area is
located within a coastal watershed
• A portion of a county or an entire county accounts
for at least 15% of a cataloging unit.
It should be noted that this NOAA report and the
other NOAA report (Culliton et al.,1990) referenced
in this Appendix differ from the NEP CCR in that the
NOAA reports include the Great Lakes region as a
coastal area. In addition, the NEP CCR. only covers
marine coastal areas in the conterminous 48 states
because none of the NEP estuaries are located in Alaska
or Hawaii. Population pressures for the one NEP
estuary located in Puerto Rico (San Juan Bay Estuary)
were evaluated separately for this NEP CCR due to a
lack of comparable population data for this region. An
overview of this evaluation is provided later in this
Appendix.
In order to determine the human population pres-
sures exerted on counties coincident with individual
NEP study areas, population data were obtained from
the U.S. Census Bureau (1991; 2001). These data were
used to calculate total population for 1960, 1970, 1980,
1990, and 2000; population density in 2000; and the
population growth rate between I960 and 2000 for the
following:
• Each NEP study area (using all NOAA-designated
coastal counties or municipalities coincident with an
individual NEP study area)
• All NEP coastal counties collectively (using the
NOAA-designated coastal counties coincident with
all 27 NEPs located in the conterminous 48 states)
• All NOAA-designated coastal counties (using both
NEP and non-NEP coastal counties in the 48 conter-
minous U.S. states and excluding coastal counties in
Puerto Rico and those adjacent to the Great Lakes)
402 National Estuary Program Coastal Condition Report
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APPENDIXA
• All non-coastal counties (using all counties in the
48 conterminous U.S. states that are not considered
NOAA-designated coastal counties, as well as the
NOAA-designated coastal counties that are adjacent
to the Great Lakes)
• All counties in the 48 conterminous U.S. states, as a
whole.
Population statistics for the study area for Puerto
Rico's NEP, the San Juan Bay Estuary Partnership
(SJBEP), were calculated differently because of variances
in available data for the region. Population data for the
SJBEP study area were only available for the year 2000.
In addition, Puerto Rico was not included in the avail-
able list of NOAA-designated coastal counties, and a
separate section in this text has been devoted to
describing the processes employed for deriving popula-
tion density estimates for the SJBEP study area. Due to
the differences in methodology and available source
data for the SJBEP study area, the results for this NEP
estuary are not included in the values cited in Chapter 1
that provide national population data for Figure 1-2.
Selection of Coastal Counties in
the NEP Study Areas
Geographic information systems (GIS) technology
was used to identify which NOAA-designated coastal
counties are spatially coincident with NEP study area
boundaries. These counties were identified using the
following steps:
• A GIS shapefile was developed delineating the
NOAA-designated coastal counties
• A separate GIS shapefile delineating the 2003
boundaries of each NEP study area was obtained
from EPA
• GIS was used to compare the two shapefiles electron-
ically and identify which NOAA-designated coastal
counties overlap the boundaries of a specific NEP
study area
• A visual inspection was conducted to refine the
selection of NOAA-designated coastal counties in
the NEP study area.
For comparison purposes in the NEP CCR, only the
NOAA-designated coastal counties in the U.S. regions
that contain NEP estuaries were processed as coastal
counties. The NOAA-designated coastal counties
bordering the Great Lakes were processed as non-coastal
counties because there are no NEP estuaries in this
region. In addition, this analysis was limited to coastal and
non-coastal counties in the conterminous United States
because no NEP-designated estuaries are located in
Alaska or Hawaii and because insufficient data were
available for the island territory of Puerto Rico.
Methodology for the 27 NEPs in the
Conterminous United States
To identify the NEP-coincident coastal counties for
the 27 NEPs in the conterminous United States, a
shapefile of NOAA-designated coastal counties was
created by electronically linking coastal county data
from NOAA (Culliton et al.,1990) to a GIS shapefile of
all U.S. counties (National Atlas of the United States,
2005). The coastal county data were obtained from the
NOAA report 50 Years of Population Change Along the
Nation's Coasts 1960-2010, A Special Earth Week Report
(Culliton et. al., 1990), which contains a table entitled
"Population and Development in Coastal Areas Coastal
Counties List," hereafter referred to as the NOAA
Coastal Counties Table. This table presents the land
area (in mi ), population, and unique Federal Informa-
tion Processing Standards (FIPS) code for each coastal
county in the conterminous United States.
The NOAA Coastal Counties Table was divided into
sections based on the waterbody associated with each
coastal county. The sections of the table associated with
Great Lakes, Hawaiian, and Alaskan waters were
excluded so that only the sections that provided data for
the Atlantic, Gulf, and Pacific coasts of the contermi-
nous United Sates were used. The FIPS codes in these
sections of the NOAA Coastal Counties Table were
linked electronically with the matching FIPS codes in
the U.S. counties shapefile to create a subset of NOAA-
designated coastal counties. This subset was saved as a
separate shapefile and used in the population calcula-
tions described below.
National Estuary Program Coastal Condition Report 403
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APPENDIXA
Once the NOAA-designated coastal counties shape-
file was created, GIS technology was used to determine
which NOAA-designated coastal counties were coinci-
dent with NEP study areas. A spatial comparison of the
NOAA-designated coastal county boundaries and the
NEP study area boundaries was performed. GIS tech-
nology automatically selected those counties from the
NOAA-designated coastal counties shapefile that
spatially intersected NEP study area polygons in the
NEP boundary shapefile obtained from EPA.
This automatic selection of spatially coincident
counties was further refined using a visual inspection in
GIS. When GIS shapefiles are obtained from different
sources, slight discrepancies in the scale or accuracy of
the polygons in the file are common. For example,
when an NEP study area boundary coincided with a
county border, the automatic selection process often
included the neighboring county due to discrepancies
between the two shapefiles. The objective of this visual
inspection was to identify any counties that were
included in the automatic selection as a result of
discrepancies between the polygonal boundaries of the
NOAA-designated coastal counties shapefile and the
NEP boundary shapefile. These counties were then
removed from the NEP-coincident coastal counties
shapefile.
Figure A-1 provides an example of how GIS analysis
was used to generate the final shapefile of NEP-coinci-
dent coastal counties. The NOAA Coastal Counties
Table was used to select all of the NOAA-designated
coastal counties (shown in yellow and purple). Note
that Highlands County (shown in orange) does not
meet the NOAA Special Projects office s definition of a
coastal county and was not included in the spatial selec-
tion. The Indian River Lagoon NEP (IRLNEP) study
area boundary polygon from EPAs NEP boundary
shapefile is outlined in green. The automatic GIS selec-
tion of coincident coastal counties generated an initial
data set that included Volusia, Brevard, Indian River,
Okeechobee, St. Lucie, Martin, and Palm Beach coun-
ties. Visual inspection of the GIS selections revealed
that the NEP boundary polygon intersected significant
portions of Volusia, Brevard, Indian River, Okeechobee,
St. Lucie, and Martin counties, and these counties were
included in the final shapefile (shown in purple).
However, the NEP boundary polygon did not intersect
a significant portion of Palm Beach County, and the
inclusion of this county was likely due to a discrepancy.
As a result, Palm Beach County was deselected and
excluded from the final NEP-coincident coastal county
shapefile for the IRLNEP.
Methodology for the San Juan Bay
Estuary Partnership (SJBEP)
Puerto Rico is divided into municipalities rather than
counties, and these municipalities were not included in
the NOAA Coastal Counties Table or the NOAA-desig-
nated coastal counties shapefile. As a result, the
methodology for determining the NEP-coincident
municipalities for the SJBEP study area differed from
the methodology used to identify the NEP-coincident
coastal counties for the other 27 NEPs. For Puerto
Rico, each NEP-coincident municipality was selected by
hand using a visual inspection. The inspection selected
all of the municipalities that significantly intersected the
boundary of the SJBEP study area polygon. The
selected municipalities were then used to create a shape-
file for the SJBEP study area.
Calculation of Population
Statistics for all U.S. NEEPs
When data were available, the total population in
1960, 1970, 1980, 1990, and 2000; population growth
rate (1960—2000); and population density in 2000 were
calculated for several geographic areas of interest. These
geographic areas are the conterminous United States, all
NOAA-designated coastal counties (collectively), all
NEP-coincident coastal counties (collectively), the
coastal counties coincident to each individual NEP
study area, and all non-coastal counties (collectively). A
unique data set of population and land area data was
created for each area of interest, and the same general
formulas were used to calculate total population, popu-
lation growth rate, and population density for each data
set. It should be noted that Puerto Rico's population
growth rate and total population figures for 1960,
1970, 1980, and 1990 were not calculated because
population data for Puerto Rico prior to 2000 were
unavailable from the U.S. Census Bureau (1991).
In order to develop a data set for the conterminous
United States, land area values and 1960, 1970, 1980,
1990, and 2000 population data for all of the states
404 National Estuary Program Coastal Condition Report
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Indian River Lagoon NEP (IRLNEP) study
area boundary
I I Indian River Lagoon Coastal Counties
(NEP coincident)
IRLNEP intersects a significant portion of these
coastal counties, which were included in the
final shapefile.
I I NOAA coastal counties
(not NEP coincident)
* Palm Beach County was included in the
automatic selection due to a discrepancy. This
county was excluded from the final data set
I I Non-NOAA-designed coastal county
Highlands County is not a NOAA-deslgnated
coastal county and was not included In
spatial selection.
Atlantic Ocean
Charlotte
Figure A-1. An example of the spatial selection process used to identify NEP-coinddent coastal counties for
the Indian River Lagoon NEP.
(excluding Puerto Rico and other commonwealths,
territories, and protectorates) were obtained from the
U.S. Census Bureau (1991; 2001). The data set was
refined to include only the 48 conterminous states by
subtracting population data and land area values for
Alaska and Hawaii.
The raw data necessary to calculate total population,
population growth rate, and population density for all
the NOAA-designated coastal counties were obtained
from several sources. The land area of each county in
2000 and the population data for each county in I960,
1970, 1980, and 1990 were obtained from the portions
of the NOAA Coastal Counties Table providing data for
the Atlantic, Gulf, and Pacific coasts. The population
data for each county in 2000 was obtained from the
U.S. Census Bureau (2001) and are hereafter referred to
as the 2000 Census Counties Table. Both tables were
linked by the county FIPS codes to create a population
data set that ranged from 1960 to 2000 for all NOAA-
designated coastal counties.
National Estuary Program Coastal Condition Report 405
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APPENDIXA
The NOAA-designated coastal counties data set was
refined to create the NEP-coincident coastal county
data set. During this process, FIPS codes were used to
link the NOAA-designated coastal counties data set
with the NEP-coincident coastal counties shapefile to
isolate the population and land area data for the NEP-
coincident coastal counties.
The NEP-coincident coastal counties shapefile
contains a field that associates each NEP-coincident
coastal county with an individual NEP. This field was
retained in the NEP-coincident coastal counties data set
and used to create the data sets for each of the 27 indi-
vidual NEPs in the conterminous United States. For the
San Juan Bay Estuary, land area and population data for
the SJBEP study area in 2000 were obtained from the
U.S. Census Bureau (2001). The SJBEP data set was
created by linking the FIPS codes in the SJBEP shape-
file to those in the data from the U.S. Census Bureau.
The non-coastal counties data set was generated
using the NOAA-designated coastal counties data set
and the data set for the conterminous United States.
The population and land area data for all of the non-
coastal counties in the 48 conterminous U.S. states were
calculated by subtracting the data for the NOAA-desig-
nated coastal counties from the data for all of the 48
conterminous U.S. states. This process is demonstrated
in the text box below.
The data in each data set were then used to calculate
the total population, population growth rate, and popu-
lation density for each geographic area of interest. The
general formulas used to calculate these statistics are
presented in the text box below. The results of these
calculations and the corresponding variables for the
conterminous United States, all NOAA-designated
coastal counties (collectively), all NEP-coincident
coastal counties (collectively), the coastal counties coin-
cident to each individual NEP study area, and all non-
coastal counties (collectively) are summarized in Table
A-l. The results for the data sets of coastal counties
coincident with each individual NEP study area are
presented in the individual NEP discussions within the
main body of the NEP CCR.
2000Popu/ot/on48Stotes- 2000Popu/ot/onCoosto/Count/es = 200QPopulationNonCoastalCounties
TotalPopulationGvenArea = I PopulationEachCounty
Population Growth Rate = 2000Popu/ot»onjota/ - 196QPopulationjotai
1960Popu/at/on70to/
2000 Population Density = 2000Popu/at;onTota/
TotalLandArea
406 National Estuary Program Coastal Condition Report
-------
APPENDIX A
Table A- 1. Comparison of U.S. Trends in Total Population, Population Growth Rate, and Population Density for
the Nation, NOAA-designated Coastal Counties, NEP-coincident Coastal Counties, and Non-coastal Counties*
Total population Growth rate
Year (millions) since 1 960 (%)
National (Conterminous
I960
1970
1980
1990
2000
U.S.)
1 78.46
202.23
225.18
247.34
279.58 56.66
Population
density
(persons/mi2)
60
68
76
84
94
Land area
(mi*)
2,959,065
NOAA-designated coastal counties
I960
1970
1980
1990
2000
70.05
82.99
92.50
105.89
119.25 70.24
181
214
239
273
308
387,473
NEP-coincident coastal counties
I960
1970
1980
1990
2000
51.42
60.55
65.48
73.68
81.91 59.28
313
368
398
448
498
164,382
Non-coastal counties
I960
1970
1980
1990
2000
108.42
119.24
132.68
141.45
1 60.33 47.88
42
46
52
55
62
2,571,592
* Excludes population data and land area from Alaska, Hawaii, and Puerto Rico and other commonwealths, territories, and
protectorates.
National Estuary Program Coastal Condition Report 407
-------
-------
'fr.
-------
410 National Estuary Program Coastal Condition Report
-------
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