Assessment of Existing Information on Atlantic Coastal Fish Habitats: 

Development of a web-based spatial bibliography, query tools, and 

data summaries 

NOAA/NOS National Centers for Coastal Ocean Science 

Center for Coastal Monitoring and Assessment 

Biogeography Branch 

February 2010 

NOAA Technical Memorandum NOS NCCOS 103 

 

 

Assessment of Existing Information on Atlantic Coastal Fish Habitats: 

Development of a web-based spatial bibliography, query tools, and 

data summaries 

February 2010 

NOAA Technical Memorandum NOS NCCOS 103 

Project Team 

David Moe Nelson 

NOAA/NOS Biogeography Branch 

Brook Herlach 

NOAA/NOS Biogeography Branch 

Tom McGrath 

NOAA/NOS Biogeography Branch 

Ken Buja 

NOAA/NOS Biogeography Branch 

Adam Zitello 

NOAA/NOS Biogeography Branch 

Andrew Oldewurtel-Ilioff 

NOAA/NOS Biogeography Branch 

Biogeography Branch N/SCI-12 

Center for Coastal Monitoring and Assessment 

NOAA/NOS National Centers for Coastal Ocean Science 

1305 East-West Hwy, 9th Floor 

Silver Spring, MD 20910 

http://ccma.nos.noaa.gov/about/biogeography/welcome.html 
 

 

Recommended Citation 

Nelson, D.M., B. Herlach, T. McGrath, K. Buja, A. Zitello, and A. Oldewurtel-Ilioff. 2010. 

Assessment of Existing Information on Atlantic Coastal Fish Habitats: Development of a 

web-based spatial bibliography, query tools, and data summaries. NOAA Technical 

Memorandum NOS NCCOS 103. 58 pp. 

For more information 

David Moe Nelson 

NOAA/NOS/NCCOS Center for Coastal Monitoring and Assessment 

1305 East-West Hwy., 9th Floor, Silver Spring, MD 20910 

phone (301) 713-3028 x154 

email david.moe.nelson@noaa.gov 

web page http://ccma.nos.noaa.gov/ecosystems/estuaries/coastalfish.html . 

Emily Greene, Coordinator 

Atlantic Coastal Fish Habitat Partnership 

1444 Eye Street NW, 6th Floor, Washington, DC 20005 

phone (202) 289-6400 

email egreene@asmfc.org 

Acknowledgements 

We thank all of the individuals who provided valuable ideas, guidance, and feedback 

throughout this project, especially Emily Greene, George Schuler, and the ACFHP 

Steering Committee and Contractor Subgroup. Special thanks are due to Suzanne 

Bricker, Kimani Kimbrough, Dave Whitall, and Virginia Engle for providing assessment 

data; Phil Herndon for guidance in developing metadata; Mark Monaco and Chris 

Caldow for review of this manuscript and helpful suggestions; and Kevin McMahon for 

editorial review and assistance with final production. 

The cover photograph of Waquoit Bay, Massachusetts, is from the NOAA Photo Library, 

http://www.photolib.noaa.gov/ . 

This project and report is a product of the Atlantic Coastal Fish Habitat Partnership 

pursuant to the U.S. Fish and Wildlife Service Grant Number DC M-60-HM. 

Mention of trade names or commercial products does not constitute endorsement or recommendation for 

their use by the United States government. 
Table of Contents 

Executive Summary 

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

The Work Plan .......................................................................................................2 

Revisions to the Work Plan 

Database Development ........................................................................................4 

 Bibliographic Information 

 Assessment Information 

 Geospatial Framework 

Web-based Tool Development .............................................................................15 

Project Home Page 

Development of the SQL Server Relational Database 

Web-based ACFHP Query Tools 

 Bibliographic Query 

 Assessment Query 

 Geospatial Query 

Metadata 

Summary of Indicators, Threats, and Actions ....................................................24 

Indicators 

Threats 

 Conservation Actions 

Discussion .............................................................................................................31 

Application of results 

Strengths and challenges 

The Way Forward ..................................................................................................33 

Coordinate efforts and foster partnerships 

Update and Improve the ACFHP Assessment of Existing Information 

Literature Cited ......................................................................................................55 

Appendices and Attachments ..............................................................................58 
List of Tables 

Table 1. Field names for each entry in the ACFHP Bibliographic Table. ................5 

Table 3. MusselWatch rankings for overall metals and organics contamination status 

Table 5. National Coastal Conditions Report (NCCR) Indices for National Estuary 

Table 6. National Coastal Conditions Report (NCCR) water quality indicators for 

Table 7. National Coastal Conditions Report (NCCR) sediment quality indicators for 

Table 10. Instances of classified threats within the Assessment Table, 

Table 11. Instances of classified threats within the Assessment Table, 

Table 12. Top three classified threats by zone and region, based on a tally of instances 

Table 14. Instances of classified actions within the Assessment Table, 

Table 15. Instances of classified actions within the Assessment Table, 

Table 16. Top three classified actions by zone and region, based on a tally of instances 

Table 2. Subset of assessment information “as reported” for one waterbody .........8 

and trends in selected ACFHP waterbodies .............................................36 

Table 4. Rankings for selected eutrophication indicators in ACFHP estuaries .......37 

Program (NEP) estuaries .........................................................................40 

National Estuary Program (NEP) estuaries ..............................................40 

National Estuary Program (NEP) estuaries ..............................................41 

Table 8. Number of indicators and threats recorded for each estuary ....................42 

Table 9. Classification of threats as recorded in the Assessment Table ................44 

tallied by region .......................................................................................45 

tallied by zone .........................................................................................46 

within the Assessment table ....................................................................47 

Table 13. Classification of actions as recorded in the Assessment Table ..............48 

tallied by region .......................................................................................49 

tallied by zone .........................................................................................50 

within the Assessment Table...................................................................51 

Table 17. Top three classified threats and actions, by zone and region .................51 
List of Figures 

Figure 1. GIS framework overview .........................................................................11 

Figure 2. North Atlantic waterbodies and watersheds ............................................12 

Figure 3. Mid-Atlantic waterbodies and watersheds...............................................13 

Figure 4. South Atlantic and South Florida waterbodies and watersheds ..............14 

Figure 5. Descriptive project web page for Assessment of Existing Information on 

Atlantic Coastal Fish Habitat ...................................................................15 

Figure 6. Database design .....................................................................................16 

Figure 7. Web front page for Atlantic Coastal Fish Habitat Database ....................17 

Figure 8. Bibliographic query window .....................................................................18 

Figure 9. Bibliographic query output .......................................................................19 

Figure 10. Assessment query window ....................................................................20 

Figure 11. Assessment query output ......................................................................21 

Figure 12. Geospatial query window with GoogleMaps interface ...........................21 

Figure 13. Geospatial query output ........................................................................23 

Figure 14. Water Quality Index for sampling stations in EPA’s National Coastal 

Conditions Report III (U.S. EPA 2008, Engle pers. comm.) ....................................52 

Figure 15. Coastal Vulnerability Index for U.S. Atlantic coastline ...........................53 

Figure 16. Overall Eutrophic Condition for 64 U.S. Atlantic coastal estuaries ........54 
EXECUTIVE SUMMARY 

The primary objective of this project, “the Assessment of Existing Information on Atlantic 

Coastal Fish Habitat”, is to inform conservation planning for the Atlantic Coastal Fish 

Habitat Partnership (ACFHP). ACFHP is recognized as a Partnership by the National 

Fish Habitat Action Plan (NFHAP), whose overall mission is to protect, restore, and 

enhance the nation’s fish and aquatic communities through partnerships that foster fish 

habitat conservation. 

This project is a cooperative effort of NOAA/NOS Center for Coastal Monitoring and 

Assessment (CCMA) Biogeography Branch and ACFHP. The Assessment includes 

three components; 1. a representative bibliographic and assessment database, 2. a 

Geographical Information System (GIS) spatial framework, and 3. a summary document 

with description of methods, analyses of habitat assessment information, and 

recommendations for further work. 

The spatial bibliography was created by linking the bibliographic table developed in 

Microsoft Excel and exported to SQL Server, with the spatial framework developed in 

ArcGIS and exported to GoogleMaps. The bibliography is a comprehensive, searchable 

database of over 500 selected documents and data sources on Atlantic coastal fish 

species and habitats. Key information captured for each entry includes basic 

bibliographic data, spatial footprint (e.g. waterbody or watershed), species and habitats 

covered, and electronic availability. Information on habitat condition indicators, threats, 

and conservation recommendations are extracted from each entry and recorded in a 

separate linked table. 

The spatial framework is a functional digital map based on polygon layers of 

watersheds, estuarine and marine waterbodies derived from NOAA’s Coastal 

Assessment Framework, MMS/NOAA’s Multipurpose Marine Cadastre, and other 

sources, providing spatial reference for all of the documents cited in the bibliography. 

Together, the bibliography and assessment tables and their spatial framework provide a 

powerful tool to query and assess available information through a publicly available web 

interface. They were designed to support the development of priorities for ACFHP’s 

conservation efforts within a geographic area extending from Maine to Florida, and from 

coastal watersheds seaward to the edge of the continental shelf. The Atlantic Coastal 

Fish Habitat Partnership has made initial use of the Assessment of Existing Information. 

Though it has not yet applied the AEI in a systematic or structured manner, it expects to 

find further uses as the draft conservation strategic plan is refined, and as regional 

action plans are developed. It also provides a means to move beyond an “assessment 

of existing information” towards an “assessment of fish habitat”, and is being applied 

towards the National Fish Habitat Action Plan (NFHAP) 2010 Assessment. Beyond the 

scope of the current project, there may be application to broader initiatives such as 

Integrated Ecosystem Assessments (IEAs), Ecosystem Based Management (EBM), and 

Marine Spatial Planning (MSP). 
INTRODUCTION 

The National Fish Habitat Action Plan (NFHAP) was launched in 2006 with the mission 

to protect, restore, and enhance the nation’s fish and aquatic communities through 

partnerships that foster fish habitat conservation (AFWA 2006). On the regional scale, 

several partnerships have been launched, with participation from federal and state 

agencies, non-governmental organizations, and local citizens, including the Atlantic 

Coastal Fish Habitat Partnership (ACFHP), recognized as a Partnership by the NFHAP 

Board (NFHAP 2009). Synthesis of existing information into a comprehensive and 

useable database and synoptic document has been identified as a crucial need at both 

the national and regional levels. 

The goal of this project is to assist the Atlantic Coastal Fish Habitat Partnership 

(ACFHP) in developing a strategy to conserve, protect, restore, and enhance aquatic 

habitats along the U.S. Atlantic Coast from Maine to Florida. To meet this goal, this 

project has developed and delivered a comprehensive database of Atlantic coastal 

habitat condition indicators, threats and stressors, as well as conservation actions and 

recommendations. This database is presented as a web-based tool to inform 

conservation planning by the Partnership. This report describes the development of the 

database and web-based tool, and summarizes results derived from information 

compiled on indicators, threats, and conservation actions. This Assessment of Existing 

Information (AEI) has three components: 

Database: A comprehensive database of bibliographic and assessment information, 

developed in Microsoft Excel and exported to other applications (SQL Server). 

Bibliographic information and spatial footprint are recorded for each entry, and relevant 

assessment information is extracted and recorded in a separate linked table. The 

database is served via the web with a user query interface developed in ASP.net. 

GIS: An ArcGIS project using NOAA’s Coastal Assessment Framework and 

MMS/NOAA’s Multipurpose Marine Cadastre provided a starting point for spatial 

organization of information. The base layer of watershed and waterbody polygons and 

their centroid points was exported to GoogleMaps for web development. Indicator data 

were imported back into ArcGIS for analysis and display together with the polygon base 

layer. 

Document: A project summary report, with a narrative description of the project, 

analyses of habitat assessment information, and recommendations for further work 

The Spatial Bibliography approach provides a powerful means of organizing existing 

information by placing it within a geographic context, while tracking it back to its original 

source. Standard bibliographies may include place names as keywords, but this 

approach tags each reference to a specific place within a defined spatial framework. 

Most standard bibliographic search engines are limited to either library holdings or to 

peer-reviewed literature, but this approach allows the addition of “gray literature” or 

other lesser-known sources that would otherwise not be found by a standard literature 

search. Spatial bibliographies have proven useful in previous literature reviews of 

biological information for the Main Hawaiian Islands (Coleman et al. 2002), Southern 

1
 
California Coastal Waters (SDNP 2003), and the Northwestern Hawaiian Islands (Taylor 

and Nelson 2006, PMNM 2009). The ACFHP Assessment of Existing Information takes 

the additional step of extracting policy-relevant information on habitat condition 

indicators, threats, and conservation actions from the assembled literature, and 

compiling it within the same spatial framework. This added value provides a means to 

move beyond an “assessment of existing information” towards an “assessment of fish 

habitat”, and may be useful in broader initiatives such as Integrated Ecosystem 

Assessments (IEAs), Ecosystem Based Management (EBM), and Marine Spatial 

Planning (MSP). 

THE WORK PLAN 

The original work plan, completed in August 2008 (NOAA/CCMA 2008) outlined a series 

of objectives and tasks following an aggressive timeline. 

Objectives to achieve this project’s goal include: 

1. With guidance from ACFHP, craft a work plan with specific tasks and 

“deliverables” that can be feasibly completed by January 2009. 

2. Using the best available search methods, assemble a comprehensive 

bibliography of existing information on Atlantic Coast habitats and species. 

3. Using the best available bibliographic methods, design and create a useable 

database to capture all of the compiled information. 

4. Develop the database as a “spatial bibliography” by linking the spatial footprint of 

each entry with a suitable framework in ArcGIS. 

5. Through close coordination with ACFHP, develop a set of topics and questions 

which can be analyzed using the database. 

6. Communicate results in a timely manner to ACFHP and NFHAP through written 

reporting, oral presentation, and live demonstration. 

7. To the extent possible, collect publicly-available versions of the entries (.pdf, 

database, GIS, and metadata files) to develop an electronic library. 

8. Explore the feasibility of future work such as deploying the Assessment 

Database with web-based platforms such as ArcIMS or SQL Server. 

Six specific tasks were identified to achieve these objectives: 

Task I. Database Development

Create a comprehensive, searchable, bibliographic database of selected documents, 

data sets, and analyses – including spatial and tabular data – relevant to the ACFHP 

priority habitats. Example database components include relevant species and 

associated habitats, identified threats, recommendations, and partners. 

2
 
Task II. Cooperatively Develop Assessment Criteria 

Work with the ACFHP Assessment Subgroup and ACFHP Coordinator to develop 

and apply objective criteria for the summary and analysis of habitat status, threat 

type and severity, conservation goals, and existing strategies to be applied in 

assessment analyses. 

Task III. Develop spatial framework in a Geographical Information System 

Develop a map of priority habitats across the range of ACFHP, and a map of ACFHP 

project sites. 

Task IV. Apply spatial analysis to habitat assessment criteria 

Conduct a spatial analysis of the status of priority habitats, the distribution and 

severity of threats to priority habitats, and the spatial distribution of existing 

conservation plan (i.e., protection, restoration, and enhancement) implementation. 

Task V. Identify data gaps 

Identify, assess, and map appropriate gaps in knowledge and actions represented in 

this existing set of information that relate to types and occurrences of habitats, 

threats, goals, and strategies to support the identification of conservation priorities 

across the Atlantic coast. 

Task VI. Deliver final report and useable data base

Compile a final report with a complete bibliography and electronic examples of 

references, base maps, the Microsoft Access database, and ESRI compatible GIS 

layers based on occurrences of priority habitats, key threats, and current 

conservation strategies across the ACFHP region. In addition, document trends and 

data gaps found in the assessment of existing information. 

Revisions to the Work Plan 

Since the project began in the summer of 2008, the work plan has evolved, with some 

course corrections and valuable lessons learned along the way: 

1. An October 2008 meeting of the ACFHP Steering Committee in Rehoboth, 

Delaware, generally concurred that the database itself would have more utility as 

a web application than as a desktop module. In addition, it would be not much 

more difficult to develop as a web application in SQL Server than in Microsoft 

Access. Availability via the web would make updates and maintenance of the 

database itself easier to distribute. 

2. The GIS base layer was developed in ArcGIS, but then exported as a KML file to 

GoogleMaps for web development. GoogleMaps is freely available to any user 

via the internet, whereas GoogleEarth requires a user to install the application on 

their computer. 

3. The project team recognized that capturing assessment information must be on a 

per-waterbody basis, not on a per-document basis, so the team designed and 

3
 
built a separate table for “assessment information as reported”. In addition, we 

realized that “assessment information as reported” doesn’t readily fit into 

predetermined assessment indices of habitat condition. 

4. Although the collection of disparate raw data sets and GIS layers was beyond the 

original scope of the project, the team acquired several processed data sets on 

water quality, contaminant, and habitat condition indicators which directly 

contributed to the table of assessment information. 

5. Some tasks, especially the development of a robust bibliographic table, and 

extraction of assessment information, took longer than expected to reach a 

workable state. The original six-month timeline may have been unrealistic to 

complete all of the tasks as originally conceived. 

6. The bibliography of 500+ references is robust and representative, but by no 

means exhaustive. It is recognized that there are documents and information 

sources that were not captured, and that new information sources are being 

continually published. 

DATABASE DEVELOPMENT 

Tasks necessary to develop the database were: 

1. Identify relevant documents and data sources, and record bibliographic 

information and “spatial footprint” within a robust bibliographic table. 

2. Extract information on indicators, threats, and actions from source documents, 

and record in a separate assessment table 

3. Develop GIS base layers to serve as a geospatial framework for organizing the 

bibliographic and assessment information. 

4. Link the bibliographic, assessment, and geospatial tables via appropriate 

common fields, creating “many-to-many relationship” sub-tables as needed. 

5. Develop a web interface for querying the database and displaying results. 

6. Develop metadata to describe the database content for interested users. 

Each of these tasks is described in more detail below. 

Bibliographic Information 

The bibliographic database table was developed to a fully functional state in May 2009, 

with records completed for 527 reference documents and data sources. Useful 

reference documents were suggested by the ACFHP Steering Committee, in addition to 

other known documents and data sources with relevant information – e.g. recent 

synoptic assessment documents from National Estuary Programs, National Estuarine 

4
 
Research Reserves, State Wildlife Action Plans, stressor-specific assessments 

(eutrophication, contaminants), online data portals and IMS sites, etc. 

These sources were tagged to their “spatial footprint” by region, state, and waterbody 

(e.g. estuary and/or watershed). Relevant habitat types (e.g. wetlands, SAV) and fish 

species considered in each document were recorded, and documents which provide 

information on habitat assessment, threats and stressors, or conservation 

recommendations were flagged for extraction of pertinent information. The bibliographic 

database was developed in Microsoft Excel and exported to SQL Server, ASP.net, and 

GoogleMaps for web development (see GIS discussion below). Table 1 provides a 

graphic description of the fields within the bibliographic table, color-coded by the type of 

information captured by each field, with notes on how the bibliographic table is linked to 

the assessment and geospatial tables. 

Table 1. Field names for each entry in the ACFHP Bibliographic Table. Fields are 

color-coded by the type of information that they capture: yellow = standard bibliographic 

information, red = electronic availability, dark blue = spatial footprint, and light blue = 

species and habitat types. 

Field Name Notes 

bibID link to assessment table 

Title 

Author(s) 

Year 

Organization 

Type of Document 

Publication Info 

Web Location "click here" to access website and/or pdf 

Filename not for inclusion on web version 

pdf available? 

electronic data available? 

Spatial Data? Rank: (0-1-2; no data-metadata-map) 

ACFHP Region(s) link to geodatabase 

State(s) link to geodatabase 

Waterbody(s) link to geodatabase and assessment table 

Type of Information 

ACFHP Species link to species info 

ACFHP Habitat Types link to habitat info 

5
 
Each field in the bibliographic table is described below 

bibID – unique identification number for each record. This is also used to link to 

information sources cited in the Assessment Criteria table. 

Title – title of report or information source (text string). 

Author(s) – as a text string in standardized format. 

Year – publication year of document or data. 

Organization – primary organization of lead author or sponsor. 

Type of document – journal article, technical report, management plan, etc. 

Publication Info – journal information, publisher, etc. 

Web location – in web version, a “click here” link is provided to access pdf or 

website from original source. 

Filename – provided in Excel version of table to keep track of documents, but not 

included in web version. 

Electronic and Spatial Data – to find original data sources for further study. 

ACFHP Region(s) – North Atlantic, Mid-Atlantic, South Atlantic, and/or South 

Florida. 

State(s) – ME, NH, MA, RI, CT, NY, NJ, PA, DE, MD, DC, VA, NC, SC, GA, FL. 

Waterbodies – reported as a unique number, and linked to geospatial table. 

Type of Information – type of information included in document or data source. 

Entries in the bibliographic database were selected because they were relevant to 

Atlantic coastal fish habitat, and were classified as to the type of information that they 

contain: 

Habitat Assessment – documents which specifically assess the quality or condition 

of specific habitat parameters, with information on indicators and threats. 

Habitat Characterization – descriptive studies of specific habitat types or 

parameters, or mapping of specific areas. 

Habitat Data – online data portals and mapping services which provide necessary 

raw or processed data for further study.
 

Species Characterization – field studies or stock assessments of fish or other 

species, not specifically linked to their habitats. 

6
 
Species/Habitat Association – life history or quantitative modeling studies which 

describe the association between species and habitat parameters. 

Conservation Plan – documents which recommend actions to manage and 

conserve species and habitats. 

Science Plan – including monitoring, research plans, etc. 

Reference – useful reference information, not pertaining to a particular location. 

ACFHP Species – common name of a species is recorded if document pertains to 

them, left blank if the source is not species-specific. 

ACFHP Habitat Types – one or more habitat types as identified in previous ACFHP 

documentation, plus additional classes to capture the water column and terrestrial 

watershed components of the ACFHP study area: 

Shellfish Beds – includes oyster and mussel beds. 

Other Sessile Fauna - includes corals, deep corals, and Sabellaria beds. 

Macroalgae – includes rockweeds and kelp. 

Submerged Aquatic Vegetation – SAV, includes seagrasses. 

Tidal Vegetation – wetlands. 

Coastal Inert Substrate – generally unconsolidated sediment. 

Riverine – freshwater above head of tide. 

Estuarine Waters – water column within estuaries. 

Marine Waters – in State or Federal waters, and not within estuaries. 

Watersheds – terrestrial component draining to rivers, estuaries, or ocean. 

The 500-plus entries in the bibliography provide a robust base of information on the 

characterization and assessment of Atlantic coastal fish habitat. In addition, since we 

have focused on assessment and synthesis documents, and not peer-reviewed 

scientific journal articles, we have identified many sources of information that would 

otherwise be missed by a standard bibliographic search. However, the bibliography is 

by no means exhaustive. There is room for growth with older peer-reviewed and “gray” 

literature, and with newly published entries. 

7
 
Assessment Information 

Of all of the types of information sources, Habitat Assessments and Conservation Plans 

provided the most pertinent information for this project. Documents and sources were 

carefully reviewed, and policy-relevant habitat assessment information (indicators, 

threats, and actions) was recorded “as reported” in a separate table, linked via 

waterbody number and reference number. 

Assessment information was captured in a separate table using these fields: 

Reference Number : links to bibID in bibliographic table. 

Waterbody Number : links to same “uniqueid” in geodatabase (digital map). 

Indicator/Threat/Action : information classified as indicator, threat, or action: 

Indicator – any measurement or assessment of a relevant parameter. 

Threat - anything adversely affecting quality of fish habitat. 

Action – any conservation action recommended or already occurring. 

Parameter : What is being measured or reported (e.g. “status of eelgrass”). 

Value : What value is reported for the parameter (e.g. “increasing”). 

In addition, digital estuarine assessment data were acquired by special request or 

downloaded from several sources, including: 

EPA’s National Coastal Conditions Report III (U.S. EPA 2008) 

NOAA’s National Status and Trends Program (Kimbrough et al. 2008) 

NOAA’s Eutrophication Project (Bricker et al. 2007) 

USGS Coastal Vulnerability Index (Hammar-Klose and Thieler 2001) 

NMFS’ Impacts to Marine Fisheries Habitat report (Johnson et al. 2008) 

These proved to be especially valuable sources of assessment information because 

they report results at a local spatial scale, but use consistent methods across regions. 

To the extent feasible, these data were incorporated directly into the Assessment Table. 

Table 2 provides a visual subset of indicator, threat, and action information captured “as 

reported” from several sources for Delaware Bay. In some cases, point data were not 

aggregated to a spatial scale readily compatible with ACFHP’s polygon-based spatial 

framework. This suggests an opportunity for further work beyond the scope of this 

immediate project (see The Way Forward, p. 33). 

Approximately half (258/527) of the sources contributed information to the Assessment 

Table. This leaves many sources (269) which are included in the Bibliographic Table, 

but did not contribute information to the Assessment Table primarily because they are 

reference documents, species characterization, or raw data not readily interpretable as 

indicators, threats, and conservation recommendations. As of May 31, 2009, the 

Assessment Table consisted of 4785 rows of information, including 1642 indicators, 

1260 threats, and 1869 actions. 

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Table 2. Subset of assessment information “as reported” for one waterbody (Delaware 

Bay) from several sources. Information is linked to the bibliographic table via 

“Reference Number”, and to the base map via “Waterbody Number.” 

Waterbody Name Reference Number Waterbody

Number

Indicator/Threat/Action Parameter

Value

Delaware Bay 152 26 indicator Water Quality Index 1 = Poor

Delaware Bay 143 26 indicator Overall Eutrophic Condition moderate

Delaware Bay 143 26 indicator Chlorophyll a ‐ Overall Expression high

Delaware Bay 143 26 indicator Dissolved Oxygen ‐ Overall Expression low

Delaware Bay 143 26 indicator Secchi Depth ‐ Overall Expression high

Delaware Bay 143 26 indicator Macroalgae ‐ Overall Expression no problem

Delaware Bay 143 26 indicator Algal Blooms ‐ Overall Expression no problem

Delaware Bay 143 26 indicator Eutrophication ‐ Impact to SAV no problem

Delaware Bay 143 26 indicator Eutrophication ‐ Impact to Living Resources no impact

Delaware Bay 152 26 indicator Sediment Quality Index 4 = Good/Fair

Delaware Bay 152 26 indicator Benthic Index 1 = Poor

Delaware Bay 152 26 indicator Fish Tissue Contaminants Index 1 = Poor

Delaware Bay 152 26 indicator Dissolved Inorganic Nitrogen (DIN) Poor

Delaware Bay 152 26 indicator Dissolved Inorganic Phosphorus (DIP) Fair

Delaware Bay 152 26 indicator Chlorophyll a Fair

Delaware Bay 152 26 indicator Water Clarity Fair

Delaware Bay 152 26 indicator Dissolved Oxygen Good

Delaware Bay 152 26 indicator Sediment Toxicity Poor

Delaware Bay 152 26 indicator Sediment Contamination Good

Delaware Bay 152 26 indicator Sediment Total Organic Carbon (TOC) Good

Delaware Bay 152 26 indicator Overall Condition 1.75 = Poor/Fair

Delaware Bay 157 26 indicator Contaminants ‐ Metals Status in Oysters Medium

Delaware Bay 157 26 indicator Contaminants ‐ Metals Trends in Oysters Stable

Delaware Bay 157 26 indicator Contaminants ‐ Organics Status in Oysters Low

Delaware Bay 157 26 indicator Contaminants ‐ Organics Trends in Oysters Stable

Geospatial Framework 

The GIS base layer was developed in ArcGIS as proposed in the original work plan, and 

is subdivided into four zones: watersheds, estuaries, nearshore marine, and offshore 

marine. It is based on NOAA’s Coastal Assessment Framework (NOAA 2007), 

including estuarine waterbodies and their associated watersheds. The Coastal 

Assessment Framework is a set of digital GIS layers, with lineage back to an earlier 

data atlas known as the National Estuarine Inventory (NEI) (NOAA 1985). The NEI and 

CAF further subdivide estuarine waters into salinity zones (tidal fresh, mixing, and 

seawater), but these subdivisions were not used for the ACFHP spatial framework. The 

CAF does not extend into marine waters, so the scheme had to be modified to meet 

ACFHP’s purposes. 

Note that there are two different types of watersheds designated within the Coastal 

Assessment Framework. An Estuarine Drainage Area (EDA) is that component of an 

estuary’s entire watershed that empties directly into the estuary and is affected by tides. 

EDAs may be composed of all or part of a single or several USGS hydrologic units and 

include all or part of the USGS cataloging unit (HUC-8) containing the most upstream 

extent of tidal influence (head-of-tide). A Coastal Drainage Area (CDA) is defined as 

that component of an entire watershed that meets the following three criteria: 1) it is not 

part of any EDA; 2) it drains directly into an ocean, an estuary, or the Great Lakes; and 

3) it is composed only of the downstream-most HUC in which the head-of-tide is found. 

9
 
In other words, CDAs are land areas that do not drain to a particular estuary, and in 

some cases are represented as multiple polygons within a state. 

Additional polygons were added for both State and Federal marine waters, based on 

legally-vetted boundary layers in the Multipurpose Marine Cadastre, a joint project of the 

U.S. Minerals Management Service, NOAA’s Coastal Services Center, and other 

partners (MMS 2008, NOAA/CSC 2008). State waters extend to the 3 nautical mile 

limit, and Federal waters extend to the 200 nmi Exclusive Economic Zone (EEZ). 

Regional breaks were selected at Cape Cod, Cape Hatteras, and Cape Canaveral, 

creating four regions: North Atlantic, Mid-Atlantic, South Atlantic, and South Florida, 

consistent with generally accepted biogeographic classifications (Briggs 1974, NOAA 

2004, Cook and Auster 2007, Spalding et al. 2007). The estuarine, watershed, and 

marine polygons were merged into a single polygon layer, 195 polygons in total, 

preserving their attributes for region, state, zone (watershed, estuarine, marine), and 

waterbody name. Figure 1 illustrates the overall spatial framework, emphasizing the 

four zones: 

Coastal watersheds - include Estuarine Drainage Areas (EDAs, n=74), and Coastal 

Drainage Areas (CDAs, n=19), based on USGS HUC-8s. 

Estuarine Waterbodies - based on NOAA’s Coastal Assessment Framework 

(n=78). 

Nearshore Marine - waters within 3 nmi, using boundaries from MMS/NOAA’s 

Multipurpose Marine Cadastre (n=15). 

Offshore Marine – Federal waters of EEZ, separated into four marine 

biogeographic regions (n=4). 

Figures 2, 3, and 4 depict the estuarine, watershed, and marine polygons for the four 

regions. Along the latitudinal gradient, the study area extends over 2000 miles from 

Passamaquoddy Bay, Maine, to the Dry Tortugas, Florida. Along the inshore-offshore 

gradient, it extends from summit-to-sea, “whitewater to blue water”, from terrestrial 

watersheds seaward to the Continental Shelf. Overall, the spatial framework provides a 

means of organizing information for a vast and diverse region into a finite number of 

spatial units. 

10
 
South 

Florida 

South 

Atlantic 

Mid-Atlantic 

North 

Atlantic 

Cape Cod 

Cape Hatteras 

Cape Canaveral 

Figure 1. GIS Framework Overview. The “summit-to-sea” study area is divided into 

four zones: watersheds, estuaries, nearshore, and offshore. Coastal watersheds 

include both Estuarine Drainage Areas (EDAs) and Coastal Drainage Areas (CDAs) 

from the Coastal Assessment Framework. 

11
 
Note that the scale of the spatial framework designates an individual waterbody, rather 

than a finer-scale habitat classification, as the fundamental spatial unit for organizing 

information. This is primarily because most of the information sources report indicators, 

threats, or conservation actions on a per-waterbody basis, e.g. “status of seagrass in 

Narragansett Bay”. Beyond the scope of this current project, data layers such as 

salinity zones from the Coastal Assessment Framework and spatial habitat classification 

schemes such as CMECS (Madden et al. 2008) can be used in a finer scale regional 

habitat characterization. 

Figure 2. North Atlantic Waterbodies and Watersheds. Polygons are color-coded by 

zone: tan = watersheds (EDAs or CDAs), greenish blue = estuaries, darker blue = 

nearshore (state) marine waters, and lighter blue = offshore (federal) marine waters. 

Note that some large marine embayments such as Cape Cod Bay and Massachusetts 

Bay are considered “estuaries” for the purposes of the ACFHP spatial framework, and 

that Passamaquoddy Bay includes Cobscook Bay. 

12
 
Figure 3. Mid-Atlantic Waterbodies and Watersheds. Polygons are color-coded by 

zone: tan = watersheds (EDAs or CDAs), greenish blue = estuaries, darker blue = 

nearshore (state) marine waters, and lighter blue = offshore (federal) marine waters. 

Chesapeake Bay has been subdivided into 19 sub-estuaries, whereas most other large 

estuaries are considered single units. Gardiners Bay, NY includes Peconic Bay. 

13
 
Figure 4. South Atlantic and South Florida Waterbodies and Watersheds. Polygons are 

color-coded by zone: tan = watersheds (EDAs or CDAs), greenish blue = estuaries, 

darker blue = nearshore (state) marine waters, and lighter blue = offshore (federal) 

marine waters. Note that in South Florida, the U.S. Exclusive Economic Zone (EEZ) 

does not extend to 200 nautical miles, but to a boundary between the adjacent EEZs of 

the Bahamas and Cuba. 

14
 
WEB-BASED TOOL DEVELOPMENT 

Project Home Page 

Figure 15 illustrates a project page entitled Assessment of Existing Information on 

Atlantic Coastal Fish Habitats , launched in October 2008 on CCMA’s website at 

http://ccma.nos.noaa.gov/ecosystems/estuaries/coastalfish.html . This page provides 

links to the workplan and other products, including the bibliographic, assessment, and 

spatial queries. This page is descriptive, providing a means to publicize the project, 

serve pdf documents, such as the original work plan and final report, and direct an 

interested user to additional sources of information. 

Figure 5. Descriptive project page for Assessment of Existing Information on Atlantic 

Coastal Fish Habitats, http://ccma.nos.noaa.gov/ecosystems/estuaries/coastalfish.html . 

15
 
Development of the SQL Server Relational Database 

The component tables (Bibliographic, Assessment, and Geospatial) were designed from 

the start so that they could be linked within a relational database application such as 

Microsoft Access, SQL Server, or Oracle, using fields that were shared between the 

tables. For example, entries in both the Bibliographic and Assessment Tables are 

tagged to specific polygon(s) in the Geospatial table. All of the tables were imported 

into SQL Server so that they could be developed into a web-based query application. 

Separate index tables were created to enable the “many-to-many” relationship between 

some fields. For example, a single document may refer to many different waterbodies, 

and vice versa. The relationships between the Bibliographic, Assessment, and 

Geospatial Tables are depicted in Figure 6. 

Figure 6. Database design (v.6.4.09). The Assessment table is linked to the 

Bibliographic Table by the bibID field. The two are also linked by a many-to-many 

relationship of Waterbody Number (uniqueid). The AssessmentTable is also linked to 

the Geospatial Table by the uniqueid (Waterbody Number) field. 

16
 
 

Web-based ACFHP Query Tools 

The web based ACFHP Query Tool includes a front page and three query modules, 

developed as subroutines within NOAA’s Benthic Habitat Viewer web tool 

(NOAA/CCMA 2007). To enable the development as a web application, the ArcGIS 

base layer was exported as a KML file to import into GoogleMaps However, we 

encountered difficulty displaying the polygon layer as-is, so we simplified it as a point 

layer by deriving a centroid lat/lon from each polygon. Using the centroid point layer, 

we developed a query module that links GoogleMaps with an ASP.Net query interface. 

Additional menu-driven query modules enable access to either the Bibliographic or 

Assessment data. 

Front Page. The front page (http://www8.nos.noaa.gov/bhv/spatbibindex.html), as 

illustrated in Figure 7, titled “Atlantic Coastal Fish Habitat Database: A Tool for 

Geospatial Assessment of Existing Information”, provides a brief explanation of content, 

and links for the three query modules under the heading “ACFHP Data Links”: 

Bibliographic Query, Assessment Query, and Geospatial Query. This page also 

provides links to related sources of information: 

1. Assessment of Existing Information on Atlantic Coastal Fish Habitats (hosted by 

CCMA) 

2. National Fish Habitat Action Plan (NFHAP) 

3. Atlantic Coastal Fish Habitat Partnership (ACFHP) 

Figure 7. Web front page for Atlantic Coastal Fish Habitat Database (v.6.17.09). 

17
 
Bibliographic Query. Clicking the link titled “Bibliographic Query” brings up a SQL 

Server query interface within a new window, as depicted in Figure 8: 

http://www8.nos.noaa.gov/bhv/spatbibQuery.aspx 

Figure 8. Bibliographic query window (v.6.17.09). 

The query is based on fields in the Bibliographic Table, and the user is prompted to 

select based on these sequential criteria within pull-down menus: 

Habitat Type: Based on a defined list of habitat types, plus the option for “All 

Types”. 

Region: Based on the four ACFHP regions, plus the option for “All Regions”. 

State: Includes Atlantic Coastal States, plus DC, NB (New Brunswick), and US 

(Federal Waters). 

Zone: Estuarine, EDA, CDA, Marine–State, and Marine-Federal. 

Waterbody: Name of waterbody (estuarine or marine) or watershed (EDA or CDA). 

Information Type: Based on a defined list of information types. 

The user also has a radio button option of viewing the results as “Grid Output” (default), 

or “Excel Download”. 

The “Query” button launches the query, and results are displayed as shown in Figure 9, 

with these fields pulled from the Bibliographic Table: 

Title 

Year 

Authors 

Organization 

Publication Info 

Habitat Type 

Information Type 

Web Location (if an item is available, a “Click Here” link is provided) 

18
 
Figure 9. Bibliographic query output (v.6.17.09). 

Note that because any given document may refer to multiple habitat types, they may 

appear in the output more than once. Additionally, a habitat type may be covered by 

the same document as a given waterbody, but may not occur in that waterbody. 

Assessment Query. Clicking the link titled “Assessment Query” brings up the SQL 

Server query interface within a new window, as illustrated in Figure 10: 

http://www8.nos.noaa.gov/bhv/spatbibAssessment.aspx . 

The query is based on fields in the Assessment Table, and the user is prompted to 

select based on these sequential criteria within pull-down menus: 

Habitat Type 

Region 

Waterbody 

The user also must select the type of assessment information with radio buttons: 

Indicator, Threat, Action, or All. 

There is also a radio button option of viewing the results as a simple GridView (default), 

or Excel Export. 

19
 
Figure 10. Assessment query window (v.6.17.09). 

The “Query” button launches the query, and results are displayed as shown below, with 

these fields pulled from the Assessment Table, Bibliographic Table, or Geographic 

Table: 

Title
 

Habitat Type
 

Waterbody Name 

Parameter 

Value 

Parameter Type 

20
 
Figure 11. Assessment query output (v.6.17.09). 

Geospatial Query. Clicking the third “ACFHP Data Link” titled “Geospatial Query” 

brings up a GoogleMaps interface within the same window, as depicted in Figure 12: 

http://www8.nos.noaa.gov/bhv/spatbibAssessment.aspx 

Figure 12. Geospatial query window with GoogleMaps interface (v6.17.09) 

21
 
The user instantly sees a map query page of the ACFHP study area, with overlapping 

ovals representing all of the waterbodies and watersheds within the ACFHP spatial 

framework. Google Maps cannot readily display the actual polygons of the spatial 

framework (i.e. waterbody and watershed boundaries), but it can create “apparent” 

polygons around the centroids of each polygon. The map interface also features 

familiar zoom and pan tools, and the option of viewing as map/satellite/hybrid/terrain 

using standard GoogleMaps base imagery layers. 

This page can be used to launch spatial queries of either the assessment or 

bibliographic data tables, similar to the corresponding queries described above. Spatial 

selection can be accomplished by: 

1. Regions can be toggled on and off using click boxes. 

2. Single waterbodies can be selected by holding CTRL and left-click on a point, 

then selecting either Assessment or Bibliographic Data as Query Type (see 

instructions on base map). 

3. Draw a rectangle and capture a subset of the waterbodies (polygon centroids), 

see instructions on base map. 

The “Query Type” radio buttons are set to “Assessment Data” or “Bibliographic Data”, 

one or the other but not both. If “Assessment Data” is selected, these fields instantly 

appear as grid output with shaded blue background: 

Reference Title 

Waterbody 

Parameter 

Value 

Parameter Type (e.g. indicator, threat, or action) 

If “Bibliographic Data” is selected, these fields instantly appear as grid output with 

shaded blue background: 

Title 

Year 

Authors 

Organization 

Publication Info 

Web Location 

An example of the grid output is shown in Figure 13, for a query of Bibliographic Data 

for South Atlantic Federal Waters. 

22
 
Figure 13. Geospatial query output (v.6.17.09) 

Metadata 

A single metadata record was developed for the public data offerings generated by the 

project, using MERMAid (Metadata Enterprise Resource Management Aid), a tool 

developed by NOAA’s National Coastal Data Development Center (NOAA/NCDDC 

2006 ). Well-written metadata can help an interested user understand the lineage and 

processing steps that went into developing a data set, and to explore and interpret the 

entities and attributes within that data set. Some software applications (e.g. ArcGIS) 

can “ingest” properly formatted FGDC-compliant metadata records, further enhancing 

the utility of the original data set. In the ACFHP metadata record, each of the tables 

within the ACFHP database (Bibliographic, Assessment, and Geospatial) are 

considered as individual entities, and each field within those tables are considered as 

attributes. After careful review, the metadata record was published to NOS’ Data 

Explorer (NOAA/NOS 2009), where it is publicly available and searchable. A link to the 

metadata record is also provided on the ACFHP query tools front page. 

23
 
SUMMARY OF INDICATORS, THREATS, AND ACTIONS 

Tables 3 through 17, and Figures 14 through 16, illustrate how information on 

indicators, threats, and actions can be integrated, summarized, and put to use to assist 

regional conservation planning. In other words, use the database to move beyond an 

“assessment of existing information on fish habitat” towards an “assessment of fish 

habitat based on existing information”. 

Indicators 

Habitat quality indicators typically focus on a single measurable parameter (e.g. 

Dissolved Inorganic Nitrogen), or in some cases report an index which has been derived 

from a set of parameters (e.g. Overall Eutrophic Condition). Although some source 

documents may ascribe a single “health score” to a given waterbody (e.g. annual State 

of the Bay reports), it is beyond the scope of this project to derive a single habitat score 

for each waterbody. On the other hand, when key indicators are developed using 

consistent methods across a set of waterbodies, they can be used for comparative 

analyses and displayed graphically. Of all the indicator data compiled within the 

Assessment Table, the most useful sources by far were those that report results at a 

local scale (e.g. individual waterbodies) within a broad spatial scope (regional or 

National). When comparing and interpreting indicator data, the user must be careful to 

consider the methods and caveats as described in the original source documents. In 

addition, the indicators themselves do not describe how fish populations actually 

respond to the underlying conditions. 

Table 3 depicts rankings for overall metals and organics contamination status in 49 

selected ACFHP waterbodies, as reported by NOAA’s National Status and Trends 

Program (Kimbrough et al. 2008). For waterbodies with multiple MusselWatch sites, the 

“worst” rankings (not averages) are reported. Waterbodies with status of medium or 

high, or trends increasing, are relatively few, but include Boston Harbor, Buzzards Bay, 

Hudson River/Raritan Bay, Delaware Bay, Patapsco/Gunpowder River (includes 

Baltimore Harbor), James River (includes Elizabeth River and Norfolk Harbor), and St. 

Johns River. Another striking result here is that in the majority of estuarine waterbodies, 

contaminant indices are low and either stable or decreasing. However, the overall 

sampling design is intended to track status and trends at representative sites, not target 

problematic “hot spots”. In addition, it is possible for individual contaminants (e.g. 

copper) to be relatively high, while the “metals index” remains relatively low. The 

“organics index” does not include contaminants of emerging concern such as 

polybrominated diphenyl ethers (PBDEs) (Kimbrough et al. 2009) or human 

pharmaceuticals (Pait et al. 2006). If a user wants to find out more about contaminants, 

the bibliographic database can direct them to the original source documents and data. 

Table 4 summarizes results from Effects of Nutrient Enrichment in the Nation’s 

Estuaries: A Decade of Change, better known as “The Eutro Report” (Bricker et al. 

2007), a cooperative study by NOAA and many partners. These indicators were 

compiled using a combination of analytical and consensus-based methods, described in 

the original report. The first column of the table summarizes the “Overall Eutrophic 

Condition”, ranked from low to high, or unknown. The list of 64 estuarine waterbodies 

24
 
corresponds closely to those used in the ACFHP spatial framework (both studies 

employ the Coastal Assessment Framework), and the color-coded rankings enable a 

quick graphic interpretation of the table. The table also includes fields which indicate 

the effects of eutrophication, such as “Impact to Living Resources”, and “Impact to 

SAV”. Table 4 is supplemented with information from a previous version of the 

eutrophication report (Bricker et al. 1999) as needed. 

Tables 5, 6, and 7 summarize information from U.S. EPA’s National Coastal Conditions 

Report series – in this case the report that focuses on eighteen National Estuary 

Program (NEP) estuaries (U.S. EPA 2006). The first column of Table 5 displays an 

“Overall Condition” score from good to poor for each estuary, along with several other 

Index scores (Water Quality, Sediment Quality, Benthic, and Fish Contaminants). Note 

that Chesapeake Bay is not included in this summary, although the National Estuary 

Program was preceded and to some extent modeled after the Chesapeake Bay 

Program. Tables 6 and 7 report individual water quality and sediment quality indicator 

rankings that are used to derive the index scores reported in Table 5. 

Table 8 addresses the question of well-studied versus poorly-studied waterbodies by 

counting the number of rows of indicator information recorded for each estuary. It must 

be recognized, however, that the Assessment Table is neither an exhaustive nor even a 

random sample of all of the indicator data that may be available, and it may contain 

some regional bias. In spite of that caveat, several trends and apparent “data gaps” can 

be qualitatively inferred: 

	 More information is available for larger estuaries (Delaware Bay, Chesapeake 

Bay, Long Island Sound) than for smaller ones (Hampton Harbor, Saco Bay, 

Waquoit Bay). 

	 More information is available for estuaries in heavily populated regions (Hudson 

River/ Raritan Bay, Delaware Bay) than for less populated regions (downeast 

Maine, portions of the Georgia coast). 

	 More information is available for National Estuary Program estuaries, largely 

because of EPA’s consistent reporting of indicator data for these waterbodies. 

	 More information is available for the larger and heavily populated Chesapeake 

sub-estuaries (Potomac and James Rivers), but much less is reported separately 

for the smaller Chesapeake sub-estuaries (e.g. Honga, Lynnhaven, 

Elk/Sassafras Rivers, tidal Susquehanna River, Eastern Bay, Ingram/Fleets 

Bays, Piankatank River/Mobjack Bay). 

	 In addition to the smaller Chesapeake sub-estuaries, little indicator information 

was found for Nassau Sound along the northern Florida coast, and Wassaw 

Sound on the Georgia coast. 

	 Although it is not evident from Table 8, there are some localized areas that are 

data-rich but are not reported separately, such as the Elizabeth River in Norfolk 

VA and the Anacostia River in Washington DC. These are relatively small subestuaries of the James and Potomac River estuaries, respectively, with largely 

urban watersheds. 

Figures 14, 15, and 16 illustrate how indicator information can be graphically displayed 

on maps, using a consistent GIS spatial template. In Figure 14, the Water Quality Index 

for sampling stations in EPA’s National Coastal Condition Report III (U.S. EPA 2008, 

25
 
Engle pers. comm., Whitall pers. comm..) is plotted as point data over the ACFHP 

spatial framework. Other parameters (indices and scores) available from this same 

dataset include: 

Sediment Quality Index

Sediment Total Organic Carbon Score 

Sediment Toxicity Score 

Sediment Contaminant Score 

Benthic Index Score 

Water Quality Index

Bottom Dissolved Oxygen Score 

Surface Chlorophyll a Score 

Surface Dissolved Inorganic Nitrogen Score 

Surface Dissolved Inorganic Phosphorus Score 

Water Clarity Score 

Tissue Contaminant Score 

Note that parameters identified as “scores” contribute to the calculation of the summary 

Sediment and Water Quality Indices. 

In Figure 15, the Coastal Vulnerability Index (CVI) for U.S. Atlantic coastline (HammarKlose and Thieler 2001) is plotted as short line segment data. This index represents the 

predicted vulnerability of a given coastline segment to the effects of sea level rise. The 

CVI is derived from a set of parameters, each of which can be mapped separately from 

the same data set, including erosion/accretion rates, tidal currents and wave climate, 

relative sea level rise, shoreline geomorphology and slope. Although these parameters 

may not be direct indicators of “fish habitat quality” per se, they may be very useful for 

conservation planning purposes. They are representative of the high-quality publicly 

available GIS data identified as “habitat data” in the spatial bibliography, and can be 

readily downloaded and used for various purposes. 

In Figure 16, Overall Eutrophic Condition for 64 U.S. Atlantic coastal estuaries (Bricker 

et al. 2007) is plotted as points representing the centroids of individual estuaries. 

Several of the parameters reported separately (Chlorophyll a, Algal Blooms, Dissolved 

Oxygen, Impact to SAV, and Macroalgae) contribute to the development of the Overall 

Eutrophic Condition (OEC) index value. Parameters from this data set that could be 

considered and mapped include 

Overall Eutrophic Condition

Chlorophyll a - Overall Expression 

Harmful Algal Blooms - Overall Expression 

Dissolved Oxygen - Overall Expression 

Eutrophication - Impact to SAV 

Macroalgae - Overall Expression 

Eutrophication - Impact to Living Resources 

Secchi Depth - Overall Expression 

Future Outlook 

Impact to Living Resources shows whether living resources (e.g. fish, shellfish, wildlife) 

are being impaired by eutrophication, but this indicator does not contribute to the OEC. 

Secchi Depth is recorded since it is a widely accepted indicator, but it does not 

contribute to the OEC since it can be affected by suspended sediment (turbidity) as well 

26
 
as nutrient enrichment and algal growth. The Harmful Algal Blooms indicator primarily 

refers to nuisance and toxic blooms (e.g. red tide, brown tide), and is therefore not 

redundant with the Chlorophyll a indicator. Some of the indicators are reported 

separately for salinity zones within individual estuaries, but this is not reflected in Table 

5 and Figure 16 of this report. Note that the Overall Eutrophic Condition for individual 

estuaries mapped in Figure 16 generally corresponds with the EPA Water Quality Index 

reported for sampling points in Figure 14. 

Threats 

Threats and Conservation Actions are more difficult to summarize and display than 

Indicator data, because they are typically reported as text information, and often in 

subjective language. They are typically associated with an individual waterbody, but are 

rarely reported consistently across a range of waterbodies. In spite of that, some 

qualitative analyses of the threats “as reported” are feasible, revealing some interesting 

results. A list of fifteen draft threat categories was developed during an ACFHP 

strategic planning session in June 2009. This process was consensus-based, and was 

independent of our compilation of threats within the Assessment Table. We read 

through the list of 1260 threats identified in the Assessment table, and quickly classified 

each with respect to the 15 ACFHP threat categories, then counted the number of 

instances of threats falling into each category, summing across regions and 

waterbodies. Table 9 presents the results of these classifications and counts of the 

threats, revealing some interesting results. 

 Water Quality and Dams and Passage are the top two categories, followed by 

Climate Change, Dredging Issues, and Contaminants. 

 Most of the threats (871 of 1260) fit clearly within the fifteen categories, but 

others are more difficult to classify, and were retained within “other” categories. 

 There are few interesting "outliers" that don’t easily fit into the classification 

scheme (e.g. light and noise pollution, unexploded ordnance). 

	 In some cases, multiple threats were reported and recorded together, and 

classified as Multiple Threats Reported. Many of these included altered 

hydrology and water quality. We did not attempt to separate them further, but 

this suggests an additional task for the next iteration of the Assessment Table 

(see The Way Forward, p. 33). 

	 Many of the threats classified as “other” belong within a larger "land use" 

classification, not just urban (i.e. impervious surfaces) but also agricultural and 

forestry practices. 

	 Regulatory Systems were identified as a threat category by the ACFHP strategic 

planning session, but no instances of threats in the assessment table were 

placed into this category. Regulations are generally considered as “actions” 

rather than “threats” within the Assessment table. 

Other classification schemes, such as those developed by IUCN (2006a), ASMFC 

(Greene et al. 2009), and The Nature Conservancy (Odell 2008), could be applied to the 

compiled list, revealing potentially different results. Some classification schemes focus 

on the sources of threats, whereas others focus on the effects, and all provide varying 

levels of detail. This demonstrates how even subjective text information can be used for 

27
 
qualitative analyses and reveal useful results if the information base is sufficiently 

robust. 

Since each individual line of information in the assessment table is tied to a particular 

waterbody, classified threats can be tallied and qualitatively compared among zones 

(watersheds, estuaries, and marine), and regions (North Atlantic, Mid-Atlantic, South 

Atlantic and South Florida). Tables 10, 11, and 12 illustrate how the classified threats 

can be broken out by zone and/or region. Because of a sparser literature base for the 

South Florida region and the Marine-Federal zone, tallies for South Florida were 

combined with the South Atlantic region, and tallies for Marine-Federal waters were 

combined with Marine-State waters for a single “Marine” zone. Several caveats must 

be kept in mind to interpret these comparisons: 

	 These tallies represent how frequently a given threat is cited in a subset of the 

existing conservation plans and other literature for a given location. It cannot be 

inferred that they represent the actual importance of a given threat. 

	 These comparisons are based on the consensus-based draft ACFHP 

classification of threats to fish habitats developed in June 2009. Applying a 

different classification scheme would likely reveal different results. 

	 For some individual waterbodies, most of the threat information comes from one 

or two documents. Comparing information on a local basis may reveal the 

biases of individual documents, rather than reveal any real differences between 

the locations. 

With those caveats in mind, several interesting results emerge and are depicted in 

Tables 10, 11, and 12. 

 Water Quality is the most-cited classified threat in all regions (North Atlantic, MidAtlantic, South Atlantic and South Florida) (Table 10). 

 Dams and Passage and Contaminants follow Water Quality as the most-cited 

classified threats in the North Atlantic region (Table 10). 

 Climate Change, Contaminants, and Invasive Species follow Water Quality as 

the most-cited classified threats in the Mid-Atlantic region (Table 10). 

	 Fishing Gear Impacts and Dams and Passage follow Water Quality as the mostcited classified threats in the South Atlantic and South Florida regions combined 

(Table 10). 

	 Dams and Passage are the top cited threat in the Watersheds zone (including 

freshwater above head-of-tide), followed by Water Quality and Impervious 

Surfaces (Table 11). 

 Water Quality is the top cited threat in the Estuaries zone, followed by 

Contaminants and Dredging Issues (Table 11). 

 Climate Change is the top cited threat in the Marine zone, followed by Fishing 

Gear Impacts and Dredging Issues (Table 11). 

	 When tallied within a region x zone matrix (Table 12), other classified threats that 

emerge in addition to the ones cited above include Water Withdrawals in North 

Atlantic watersheds, Invasive Species in Mid-Atlantic estuaries, and Boating 

Issues in South Atlantic and South Florida marine waters. 

28
 
Conservation Actions 

Conservation actions and recommendations as reported in the existing literature, are 

recorded in the Assessment Table as 1860 instances of text information in a format 

similar to that for threats. In Table 13, a classification scheme is applied based on 

themes that emerged from visual inspection of the information. It could be considered 

an “emergent scheme”, admittedly subject to the biases (e.g. “splitter” vs. “lumper”) of 

the viewer, and not based on any group consensus. In spite of that, several trends are 

evident: 

	 Most conservation actions either refer to a specific threat (e.g. “stop pollution”), or 

to a specific habitat type (e.g. “restore wetlands”), or involve the designation of 

an area for a specific purpose, such as Marine Protected Areas (MPA) or 

Essential Fish Habitat (EFH). 

	 The most often cited types of recommended conservation actions involve Area 

Designation, Water Quality, Wetlands, and Fish Passage. Again, these are 

categories that emerged based on actions and habitat types as reported. “Area 

Designation” includes Marine Protected Areas (MPAs), Essential Fish Habitat 

(EFH), Habitat Areas of Particular Concern (HAPC), National Wildlife Refuges 

(NWR), etc. 

	 Water quality and fish passage issues were prominent as both threats and 

conservation recommendations, and to a lesser extent, fishing gear impacts and 

fishery regulation. 

	 Except for the recent Presidential Executive Order on restoration of the 

Chesapeake (The White House 2009), few actions specifically address Climate 

Change, even though it was widely cited as a threat, especially in marine waters. 

	 Some conservation recommendations were stated in such general terms that 

they couldn't be tagged to a specific threat, habitat type, or species of interest 

(e.g. “conserve fish habitat”), and were classified as “General Habitat 

Conservation”. 

 Two or more distinct actions were sometimes reported together, and were 

classified as “Multiple Recommendations”. 

	 There were several interesting and specific "outlier" recommendations which 

didn’t readily fit into the emergent classification scheme. One in particular 

recommended “experimental restoration in shallow, low-salinity areas to reach 

recovery threshold”, with the premise that rapid and demonstrable restoration of 

an entire estuarine waterbody may not be feasible (Kemp and Goldman 2008). 

In Tables 14, 15, and 16, the classified and tallied conservation actions are split out by 

zone and/or region. As with the analysis of threats, tallies for South Florida were 

combined with the South Atlantic region, and tallies for Marine-Federal waters were 

combined with Marine-State waters for a single Marine zone. Similar caveats apply as 

well: 

	 Conservation recommendations are often reported in the existing literature in 

language more subjective than that for threats or indicators, and their 

classification is likely to be more subjective also. 

	 These tallies represent how frequently a given conservation recommendation is 

identified in a subset of the existing conservation plans and other literature for a 

29
 
given location. It cannot be inferred that they represent the actual priority or 

importance of a given action. 

	 These comparisons are based on an emergent scheme, and applying a 

predetermined or consensus-based classification scheme (e.g. IUCN 2006b) 

would likely reveal different results. 

	 For some individual waterbodies, the conservation actions may come from one or 

two documents. Comparing information on a local basis may merely reveal the 

biases of individual documents, rather than reveal any real differences between 

the locations. 

In spite of these caveats, several interesting results emerge and are evident in Tables 

14, 15, and 16: 

 Area Designation emerged as the most-cited action in all regions (North Atlantic, 

Mid-Atlantic, South Atlantic and South Florida), except that it is tied with Water 

Quality – Protect and Restore in the Mid-Atlantic region (Table 14). 

	 Improve Fish Passage is the top cited action in the Watersheds zone (including 

freshwater above head-of-tide), followed by Riparian Buffers – Conserve and 

Restore and Area Designation (Table 15). 

	 Area Designation is the top cited action in the Estuaries zone, followed by 

Wetlands – Protect and Restore, and Water Quality – Protect and Restore 

(Table 15). 

	 Area Designation is the top cited action in the Marine zone, followed by 

Monitoring and Assessment and Fishery Regulation (Table 15). 

	 The widespread prominence of Area Designation as a conservation 

recommendation illustrates the emergence of Marine Spatial Planning in 

resource management. 

	 When tallied within a region x zone matrix (Table 12), other classified actions that 

emerge in addition to the ones cited above include Watersheds – Conserve and 

Restore in North Atlantic watersheds, Conserve Species in South Atlantic and 

South Florida watersheds (e.g. actions taken to benefit individual species of 

concern), Control Invasive Species and SAV – Protect and Restore in MidAtlantic estuaries. 

Table 17 combines the content of Tables 12 and 16, so that the top three classified 

threats and actions can be viewed together within a region x zone matrix. Although 

threats and actions are treated as independent rows of information within the database, 

this view enables a few observations: 

 In many cases, the top threats and actions for a given region and zone are 

related, e.g. Dams and Passage and Improve Fish Passage in North Atlantic 

Watersheds, Water Quality and Water Quality – Protect and Restore in MidAtlantic Estuaries, Fishing Gear Impacts and Fishery Regulation in South 

Atlantic/South Florida Marine Waters. 

	 In some cases, threats and actions for a given region and zone are not directly 

related. Climate Change scores as one of the top three threats in the Marine 

Zone of all regions, but there are few conservation actions which specifically 

address it. Area Designation is a widely cited conservation action, but it is often 

intended to address multiple threats. 

30
 
DISCUSSION 

Application of the results 

The Atlantic Coastal Fish Habitat Partnership has made initial use of the Assessment of 

Existing Information (AEI) as described below. The Partnership has not yet applied the 

AEI in a systematic or structured manner, but expects to find further uses as the draft 

conservation strategic plan is refined, and as regional action plans are developed 

(Greene pers. comm.). 

The Partnership developed a version of Table 9 (Classification of Threats, p. 44), 

modified to combine threats into categories defined in its draft conservation strategic 

plan where possible. Threats that were not combined into categories defined in the 

draft conservation plan, were still included in the table, in some cases in a modified 

format. The modified table was included in the Partnership’s draft conservation 

strategic plan, along with language on how the AEI results and modified table were 

used in relation to the threat categories discussed in the draft plan. This information will 

need to be reviewed and approved in order to be included in ACFHP’s final strategic 

conservation plan. It is important to note that the AEI results and the modified threat 

table haven’t been thoroughly compared to the threat categories discussed in the draft 

plan. 

To help inform the strategic planning process, indicator data from the EPA's National 

Coastal Conditions Report (provided in the AEI) were displayed on maps, in addition to 

other data sets not included in the AEI. Some ACFHP steering committee members 

considered the information displayed on these maps during deliberations regarding the 

selection of proposed areas of opportunity, noted in the Partnership’s draft conservation 

strategic plan. The Partnership is still discussing questions of using geographic areas 

as a means of setting priorities. 

The approach and results are also being adapted and used for other purposes. A 

similar spatial framework and National sources of indicator data are being developed to 

complete the coastal component of the National Fish Habitat Action Plan assessment 

targeted for completion in 2010 (NFHAP 2008). Beyond this, the approach may prove 

useful in broader initiatives, such as Integrated Ecosystem Assessments (IEAs) (Levin 

et al. 2008), Ecosystem Based Management (EBM) (Burgess et al. 2005), and Marine 

Spatial Planning (MSP) (NOAA/EGT 2009, CEQ 2009). 

Strengths and challenges 

The approach used here, developing a bibliography and fitting assessment information 

into a defined spatial framework, has some inherent strengths and presents some 

unique challenges: 

• The assessment provides no information above and beyond what is already available, 

since it is based on existing sources. However, while the content by itself is not new, 

the way that it is organized reveals patterns that could not be discerned from the 

31
 
original sources alone. Taking local information and zooming out to a regional scale 

can reveal “emergent properties” which would otherwise not be evident. 

• This assessment does not attempt to derive a single overall condition score for each 

waterbody, as do some other assessment programs. The available information for 

any given waterbody comes from a diverse set of sources, and the amount of 

information available varies greatly between waterbodies. Although a scheme which 

reports single scores can be useful for comparing locations, it can also serve to 

conceal rather than reveal the underlying information that contributes to the scores. 

• Much of the information captured is text, not numeric data. However, the analysis of 

threats and conservation actions demonstrates how even subjective information can 

be categorized, quantified, analyzed, and applied. 

• All entries in the bibliographic and assessment tables are considered equally – no one 

source of data on indicators, threats, and conservation actions are given priority. As a 

result, the tallies of threats and conservation actions in Tables 9 through 17 only 

summarize how often they appear in the literature base – they do not infer the actual 

importance of a given threat or conservation action. 

• The spatial framework cannot be instantly adjusted from a local to a National scale, 

since it is based on a static layer of polygons at a defined scale. Some data sets are 

inherently more “scaleable” than others, for example remotely sensed oceanographic 

data can be aggregated to multiple scales as needed, while other assessment 

information is only applicable to a single site. 

• To some extent, the approach duplicates existing bibliographic databases such as 

NOAA’s library holdings and Aquatic Sciences and Fisheries Abstracts. However, the 

ACFHP database provides three important advantages: 1. Includes “gray literature” 

and conservation plans that are not likely to be captured by searches of other 

databases, 2. Extracts and records the content of documents cited on habitat 

indicators, threats, and conservation actions, and 3. Links this information to a 

particular place via a defined spatial framework. 

• The system is potentially “high-maintenance”. New relevant information is being 

continually published, and must be reviewed and entered into the system if it is to be 

useful as a source of up-to-date assessment information. This is a legitimate issue, 

since many of the assessment reports cited are revised and reissued annually. 

• The information on indicators, threats, and actions is not an exhaustive sample, nor 

even a random sample, of what is potentially available from the existing literature. It is 

recognized that there may be inherent biases in the information captured, as artifacts 

of the sources that are selected. 

• The literature base is not comprehensive, and peer-reviewed scientific articles are 

underrepresented. The literature search deliberately sought synoptic regional and 

national-scale sources, whereas many peer-reviewed research articles are sitespecific. Since the spatial bibliography is not comprehensive, it is best used in 

32
 
combination with other search engines and databases of library holdings and scientific 

publications such as Aquatic Sciences and Fisheries Abstracts. 

• The spatial bibliography can serve purposes not originally intended, for example as a 

literature review for planning scientific research in a particular location. Spatial 

bibliographies have been developed and applied in other regions for this purpose 

(SDNP 2003, Taylor and Nelson 2006, PMNM 2009). 

• The bibliography and assessment database reveals data gaps. Some regions are 

well-studied, and others are less so. Synoptic national or regional assessments have 

been completed for some parameters (water and sediment quality), but not for other 

dimensions of fish habitat such as the status of SAV, oyster reef and mussel bed 

habitats. 

• This approach represents a cost-effective and timely means of compiling a large 

amount of information. No original field research is required, and there is very little 

travel expense. Most of the work could be accomplished by a small team in one place 

with access to a research library, computer resources, and web development 

capabilities. 

• The online web query tools do not provide the original source documents as pdfs, but 

point the user towards them with a “click here” link where possible. Web links to 

sources cited can become broken, generating “file not found” errors when running the 

web query tools. Fixing these broken links is part of the necessary system 

maintenance, along with updating bibliographic and assessment information. 

THE WAY FORWARD 

Based on our experience in developing the ACFHP database and developing the web tools, 

we offer these concise recommendations. 

Coordinate efforts and foster partnerships 

• Promote the database and web tools within the larger conservation community to maximize 

their use and to advance the goals of ACFHP. 

• Gather feedback from users of the ACFHP database and web tools on the strengths and 

limitations, and develop a plan to periodically improve the content and function. 

• Keep track of related efforts such as NFHAP’s decision support tools, NOAA’s regional 

ecosystem spatial databases, data portals, IMS sites, IOOS, and EBM tools so as to 

complement and not duplicate their capabilities. 

• Engage with groups such as NFHAP and other regional Fish Habitat Partnerships, Restore 

America’s Estuaries (RAE), NOAA’s Community-based Restoration Program, 

NatureServe’s Ecosystem Based Management (EBM) Tools Network, American Fisheries 

Society, and Society for Conservation GIS to extend results and survey user needs, giveand-take feedback, provide value-added, and avoid duplication of efforts. 

33
 
• Extend these results to assist the coastal component of the NFHAP Assessment 

targeted for completion in 2010, using a similar spatial framework and National-scale 

synoptic sources of indicator data. 

• Adapt this approach to assist broader initiatives such as Ecosystem Based 

Management (EBM), Integrated Ecosystem Assessments (IEAs), and Marine Spatial 

Planning (MSP). 

Update and Improve the ACFHP Assessment of Existing Information 

• Expand the bibliographic table with sources missed in the current version, including 

entries from existing bibliographies, and updated systematic searches of peerreviewed literature and library holdings. 

• Periodically update both the Bibliographic and Assessment tables with new and 

corrected information. Note that some indicator reports (e.g. “State of the Bay”) are 

issued annually, and web links to documents must be checked and fixed as needed. 

• Revisit and revise specific anomalies in the Bibliographic and Assessment tables, such 

as cases where multiple habitat threats or conservation recommendations are 

reported together, referring back to the original source documents. 

• Explore the feasibility of migrating the relational database, its functionality and 

underlying data tables, into a new interactive ACFHP website. 

• Re-classify threats and actions to meet the needs of ACFHP’s planning process. 

Classification could be based on schemes developed by IUCN (2006a, 2006b), a 

modified scheme for marine and estuarine waters (Odell 2008), and/or ASMFC’s 

recent Diadromous species review (Greene et al. 2009). Applying consistent schema 

could help integrate and “connect the dots” between the sometimes disparate 

indicator, threat, and conservation action information. 

• Develop new ways to report and display information from the database, such as onepage summaries of indicator, threat, and conservation action information for each 

waterbody. Such a summary would likely include baseline characterization 

information from sources such as the National Estuarine Inventory Atlas and Coastal 

Assessment Framework (NOAA 1985, 1997), consistently reported core indicator 

information (U.S. EPA 2008, Bricker et al. 2007, Kimbrough et al. 2008), and brief 

summaries of threats and conservation recommendations. 

• Explore the use of data portals and internet map services to assist conservation 

planning. Many of these are identified in the bibliography, and they may provide a 

low-cost and user-friendly way to meet mapping and data needs. 

• Explore the use of desktop GIS to meet the mapping and analysis needs of Fish 

Habitat Partnerships. Data can be downloaded from sources identified, and imported 

into ArcGIS, ArcReader, or other low-cost GIS applications. 

34
 
• Explore the feasibility of applying further analysis to indicator data sets such as EPA 

Coastal Conditions, NOAA’s MusselWatch and Estuarine Eutrophication, etc. 

Intersect point layer data with the ACFHP polygon layer to “bin” the point data into the 

spatial framework. Consult with original authors and other experts on caveats, 

interpretation of results, and potential anomalies when attributing point data to a perwaterbody basis. 

• Fix anomalies identified in the GIS base layers. Merge U.S. and Canada portions of 

Passamaquoddy Bay, and delineate disjunct CDAs treated as a single polygon. 

• Review and revise the spatial framework within the Chesapeake Bay region. 

Determine which of the nineteen sub-estuaries can be combined without losing spatial 

resolution of the available data, and which areas should be considered as distinct. In 

the section on Indicators above on p. 24, it is noted that little information is reported 

separately for some of the smaller Chesapeake sub-estuaries. In contrast, there may 

be other data-rich areas that warrant distinct consideration, such as the Elizabeth 

River in Norfolk VA and the Anacostia River in Washington DC. 

35
 
Table 3. MusselWatch rankings for overall metals and organics contamination status 

and trends in selected ACFHP waterbodies. For waterbodies with multiple 

MusselWatch sites, the “worst” rankings (not averages) are reported. Waterbodies with 

status of medium or high, or trends increasing, are highlighted for emphasis. Source: 

Kimbrough et al. 2008, Kimbrough pers. comm. 

ACFHP Metals Metals Organics Organics 

State ACFHP Waterbody Status Trends Status Trends 

ME Penobscot Bay low decreasing low stable 

ME Casco Bay low stable low decreasing 

ME Maine State Waters low stable low decreasing 

NH Great Bay low stable low stable 

MA Massachusetts State Waters low stable low decreasing 

MA Boston Harbor low stable medium decreasing 

MA Massachusetts Bay low stable low stable 

MA Cape Cod Bay low stable low decreasing 

MA Massachusetts State Waters low stable low stable 

MA Buzzards Bay low increasing low stable 

RI Narragansett Bay low stable low decreasing 

RI Rhode Island State Waters low stable low decreasing 

CT Connecticut River low stable low decreasing 

NY Long Island Sound low stable low stable 

NY Gardiners Bay low stable low stable 

NY Great South Bay low stable low stable 

NY Hudson River/Raritan Bay low stable high stable 

NJ New Jersey State Waters low stable low decreasing 

NJ Barnegat Bay low stable low decreasing 

NJ New Jersey Inland Bays low stable low stable 

NJ Delaware Bay medium stable low stable 

MD Patapsco/Gunpowder Rivers medium stable low decreasing 

MD Chesapeake Bay low stable low decreasing 

MD Severn River low stable low decreasing 

MD Choptank River low stable low decreasing 

MD Patuxent River low stable low decreasing 

MD Potomac River low stable low stable 

VA Rappahannock River low stable low decreasing 

VA Poquoson/Back Rivers low stable low decreasing 

VA James River medium decreasing low decreasing 

VA Virginia Eastern Shore low stable low decreasing 

VA Chincoteague Bay low stable low stable 

VA Virginia State Waters low stable low stable 

NC Albemarle Sound low stable low decreasing 

NC Pamlico Sound low stable low decreasing 

NC Pamlico/Pungo Rivers low decreasing low stable 

NC Neuse River low stable low stable 

NC Bogue Sound low stable low decreasing 

NC Cape Fear River low stable low decreasing 

SC Winyah Bay low stable low stable 

SC North/South Santee Rivers low stable low stable 

SC Charleston Harbor low stable low decreasing 

GA Savannah River low stable low decreasing 

GA St. Catherines/Sapelo Sound low stable low decreasing 

GA Altamaha River low stable low stable 

FL St. Johns River low increasing low stable 

FL Florida State Waters - North low stable low stable 

FL Indian River low stable low stable 

FL Biscayne Bay low stable low stable 

36
 
Table 4. Rankings for selected eutrophication indicators in ACFHP waterbodies from the National Estu

Eutrophication Assessment. The first column (Overall Eutrophic Condition) provides a synoptic assesswaterbody, color-coded (red to blue) for easy interpretation. Rankings are from the 2007 report unless 1999. Sources: Bricker et al. 2007, Bricker et al. 1999, Bricker pers. comm. 

Eu

ACFHP Overall Eutrophic Chlorophyll a - Harmful Algal Blooms Dissolved Oxygen - Eutrophication - Macroalgae - Im

State(s) ACFHP Waterbody Condition Future Outlook Overall Expression - Overall Expression Overall Expression Impact to SAV Overall Expression Re

ME NB Passamaquoddy Bay Moderate Large improvement low low no problem no problem high no 

ME Englishman / Machias Bay Moderate High (1999) unknown moderate (1999) moderate (1999) no problem (1999) unknown high (1999) un

ME Narraguagus Bay Moderate High (1999) unknown moderate (1999) high (1999) no problem (1999) unknown no problem (1999) un

ME Blue Hill Bay Low Small Deterioration low low no problem no problem no problem no 

ME Penobscot Bay Low unknown low no problem no problem unknown no problem un

ME Muscongus Bay Moderate Low (1999) unknown moderate (1999) low (1999) low (1999) unknown no problem (1999) un

ME Damariscotta River Low No Change unknown low unknown unknown no problem un

ME Sheepscot Bay Moderate High (1999) unknown moderate (1999) high (1999) low (1999) unknown moderate (1999) un

ME Kennebec / Androscoggin River Moderate Low (1999) unknown moderate (1999) no problem (1999) low (1999) unknown no problem (1999) un

ME Casco Bay Moderate High (1999) Small Deterioration moderate (1999) low no problem no problem unknown un

ME Saco Bay Moderate (1999) unknown low (1999) low low (1999) unknown unknown un

ME Wells Bay Low Small Deterioration low no problem low no problem no problem un

NH ME Great Bay Moderate Large Deterioration low low no problem low high sli

NH Hampton Harbor Moderate Small Deterioration low low no problem no problem high un

MA Merrimack River unknown unknown unknown unknown unknown moderate (1999) unknown un

MA Plum Island Sound Moderate High Large Deterioration high moderate no problem no problem (1999) unknown un

MA Massachusetts Bay Moderate Large improvement high low no problem low (1999) unknown un

MA Boston Harbor Low Large Deterioration low no problem no problem no problem no problem mo

MA Cape Cod Bay Moderate Large Deterioration high low no problem unknown moderate un

MA Waquoit Bay Moderate Small Deterioration moderate no problem low low high coMA Buzzards Bay Moderate Large Deterioration low moderate low low moderate mo

37
Table 4, continued. Rankings for selected eutrophication indicators in ACFHP waterbodies from the N

Eutrophication Assessment. The first column (Overall Eutrophic Condition) provides a synoptic assesswaterbody, color-coded (red to blue) for easy interpretation. Rankings are from the 2007 report unless 1999. Sources: Bricker et al. 2007, Bricker et al. 1999, Bricker pers. comm. 

Eu

ACFHP Overall Eutrophic Chlorophyll a - Harmful Algal Blooms Dissolved Oxygen - Eutrophication - Macroalgae - Im

State(s) ACFHP Waterbody Condition Future Outlook Overall Expression - Overall Expression Overall Expression Impact to SAV Overall Expression Re

RI MA Narragansett Bay High Large improvement moderate moderate high no problem high co

CT Connecticut River Low Large improvement unknown no problem no problem no problem no problem sli

NY CT Long Island Sound High Small improvement high low high low no problem mo

NY Peconic / Gardiners Bay Low No Change low low no problem high (1999) no problem un

NY Great South Bay Moderate High No Change high moderate no problem moderate (1999) high moNY NJ Hudson River / Raritan Bay Moderate Small improvement high moderate (1999) low no problem (1999) low (1999) co

NJ Barnegat Bay High Small improvement high high no problem moderate high co

NJ New Jersey Inland Bays High Large Deterioration low low no problem high high coDE Delaware Inland Bays Moderate No Change moderate low low no problem high mo

DE NJ Delaware Bay Moderate No Change high no problem low no problem no problem no 

MD DE Maryland Inland Bays Moderate Large Deterioration high low low low moderate un

MD VA Chincoteague Bay High Small Deterioration high high no problem low moderate un

MD VA Chesapeake Bay High Small improvement high high high high moderate co

MD Chester River High Small improvement high no problem (1999) high no problem no problem (1999) un

MD Choptank River High Small improvement high high low no problem no problem co

MD VA Tangier / Pocomoke Sound Moderate High Small Deterioration high low (1999) no problem moderate high (1999) coMD Patuxent River High Small Deterioration high moderate high no problem no problem (1999) co

MD DC VA Potomac River High Small Deterioration high high moderate no problem low (1999) co

VA Rappahannock River Moderate High No Change high moderate moderate moderate no problem mo

VA York River Moderate High No Change high moderate low no problem moderate mo

VA James River Moderate High No Change high moderate no problem no problem no problem mo

38
Table 4, continued. Rankings for selected eutrophication indicators in ACFHP waterbodies from the N

Eutrophication Assessment. The first column (Overall Eutrophic Condition) provides a synoptic assesswaterbody, color-coded (red to blue) for easy interpretation. Rankings are from the 2007 report unless 1999. Sources: Bricker et al. 2007, Bricker et al. 1999, Bricker pers. comm. 

Eu

ACFHP Overall Eutrophic Chlorophyll a - Harmful Algal Blooms Dissolved Oxygen - Eutrophication - Macroalgae - Im

State(s) ACFHP Waterbody Condition Future Outlook Overall Expression - Overall Expression Overall Expression Impact to SAV Overall Expression Re

NC VA Albemarle Sound unknown unknown low (1999) low (1999) low (1999) low (1999) no problem (1999) un

NC Pamlico Sound unknown Large Deterioration moderate (1999) moderate low (1999) low (1999) no problem (1999) un

NC Pamlico / Pungo Rivers unknown unknown unknown unknown unknown moderate (1999) no problem (1999) unNC Neuse River High Small Deterioration high high low low (1999) no problem (1999) co

NC Bogue Sound unknown unknown unknown unknown unknown unknown no problem (1999) un

NC New River Moderate No Change high low low unknown no problem mo

NC Cape Fear River Moderate Low Small Deterioration moderate no problem low unknown no problem mo

SC Winyah Bay Moderate Large Deterioration moderate no problem moderate no problem (1999) no problem (1999) un

SC North / South Santee Rivers Moderate unknown moderate low moderate unknown no problem (1999) un

SC Charleston Harbor Moderate Low Large Deterioration moderate low no problem no problem (1999) moderate (1999) un

SC Stono / North Edisto Rivers Moderate Small Deterioration moderate low moderate no problem (1999) no problem (1999) un

SC St. Helena Sound Moderate Small Deterioration moderate low moderate unknown unknown unSC Broad River Moderate Low Large Deterioration moderate no problem low unknown unknown un

GA SC Savannah River Moderate Large Deterioration moderate no problem moderate no problem no problem unGA Ossabaw Sound Moderate Low Small Deterioration unknown no problem moderate no problem no problem no 

GA St. Catherines / Sapelo Sounds Moderate Low (1999) unknown moderate (1999) no problem (1999) low (1999) no problem (1999) no problem (1999) un

GA Altamaha River Low Large Deterioration moderate (1999) no problem low no problem no problem un

GA St. Andrew / St. Simons Sounds Low Large Deterioration moderate (1999) no problem low (1999) no problem no problem un

GA FL St. Marys River / Cumberland Sound Moderate Low Small Deterioration moderate (1999) no problem moderate no problem no problem no FL St. Johns River High Small improvement high high moderate no problem high co

FL Indian River Moderate Small Deterioration low moderate low no problem moderate moFL Biscayne Bay Moderate Low No Change low no problem moderate no problem no problem sli

39
Table 5. National Coastal Condition Report (NCCR) Indices for U.S. EPA National 

Estuary Program (NEP) estuaries. Source: U.S. EPA 2006. 

Fish Tissue 

ACFHP Overall Water Quality Sediment Contaminants 

State ACFHP Waterbody Condition Index Quality Index Benthic Index Index 

ME Casco Bay 5 = Good 5 = Good 5 = Good 5 = Good unknown 

MA Boston Harbor 2.5 = Fair/Poor 5 = Good 1 = Poor 1 = Poor 3 = Fair 

MA Cape Cod Bay 2.5 = Fair/Poor 5 = Good 1 = Poor 1 = Poor 3 = Fair 

MA Buzzards Bay 3.25 = Fair/Good 5 = Good 3 = Fair 4 = Good/Fair 1 = Poor 

RI Narragansett Bay 1.75 = Poor/Fair 3 = Fair 1 = Poor 2 = Fair/Poor 1 = Poor 

CT Connecticut River 1.5 = Poor/Fair 3 = Fair 1 = Poor 1 = Poor 1 = Poor 

NY Long Island Sound 1.5 = Poor/Fair 3 = Fair 1 = Poor 1 = Poor 1 = Poor 

NY Peconic (Gardiners) Bay 4.33 = Good/Fair 5 = Good unknown 3 = Fair 5 = Good 

NY Hudson River/Raritan Bay 1 = Poor 1 = Poor 1 = Poor 1 = Poor 1 = Poor 

NJ Barnegat Bay 3.5 = Fair/Good 4 = Good/Fair 4 = Good/Fair 3 = Fair 3 = Fair 

DE Delaware Inland Bays 2.5 = Fair/Poor 3 = Fair 1 = Poor 1 = Poor 5 = Good 

DE Delaware Bay 1.75 = Poor/Fair 1 = Poor 4 = Good/Fair 1 = Poor 1 = Poor 

MD Chincoteague Bay 3.5 = Fair/Good 1 = Poor 5 = Good 3 = Fair 5 = Good 

NC Albemarle Sound 4 = Good/Fair 5 = Good 4 = Good/Fair 3 = Fair 4 = Good/Fair 

NC Pamlico Sound 4 = Good/Fair 5 = Good 4 = Good/Fair 3 = Fair 4 = Good/Fair 

NC Pamlico/Pungo Rivers 4 = Good/Fair 5 = Good 4 = Good/Fair 3 = Fair 4 = Good/Fair 

NC Neuse River 4 = Good/Fair 5 = Good 4 = Good/Fair 3 = Fair 4 = Good/Fair 

FL Indian River 5 = Good 5 = Good 5 = Good 5 = Good unknown 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Table 6. National Coastal Condition Report (NCCR) water quality indicators for U.S. 

EPA National Estuary Program (NEP) estuaries. These are the indicators that 

contribute to the “Water Quality Index” reported in Table 5. Source: U.S. EPA 2006. 

ACFHP 

State ACFHP Waterbody 

Dissolved 

Inorganic 

Nitrogen (DIN) 

Dissolved 

Inorganic 

Phosphorus 

(DIP) 

Dissolved 

Oxygen Chlorophyll a Water Clarity 

ME Casco Bay Good Good Good Good Good 

Boston Harbor Good Good Good Good Good 

Cape Cod Bay Good Good Good Good Good 

Buzzards Bay Good Fair Good Good Good 

Narragansett Bay Good Fair Good Fair Good 

Connecticut River Good Fair Fair Good Good 

Long Island Sound Good Fair Fair Good Good 

Peconic (Gardiners) Bay Good Fair Good Good Good 

Hudson River/Raritan Bay Fair Poor Good Good Good 

Barnegat Bay Good Good Good Good Poor 

Delaware Inland Bays Fair Fair Good Fair Good 

Delaware Bay Poor Fair Good Fair Fair 

Chincoteague Bay Poor Poor Good Fair Poor 

Albemarle Sound Good Good Fair Fair Good 

Pamlico Sound Good Good Fair Fair Good 

Pamlico/Pungo Rivers Good Good Fair Fair Good 

Neuse River Good Good Fair Fair Good 

Indian River Good Good Fair Fair Good 

MA 

MA 

MA 

RI 

CT 

NY 

NY 

NY 

NJ 

DE 

DE 

MD 

NC 

NC 

NC 

NC 

FL 

40
 
Table 7. National Coastal Condition Report (NCCR) sediment quality indicators for U.S. 

EPA National Estuary Program (NEP) estuaries. These are the indicators that 

contribute to the “Sediment Quality Index” reported in Table 5. Source: U.S. EPA 2006. 

ACFHP 

State ACFHP Waterbody 

Sediment 

Total Organic 

Carbon (TOC) 

Sediment 

Contamination 

Sediment 

Toxicity 

ME Casco Bay Good Good Good 

MA Boston Harbor Good Fair Poor 

MA Cape Cod Bay Good Fair Poor 

MA Buzzards Bay Good Fair Poor 

RI Narragansett Bay Good Fair Poor 

CT Connecticut River Good Poor Poor 

NY Long Island Sound Good Poor Poor 

NY Peconic (Gardiners) Bay unknown unknown unknown 

NY Hudson River/Raritan Bay Good Poor Poor 

NJ Barnegat Bay Good Good Good 

DE Delaware Inland Bays Good Good Poor 

DE Delaware Bay Good Good Poor 

MD Chincoteague Bay Good Good Good 

NC Albemarle Sound Good Good Good 

NC Pamlico Sound Good Good Good 

NC Pamlico/Pungo Rivers Good Good Good 

NC Neuse River Good Good Good 

FL Indian River Good unknown unknown 

41
 
       

   

     

   

   

   

   

   

   

         

         

     

     

           

         

     

   

   

   

     

     

   

     

   

   

   

     

     

     

     

Table 8. Number of indicators and threats recorded for each estuary. Sorted in 

descending order (of indicators recorded), with NEP and NERR designation noted. 

Estuary Name

Number of

Indicators

Number of

Threats NEP? NERR?

Delaware Bay 65 21 Yes

Chesapeake Bay 53 29 Yes (Chesapeake Bay Program)

Long Island Sound 44 9 Yes Yes

Casco Bay 40 21 Yes

Albemarle Sound 36 7 Yes Yes

Chincoteague Bay 35 8 Yes

Barnegat Bay 34 10 Yes

Great Bay 33 24 Yes Yes

Hudson River/Raritan Bay 33 19 Yes Yes

Indian River 30 11 Yes

Narragansett Bay 30 10 Yes

Buzzards Bay 29 11 Yes

Pamlico Sound 29 9 Yes

Cape Cod Bay 29 7 Yes (Massachusetts Bays) Yes

Boston Harbor 28 9 Yes (Massachusetts Bays)

James River 27 12 Yes (sub‐estuary of Chesapeake Bay)

Savannah River 27 11 Yes

Neuse River 27 10 Yes (sub‐estuary of Pamlico Sound)

Pamlico/Pungo Rivers 27 6 Yes (sub‐estuary of Pamlico Sound) Yes

Peconic (Gardiners) Bay 27 4 Yes

Connecticut River 26 8 Yes (sub‐estuary of Long Island Sound)

Potomac River 24 11 Yes (sub‐estuary of Chesapeake Bay)

Cape Fear River 22 10

Bogue Sound 22 4

Delaware Inland Bays 22 4 Yes

Maryland Inland Bays 19 9 Yes

New Jersey Inland Bays 18 7

Patuxent River 18 4 Yes (sub‐estuary of Chesapeake Bay) Yes

Charleston Harbor 17 11

North/South Santee Rivers 17 8

Winyah Bay 17 8

Massachusetts Bay 17 6 Yes (Massachusetts Bays)

Altamaha River 17 5 Yes

St. Catherines/Sapelo Sounds 16 2

Biscayne Bay 15 11

Penobscot Bay 14 23

St. Marys River/Cumberland Sound 14 7

St. Johns River 13 13

Rappahannock River 13 6 Yes (sub‐estuary of Chesapeake Bay)

Choptank River 13 3 Yes (sub‐estuary of Chesapeake Bay)

Great South Bay 13 3

42
 
       

     

   

   

   

   

   

   

     

   

     

     

     

   

         

   

   

     

   

   

         

     

         

     

     

         

         

     

     

         

         

Table 8, continued. Number of indicators and threats recorded for each estuary. 

Sorted in descending order (of indicators recorded), with NEP and NERR designation 

noted. 

Estuary Name

Number of

Indicators

Number of

Threats NEP? NERR?

St. Andrew/St. Simons Sounds 12 6

Ossabaw Sound 12 5

Sheepscot Bay 11 12

Passamaquoddy Bay 10 15 Yes

Wells Bay 10 12

Merrimack River 10 4

Broad River 10 3 Yes

Plum Island Sound 10 2

Kennebec/Androscoggin River 9 16

Englishman/Machias Bay 9 15 Yes

Hampton Harbor 9 12 Yes

Saco Bay 9 11 Yes

Tangier/Pocomoke Sound 9 10 Yes (sub‐estuary of Chesapeake Bay)

York River 9 8 Yes (sub‐estuary of Chesapeake Bay)

Stono/North Edisto Rivers 9 5

Waquoit Bay 9 5

Chester River 9 3 Yes (sub‐estuary of Chesapeake Bay)

New River 9 3

St. Helena Sound 9 3

Blue Hill Bay 8 14 Yes

Damariscotta River 8 14

Muscongus Bay 8 14

Narraguagus Bay 8 13

Patapsco/Gunpowder Rivers 8 7 Yes (sub‐estuary of Chesapeake Bay) Yes

Severn River 7 2 Yes (sub‐estuary of Chesapeake Bay)

Wassaw Sound 5 3

Virginia Eastern Shore 5 1 Yes (sub‐estuary of Chesapeake Bay)

Poquoson/Back Rivers 4 5 Yes (sub‐estuary of Chesapeake Bay)

Nassau Sound 1 5

Ingram/Fleets Bays 1 4 Yes (sub‐estuary of Chesapeake Bay)

Lynnhaven River 1 4 Yes (sub‐estuary of Chesapeake Bay)

Eastern Bay 1 3 Yes (sub‐estuary of Chesapeake Bay)

Piankatank River/Mobjack Bay 1 3 Yes (sub‐estuary of Chesapeake Bay)

Elk/Sassafras Rivers 1 2 Yes (sub‐estuary of Chesapeake Bay)

Honga River 1 2 Yes (sub‐estuary of Chesapeake Bay) Yes

Susquehanna River 1 2 Yes (sub‐estuary of Chesapeake Bay)

43
 
   

           

               

         

         

       

             

         

       

                   

         

       

         

               

             

               

               

               

   

   

         

   

           

           

     

         

     

     

           

     

     

Table 9. Classification of Threats as recorded in the Assessment Table (total n=1260). 

The classification scheme was developed by discussions of the ACFHP Steering 

Committee, June 2009. Threats include those attributed to estuaries, watersheds, and 

marine waters. 

Classified Threat Number of Instances Notes

2. Water Quality 225 including nutrients, eutrophication, DO, BOD

1. Dams and Passage 106 including all barriers to fish migration

5. Climate Change 97 including Sea Level Rise

6. Dredging Issues 89 including dredge spoil disposal

7. Contaminants 84 generally in sediments or tissues

8. Fishing Gear 73 impacts of bottom tending fishing gear

4. Impervious Surfaces 64 also Urban Land Development

9. Invasive Species 54 also Non‐Native Species

11. Water Withdrawals 25 when reported separately from Altered Hydrology / Multiple Threats

13. Aquaculture 17

10. Boating issues 15 Vessel damage, sewage discharge

3. Energy Development 9 Wind, tidal, hydro

15. Temperature 8 when reported separately from Climate Change

12. Groundwater 5 when reported separately from Altered Hydrology / Multiple Threats

14. Regulatory Systems 0 these were generally classified as "Actions"

Multiple Threats Reported 96 many include altered hydrology and water quality

Other ‐ Habitat Loss 47 reported as a threat ‐ but can be considered a result

Other ‐ Algal blooms 23 may or may not be related to water quality

Other ‐ Forestry Practices 23 watershed land use

Other ‐ Stormwater Issues 22 non‐point source

Other ‐ Agricultural Runoff 20 non‐point source

Other ‐ Marine Debris 19

Other ‐ Agricultural Practices 17 watershed land use

Other ‐ Tidal Restriction 17 hydrology

Other ‐ Bacterial Contamination 16 distinct from water quality and contaminants?

Other ‐ Riparian Buffers 14 watershed land use?

Other ‐ Sedimentation 14 Distinct threat?

Other ‐ Disease of Biotic Habitats 10 group with bacterial contamination, pathogens?

Other ‐ Shoreline Erosion 10

Other ‐ Sewage and Septic Issues 9 associated with Water Quality?

Other ‐ Marine Infrastructure 5 associated with Dredging Issues?

Other ‐ Intakes and Impingement 3 associated with Water Withdrawals?

Other ‐ Storm Events 3

Other ‐ Unexploded Ordnance 3

Other ‐ Nuisance Macroalgae 2 group with Algal Blooms?

Other ‐ Ocean Noise 2 impacts to marine mammals

Other ‐ Lighting on Beaches 1 impacts to nesting sea turtles

Other ‐ Recreational Vehicles 1 in wetlands and beaches

Other ‐ Shoreline Hardening 1 associated with Altered

44
 
Table 10. Instances of classified threats within the Assessment Table (total n=1260), 

tallied by region. Results for the South Atlantic and South Florida are combined. 

South Atlantic

Classified Threat North Atlantic Mid‐Atlantic + South Florida

01. Dams and Passage 39 32 35

02. Water Quality 90 87 48

03. Energy Development 7 2

04. Impervious Surfaces 18 28 18

05. Climate Change 23 52 22

06. Dredging Issues 29 28 32

07. Contaminants 33 33 18

08. Fishing Gear 9 20 44

09. Invasive Species 16 33 5

10. Boating issues 5 5 5

11. Water Withdrawals 14 6 5

12. Groundwater 1 4

13. Aquaculture 15 2

14. Regulatory Systems

15. Temperature 1 7

Multiple Threats Reported 20 41 35

Other ‐ Acid Rain 2

Other ‐ Agricultural Practices 13 4

Other ‐ Agricultural Runoff 2 3 15

Other ‐ Algal blooms 5 16 2

Other ‐ Altered Hydrology 2

Other ‐ Bacterial Contamination 9 7

Other ‐ Disease of Biotic Habita 2 7 1

Other ‐ Fish Waste Disposal 1 1

Other ‐ Forestry Practices 12 11

Other ‐ Habitat Loss 31 7 9

Other ‐ Intakes and Impingemen 1 2

Other ‐ Lighting on Beaches 1

Other ‐ Marine Debris 17 2

Other ‐ Marine Infrastructure 3 1 1

Other ‐ Nuisance Macroalgae 2

Other ‐ Ocean Noise 1 1

Other ‐ Recreational Vehicles 1

Other ‐ Riparian Buffers 14

Other ‐ Sedimentation 11 3

Other ‐ Sewage and Septic Issue 4 5

Other ‐ Shoreline Erosion 6 1 3

Other ‐ Shoreline Hardening 1

Other ‐ Storm Events 1 2

Other ‐ Stormwater Issues 4 9 9

Other ‐ Tidal Restriction 5 12

Other ‐ Unexploded Ordnance 3

45
 
Table 11. Instances of classified threats within the Assessment Table (total n=1260), 

tallied by zone. Results for the Marine-State and Marine-Federal zones are combined. 

Classified Threat Watersheds Estuaries Marine

01. Dams and Passage 100 6

02. Water Quality 51 164 9

03. Energy Development 5 4

04. Impervious Surfaces 51 11 2

05. Climate Change 13 32 52

06. Dredging Issues 5 58 26

07. Contaminants 6 68 10

08. Fishing Gear 1 41 31

09. Invasive Species 16 37 1

10. Boating issues 8 7

11. Water Withdrawals 18 7

12. Groundwater 5

13. Aquaculture 13

14. Regulatory Systems

15. Temperature 8

Multiple Threats Reported 30 63 3

Other ‐ Habitat Loss 9 37 1

Other ‐ Algal blooms 17 6

Other ‐ Forestry Practices 23

Other ‐ Stormwater Issues 13 5 4

Other ‐ Agricultural Runoff 11 5 4

Other ‐ Marine Debris 16 3

Other ‐ Agricultural Practices 17

Other ‐ Tidal Restriction 6 6 5

Other ‐ Bacterial Contamination 12 4

Other ‐ Riparian Buffers 14

Other ‐ Sedimentation 2 12

Other ‐ Disease of Biotic Habitats 9 1

Other ‐ Sewage and Septic Issue 1 2 7

Other ‐ Shoreline Erosion 3 2 5

Other ‐ Marine Infrastructure 1 4

Other ‐ Intakes and Impingement 1 2

Other ‐ Unexploded Ordnance 1 1 1

Other ‐ Storm Events 3

Other ‐ Acid Rain 2

Other ‐ Altered Hydrology 2

Other ‐ Fish Waste Disposal 2

Other ‐ Nuisance Macroalgae 2

Other ‐ Ocean Noise 2

Other ‐ Lighting on Beaches 1

Other ‐ Recreational Vehicles 1

Other ‐ Shoreline Hardening 1

46
 
   

          

        

         

    

   

         

        

   

          

       

        

         

    

   

         

        

   

                

       

        

         

        

   

         

        

        

   

Table 12. Top three classified threats by zone and region, based on a tally of instances 

within the Assessment Table (total n=1260). Tallies for the South Atlantic and South 

Florida regions are combined, as are tallies for the Marine-State and Marine-Federal 

zones. Results are displayed within a region x zone matrix. 

Region / Zone Watersheds Estuaries Marine (S+F)

North Atlantic

Dams and Passage (37)

Water Quality (28)

Water Withdrawals (14)

Water Quality (55)

Contaminants (23)

Dredging Issues (16)

Dredging Issues (13)

Climate Change (11)

Fishing Gear (8)

Mid‐Atlantic

Dams and Passage (32)

Impervious Surfaces (25)

Water Quality (16)

Water Quality (70)

Contaminants (28)

Invasive Species (19)

Climate Change (23)

Fishing Gear (11)

Dredging Issues (9)

South Atlantic +

South Florida

Dams and Passage (31)

Impervious Surfaces (17)

Water Quality (7)

Water Quality (40)

Fishing Gear (31)

Dredging Issues (26)

Climate Change (18)

Fishing Gear (12)

Dredging Issues (4)

Boating Issues (4)

47
 
   

           

   

   

       

           

       

   

   

                     

   

   

     

             

       

           

     

           

                       

   

             

       

           

       

     

   

   

   

   

        

   

     

Table 13. Classification of Actions as recorded in the Assessment Table (total n=1860). 

The classification scheme is based on themes that emerged from the data itself. Most 

actions address either a particular habitat type (e.g. “restore wetlands”) or a particular 

threat (e.g. “improve fish passage”). Actions include those attributed to estuaries, 

watersheds, and marine waters. 

Classified Action

Number of

Instances Notes

Area Designation 304 Includes MPAs, EFH, HAPCs, Conservation Priority Areas

Water Quality ‐ Protect and Restore 134

Wetlands ‐ Protect and Restore 121

Improve Fish Passage 109 Includes barrier removal

Monitoring and Assessment 93 Includes Mapping and Research Recommendations

Conservation Planning 89 Includes policy, legislation, and enforcement

Riparian Buffers ‐ Conserve and Restore 86

Control Invasive Species 81

General Habitat Conservation 79 Actions not specific towards a threat, habitat type, orspecies

SAV ‐ Protect and Restore 79

Watersheds ‐ Conserve and Restore 73

Fishery Regulation 68 Some overlap with MPAs

Clean Boating 47 Includes no discharge zones, pumpouts, vessel groundings, etc.

Improve Stormwater Management 47 Includes urban runoff

Hydrology ‐ Protect and Restore 46 Includes freshwater and tidal flow

Education, Outreach, and Partnerships 45

Improve Wastewater Management 45 Includes sewage and septic issues

Beaches and Shorelines ‐ Protect and Restore 44 Includes dune restoration, some beach nourishment (also a threat?)

Shellfish Beds ‐ Protect and Restore 42

Conserve Species 34 Actions directed towards individual species (e.g. shortnose sturgeon)

Agricultural Conservation BMPs 31

Multiple Recommendations 29 Several recommendations reported in single item

Forestry BMPs 26 Some overlap with Watershed and Agricultural BMPs

Dredging Regulation 24

Prepare for Climate Change Impacts 22

Clean Up Marine Debris 21

Clean Up Contaminants 14

Improve Public Access 8

Reduce Sedimentation 7

Other ‐ Threat misclassified as Action? 5

Other ‐ mine drainage mitigation 2

Other ‐ preserve historic resources 1

Other ‐ experimental restoration 1

Other ‐ improve benthic productivity 1

Other ‐ respond to natural disasters 1

48
 
Table 14. Instances of classified actions within the Assessment Table (total n=1860), 

tallied by region. Results for the South Atlantic and South Florida are combined. 

South Atlantic

Classified Action North Atlantic Mid‐Atlantic + South Florida

Area Designation 56 106 142

Water Quality ‐ Protect and Restore 11 106 17

Wetlands ‐ Protect and Restore 53 58 10

Improve Fish Passage 38 42 29

Monitoring and Assessment 33 42 18

Conservation Planning 16 67 6

Riparian Buffers ‐ Conserve and Restore 21 60 5

Control Invasive Species 8 67 5

General Habitat Conservation 26 42 11

SAV ‐ Protect and Restore 13 61 5

Watersheds ‐ Conserve and Restore 31 40 2

45

3

Fishery Regulation 6 17

Clean Boating 23 21

Improve Stormwater Management 9 31 7

Hydrology ‐ Protect and Restore 18 17 11

Education, Outreach, and Partnerships 30 15

Improve Wastewater Management 7 37 1

Beaches and Shorelines ‐ Protect and Restore 11 28 5

Shellfish Beds ‐ Protect and Restore 14 21 7

Conserve Species 6 15 1

Agricultural Conservation BMPs 25 6

Multiple Recommendations 5 18 6

Forestry BMPs 26

Dredging Regulation 8 1

Prepare for Climate Change Impacts 22

Clean Up Marine Debris 14 4 3

Clean Up Contaminants 2 11 1

Improve Public Access 8

Reduce Sedimentation 1 6

Other ‐ Threat misclassified as Action? 5

Other ‐ mine drainage mitigation 2

Other  ‐ preserve historic resources 1

Other ‐ experimental restoration 1

Other ‐ improve benthic productivity 1

Other ‐ respond to natural disasters 1

4

6

49
 
Table 15. Instances of classified actions within the Assessment Table (total n=1860), 

tallied by zone. Results for the Marine-State and Marine-Federal zones are combined. 

Classified Action Watersheds Estuaries Marine

Area Designation 69 128 107

Water Quality ‐ Protect and Restore 51 79 4

Wetlands ‐ Protect and Restore 15 98 8

Improve Fish Passage 97 12

Monitoring and Assessment 8 43 42

Conservation Planning 30 46 13

Riparian Buffers ‐ Conserve and Restore 81 4 1

Control Invasive Species 6 73 2

SAV ‐ Protect and Restore 2 75 2

Watersheds ‐ Conserve and Restore 55 16 2

General Habitat Conservation 42 26 1

Fishery Regulation 1 39 28

Clean Boating 1 36 10

Improve Stormwater Management 30 15 2

Hydrology ‐ Protect and Restore 22 24

Education, Outreach, and Partnerships 21 18 6

Improve Wastewater Management 21 22 2

Beaches and Shorelines ‐ Protect and Restore 4 23 17

Shellfish Beds ‐ Protect and Restore 1 40 1

Conserve Species 24 10

Agricultural Conservation BMPs 31

Multiple Recommendations 13 16

Forestry BMPs 26

Dredging Regulation 1 23

Prepare for Climate Change Impacts 20 2

Clean Up Marine Debris 17 4

Clean Up Contaminants 3 11

Improve Public Access 2 6

Reduce Sedimentation 1 6

Other ‐ Threat misclassified as Action? 5

Other ‐ mine drainage mitigation 2 1

Other  ‐ preserve historic resources 1

Other ‐ experimental restoration 1

Other ‐ respond to natural disasters 1

Other ‐ improve benthic productivity 1

50
 
   

                                        

                  

           

                       

                                       

              

                                      

                            

           

         

                  

     

                                

                   

              

                                      

                             

   

                                             

                                           

            

                                         

                                             

            

                                      

                                         

     

   

                                                          

                                         

                                           

                                                          

                                     

                                           

   

                                                          

                                              

                                         

   

                                                         

                                        

                  

           

                                                         

                       

                                       

              

                                                         

                                      

                            

           

                                                          

                               

                                   

        

                                                          

                             

                                        

   

                                                          

                                     

                                              

   

                                                         

         

                  

     

                                                         

                                

                   

              

                                                         

                                      

                             

   

     

                                                          

                           

                                         

        

                                                          

                                             

                                                  

   

                                                          

                                          

                                            

         

                                                         

                                       

                                           

            

                                                         

                                         

                                             

            

                                                         

                                      

                                         

     

Table 16. Top three classified actions by zone and region, based on a tally of instances 

within the Assessment Table (total n=1860). Tallies for the South Atlantic and South 

Florida regions are combined, as are tallies for the Marine-State and Marine-Federal 

zones. Results are displayed within a region x zone matrix. 

Region / Zone Watersheds Estuaries Marine (State+Federal)

North Atlantic

Improve Fish Passage (38)

Watersheds ‐ Conserve and Restore (24)

Riparian Buffers ‐ Conserve and Restore (21)

Wetlands ‐ Protect and Restore (38)

Area Designation (27)

Monitoring and Assessment (25)

Area Designation (15)

Wetlands ‐ Protect and Restore (7)

Monitoring and Assessment (7)

Mid‐Atlantic

Riparian Buffers ‐ Conserve and Restore (55)

Water Quality ‐ Protect and Restore (45)

Improve Fish Passage (30)

Control Invasive Species (61)

Water Quality ‐ Protect and Restore (60)

SAV ‐ Protect and Restore (59)

Area Designation (33)

Monitoring and Assessment (28)

Fishery Regulation (12)

South Atlantic +

South Florida

Improve Fish Passage (29)

Area Designation (28)

Conserve Species (13)

Area Designation (55)

Fishery Regulation (33)

Dredging Regulation (15)

Area Designation (59)

Fishery Regulation (12)

Monitoring and Assessment (7)

Table 17. Top three classified threats and actions, by zone and region, based on tallies 

of instances within the Assessment Table. Results for Tables 12 and 16 are combined, 

so that the top three classified threats and actions can be viewed together. Results are 

displayed within a region x zone matrix, and are combined for the South Atlantic and 

South Florida regions, and for the Marine-State and Marine-Federal zones. 

Region / Zone Watersheds Estuaries Marine (State+Federal)

North Atlantic

Threats:

Dams and Passage (37)

Water Quality (28)

Water Withdrawals (14)

Actions:

Improve Fish Passage (38)

Watersheds ‐ Conserve and Restore (24)

Riparian Buffers ‐ Conserve and Restore (21)

Threats:

Water Quality (55)

Contaminants (23)

Dredging Issues (16)

Actions:

Wetlands ‐ Protect and Restore (38)

Area Designation (27)

Monitoring and Assessment (25)

Threats:

Dredging Issues (13)

Climate Change (11)

Fishing Gear (8)

Actions:

Area Designation (15)

Wetlands ‐ Protect and Restore (7)

Monitoring and Assessment (7)

Mid‐Atlantic

Threats:

Dams and Passage (32)

Impervious Surfaces (25)

Water Quality (16)

Actions:

Riparian Buffers ‐ Conserve and Restore (55)

Water Quality ‐ Protect and Restore (45)

Improve Fish Passage (30)

Threats:

Water Quality (70)

Contaminants (28)

Invasive Species (19)

Actions:

Control Invasive Species (61)

Water Quality ‐ Protect and Restore (60)

SAV ‐ Protect and Restore (59)

Threats:

Climate Change (23)

Fishing Gear (11)

Dredging Issues (9)

Actions:

Area Designation (33)

Monitoring and Assessment (28)

Fishery Regulation (12)

South Atlantic +

South Florida

Threats:

Dams and Passage (31)

Impervious Surfaces (17)

Water Quality (7)

Actions:

Improve Fish Passage (29)

Area Designation (28)

Conserve Species (13)

Threats:

Water Quality (40)

Fishing Gear (31)

Dredging Issues (26)

Actions:

Area Designation (55)

Fishery Regulation (33)

Dredging Regulation (15)

Threats:

Climate Change (18)

Fishing Gear (12)

Dredging Issues (4), Boating Issues (4)

Actions:

Area Designation (59)

Fishery Regulation (12)

Monitoring and Assessment (7)

51
 
Legend 

NCCRIII National Indices (US EPA) 

<all other values> 

EUTROINDEX 

0 0 = Poor 

<Null> 

3 3 = Fair 

5 5 = Good 

SpatialFramework 

Zone 

CDA 

EDA 

Estuarine 

Created by D.M. Nelson, NOAA/NOS 

for Atlantic Coast Fish Habitat Partnership (ACFHP) Marine - Federal 

April 22, 2009 

Data from U.S. EPA 2008 Marine - State 

National Coastal Condition Report III 

provided by Virginia Engle, U.S. EPA, Gulf Breeze FL states2m polygon 

Figure 14. Water Quality Index for sampling stations in EPA’s National Coastal 

Condition Report III (U.S. EPA 2008, Engle pers. comm.), overlaid on the ACFHP base 

map. filename: NCCR3_EutroIndex_June18.emf 

52
 
Created by D.M. Nelson, NOAA/NOS, April 22, 2009
 

for Atlantic Coast Fish Habitat Partnership (ACFHP)
 

Data from USGS (Hammar-Klose and Thieler 2001)
 

USGS Coastal Vulnerability Index 

Coastal vulnerability to sea level rise, based on
 

geomorphology, slope, wave and tide climate, erosion/accretion.

Legend
 

Coastal Vulnerability Index (USGS)
 

<all other values> 

CVI 

High
 

Low
 

Moderate
 

Very High
 

SpatialFramework 

Zone 

CDA
 

EDA
 

Estuarine
 

Marine - Federal
 

Marine - State
 

states2m polygon
 

Figure 15. Coastal Vulnerability Index for U.S. Atlantic coastline (Hammar-Klose and 

Thieler 2001), overlaid on the ACFHP base map. filename: USGS_CVI_June18.emf 

53
 
Passamaquoddy Bay 

Englishman/Machias Bay 

Penobscot Bay 

Damariscotta River Sheepscot Bay 

Muscongus Bay 

Wells BaySaco Bay 

Great Bay Hampton Harbor 

Merrimack River 

Boston Harbor Plum Island Sound 

Massachusetts Bay Cape Cod Bay 

Buzzards Bay Waquoit Bay Connecticut River Narragansett Bay Long Island Sound Peconic Bay Hudson River/Raritan Bay 

Great South Bay 

Barnegat Bay 

New Jersey Inland Bays 

Delaware Bay Chester River 

Choptank River Patuxent River Maryland Inland Bays Potomac River 

Chesapeake Bay Rappahannock River Chincoteague Bay 

York River 

James River 

Albemarle Sound 

Pamlico/Pungo Rivers 

Neuse River 

New River 

Bogue Sound 

Cape Fear River 

Winyah Bay North/South Santee Rivers
 

Charleston Harbor
 

St. Helena Sound Legend Broad River
 

Savannah River
 

Ossabaw Sound EutroData
 

<all other values> 

St. Andrew/St. Simons Sounds 

Altamaha River 

Overall_Eutrophic_Condition St. Marys River/Cumberland Sound 

high 

low 

moderate 

moderate high 

Indian River moderate low 

unknown 

St. Johns River 

SpatialFramework 

Zone 

CDA 

EDA Biscayne Bay 

Estuarine 

Created by D.M. Nelson, NOAA/NOS, June 18, 2009 Marine - Federal for Atlantic Coast Fish Habitat Partnership (ACFHP) 

Data from NOAA (Bricker et al. 2007) Marine - State Effect of Nutrient Enrichment in the Nation's Estuaries: 

A Decade of Change states2m polygon 

Figure 16. Overall Eutrophic Condition for 64 U.S. Atlantic coastal estuaries (Bricker et 

al. 2007), overlaid on the ACFHP base map. filename: EutroCondition_June18.emf 

54
 
 

 

 

 

 

 

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AFWA. 2006. National Fish Habitat Action Plan (NFHAP). Association of Fish and Wildlife Agencies, 

Washington DC. http://www.fishhabitat.org/documents/plan/National_Fish_Habitat_Action_Plan.pdf 

Bricker S.B., C.G. Clement, D.E. Pirhalla, S.P. Orlando, and D.R.G. Farrow. 1999. National Estuarine 

Eutrophication Assessment. Effects of Nutrient Enrichment in the Nation's Estuaries. NOAA/NOS Special 

Projects Office and National Centers for Coastal Ocean Science, Silver Spring, MD. 71 pp. 

http://coastalscience.noaa.gov/publications/eutro_report.pdf 

Bricker, S., B. Longstaff, W. Dennison, A. Jones, K. Boicourt, C. Wicks, and J. Woerner. 2007. Effects of 

Nutrient Enrichment in the Nation's Estuaries: A Decade of Change. NOAA/NOS Center for Monitoring 

and Assessment. NOAA Coastal Ocean Program Decision Analysis Series No. 26. 322 pp. 

http://ccma.nos.noaa.gov/publications/eutroupdate/ . 

Bricker, Suzanne, pers. comm. 2009. NOAA/NOS Center for Coastal Monitoring and Assessment, Silver 

Spring, MD. 

Briggs, J.C. 1974. Marine Zoogeography. McGraw-Hill, New York. 475 p. 

Burgess, J., J.H. Dunnigan, J.S. Mechling, and E.C. Norton. 2005. NOAA’s Ecosystem Approach to 

Management. OCEANS 2005, Proceedings of MTS/IEEE, pp. 1-4. 

CEQ. 2009. Interim Framework for Effective Coastal and Marine Spatial Planning. The White House 

Council on Environmental Quality, Interagency Ocean Policy Task Force. December 9, 2009. 32 pp. 

http://www.whitehouse.gov/sites/default/files/microsites/091209-Interim-CMSP-Framework-TaskForce.pdf 

Coleman, D.E., P. Jokiel, E. Hill, and N. Bentivoglio. 2002. Better document management through 

georeferencing. ArcUser Online, Apri-June 2002. Environmental Science Research Institute, Redlands, 

CA. http://www.esri.com/news/arcuser/0402/docmanage1of3.html 

Cook, R.R., and P.J. Auster. 2007. A Bioregional Classification of the Continental Shelf of Northeastern 

North America for Conservation Analysis and Planning Based on Representation. Marine Sanctuaries 

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14 pp. http://sanctuaries.noaa.gov/science/conservation/continental.html 

Engle, Virginia. pers. comm. 2009. U.S. EPA, Gulf Breeze, FL. 

Greene, Emily. pers comm.. 2009. Atlantic States Marine Fisheries Commission, Washington, DC. 

Greene, K.E., J.L. Zimmerman, R.W. Laney, and J.C. Thomas-Blate. Atlantic Coast Diadromous Fish 

Habitat: A Review of Utilization, Threats, Recommendations for Conservation, and Research Needs. 

ASMFC Habitat Management Series #9. Atlantic States Marine Fisheries Commission, Washington, DC. 

464 p. 

Hammar-Klose, E.S., and E.R. Thieler. 2001. Coastal Vulnerability to Sea-Level Rise: A Preliminary 

Database for the U.S. Atlantic, Pacific and Gulf of Mexico Coasts. USGS Digital Data Series – 68. 

USGS Coastal and Marine Geology Program, Woods Hole, MA. http://pubs.usgs.gov/dds/dds68/ 

IUCN. 2006a. IUCN-CMP Unified Classification of Direct Threats, Version 1.0 – June 2006. IUCN – The 

World Conservation Union, CMP – The Conservation Measures Partnership. 

IUCN. 2006b. IUCN-CMP Unified Classification of Conservation Actions, Version 1.0 – June 2006. 

IUCN – The World Conservation Union, CMP – The Conservation Measures Partnership. 

55
 
 

 

 

 

 

 

 

Johnson, M.R., C. Boelke, L.A. Chiarella, P.D. Colosi, K. Greene, K. Lellis, H., Ludemann, M. Ludwig, S. 

McDermott, J. Ortiz, D. Rusanowsky, M. Scott, and J. Smith. 2008. Impacts to marine fisheries habitat 

from nonfishing activities in the Northeastern United States. NOAA/NMFS Northeast Fisheries Science 

Center, Woods Hole, MA. NOAA Tech. Memo. NMFS NE 209 

http://www.nefsc.noaa.gov/publications/tm/tm209/index.html 

Kemp, W.M., and E.B. Goldman. 2008. Thresholds in the Recovery of Eutrophic Coastal Ecosystems - 

A Synthesis of Research and Implications for Management. Maryland Sea Grant Publication Number 

UM-SG-TS-2008-01, Scientific and Technical Advisory Committee (STAC) Publication Number 08-002. 

http://www.mdsg.umd.edu/members/sandy/images/Thresholds_Report_web.pdf 

Kimbrough, K.L., W.E. Johnson, G.G. Lauenstein, J.D. Christensen, and D.A. Apeti. 2008. An 

Assessment of Two Decades of Contaminant Monitoring in the Nation's Coastal Zone. NOAA/NOS 

Center for Coastal Monitoring and Assessment, Silver Spring MD. NOAA Tech. Memo. NOS NCCOS 74. 

105 pp. http://ccma.nos.noaa.gov/stressors/pollution/nsandt/welcome.html . 

Kimbrough, K.L., W.E Johnson, G.G. Lauenstein, J.D. Christensen, and D.A. Apeti. 2009. An 

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Zone. NOAA/NOS Center for Coastal Monitoring and Assessment, Silver Spring MD. NOAA Tech. 

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Kimbrough, Kimani, pers. comm. 2009. NOAA/NOS Center for Coastal Monitoring and Assessment, 

Silver Spring, MD. 

Levin, P.S., M.J. Fogarty, G.C. Matlock, and M. Ernst. 2008. Integrated Ecosystem Assessments. NOAA 

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http://www.nwfsc.noaa.gov/assets/25/6801_07302008_144647_IEA_TM92Final.pdf 

Madden, C., K. Goodin, B. Allee, M. Finkbeiner, and D. Bamford. 2008. Coastal and Marine Ecological 

Classification Standard - DRAFT Version III. NOAA/NOS Coastal Services Center and NatureServe. 77 

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APPENDICES AND ATTACHMENTS 

Bibliographic Table – filename ACFHP_Biblio_Table_May29.xlsx 

Assessment Table – filename ACFHP_Assessment_Table_June1.xlsx 

Geospatial Table – filename ACFHP_Polygons_Table.xlsx 

Data Summary Tables – filenames Visual_Indicator_Summaries_Jun4.xlsx, ACFHP_Threats.xlsx, 

ACFHP_Actions.xlsx 

Metadata – filename ACFHP_Metadata.txt 

Microsoft Excel versions of these data tables are available upon request. 

Appendix 1: Timeline for the completion of this project 

June 2008 - Project proposal to ACFHP Steering Committee, Manchester NH. 

August 2008 - Workplan developed by ASMFC, CSS, and NOAA. 

October 2008 - ACFHP Steering Committee, Rehoboth DE. 

March 3, 2009: Poster presentation titled “A Geospatial Bibliography to Assess Existing Information on 

Atlantic Coastal Fish Habitat” at Coastal GeoTools Conference, Myrtle Beach SC. Proceedings available 

at http://www.csc.noaa.gov/geotools/documents/2009_preceedings.pdf
 

March 13, 2009: Deliver bibliographic and assessment tables and written status update to ASMFC, and 

launch first version publicly-available web application. 

March 19, 2009: Meet with ASMFC staff, and ACFHP Assessment Subcommittee (via WebEx and conf 

call), to present the work products (bibliography, assessment information, and web application) 

April 3, 2009: After making revisions based on Subcommittee’s comments, deliver final draft work 

products to ASMFC. 

April 21, 2009: Present work products (bibliography, assessment information, and web application) to 

ACFHP Steering Committee 

April 26, 2009: Oral presentation to Northeast Association of Fish and Wildlife Agencies (NEAFWA) 

conference, Symposium on Habitat Assessment, Lancaster PA, titled “Assessment of Existing Atlantic 

Coastal Fish Habitat Information Using a Bibliographic and Spatial Framework”. http://www.neafwa.org/ . 

May 31, 2009: After receiving feedback from the ACFHP Assessment Subcommittee and Steering 

Committee, final work products (data tables) delivered to ASMFC. 

June 2009 – Launch revised web-based queryable database for use by ACFHP 

July 6, 2009 - Draft final report delivered to ACFHP. 

July 21, 2009 – Poster presentation at CoastalZone’09, Boston MA, titled “A Spatial Bibliography to 

Assess Existing Information on Atlantic Coastal Fish Habitat”. Proceedings available at 

http://www.csc.noaa.gov/cz/ . 

July 23, 2009 – Oral presentation and discussion titled “A Spatial Bibliography to Assess Existing 

Information on Atlantic Coastal Fish Habitat” at NFHAP Coastal Assessment meeting, Grand Haven MI. 

July 31, 2009 - Final project summary report delivered to ACFHP for use in conservation planning. 

February 2010 – Results published as NOAA Tech. Memo., and final web query application launched. 

58
 
 

United States Department of Commerce 

Gary F. Locke 

Secretary 

National Oceanic and Atmospheric Administration 

Jane Lubchenco, Ph.D. 

Under Secretary of Commerce for Oceans and Atmosphere 

National Ocean Service 

John H. Dunnigan 

Assistant Administrator for Ocean Service and Coastal Zone Management