NOAA Technical Memorandum NOS NCCOS 129

Ecological Condition of Coastal Ocean Waters within 

Stellwagen Bank National Marine Sanctuary: 2008

NOAA Technical Memorandum NOS NCCOS 129

Ecological Condition of Coastal Ocean Waters within 

Stellwagen Bank National Marine Sanctuary: 2008

May 2011

U.S. Department of 

Commerce

National Oceanic and 

Atmospheric Administration

National Ocean Service

Silver Spring, MD 20910

Ecological Condition of Coastal Ocean Waters within Stellwagen Bank National Marine 

Sanctuary: 2008

May 2011

Prepared By

W. Leonard Balthis1, Jeffrey L. Hyland1, Cynthia Cooksey1, Michael H. Fulton1, Edward F. 

Wirth1, Donald Cobb2, David N. Wiley3

Author Affiliations

1 Center for Coastal Environmental Health and Biomolecular Research

National Oceanic and Atmospheric Administration

219 Fort Johnson Road

Charleston, SC 29412-9110

2 U.S. Environmental Protection Agency

ORD/NHEERL Atlantic Ecology Division

27 Tarzwell Drive

Narragansett, RI 02882

3 National Oceanic and Atmospheric Administration

Stellwagen Bank National Marine Sanctuary

175 Edward Foster Road

Scituate, MA 02066
ii

Preface

This document presents the results of an assessment of ecological condition and potential 

stressor impacts in coastal-ocean waters of the Stellwagen Bank National Marine Sanctuary 

(SBNMS), based on sampling conducted in June 2008. The project was a collaborative effort by 

the U.S. Environmental Protection Agency (EPA) and the National Oceanic and Atmospheric 

Administration (NOAA). It represents one of a series of studies, similar in protocol and design 

to EPA’s Environmental Monitoring and Assessment Program (EMAP) and subsequent National 

Coastal Assessment (NCA), which extend these prior efforts in estuaries and inland waters out to 

the coastal shelf, from navigable depths along the shoreline seaward to the shelf break 

(approximate 100 m depth contour). Ecological assessments in National Marine Sanctuaries 

provide a basis for comparing conditions in these protected areas to surrounding non-sanctuary 

waters.

The appropriate citation for this report is:

Balthis, W. L., J. L. Hyland, C. Cooksey, M. H. Fulton, E. F. Wirth, D. Cobb, D. N. Wiley. 2011. 

Ecological Condition of Coastal Ocean Waters within Stellwagen Bank National Marine 

Sanctuary: 2008. NOAA Technical Memorandum NOS NCCOS 129, NOAA National Ocean 

Service, Charleston, SC 29412-9110. 59 pp.

Disclaimer

This document has been subjected to review by the National Ocean Service of NOAA and the 

National Health and Environmental Effects Research Laboratory of EPA and approved for 

publication. Approval does not signify that the contents reflect the official views of these 

agencies, nor does mention of trade names or commercial products constitute endorsement or 

recommendation for use.
iii

Acknowledgments

This study was made possible through the coordination of resources and staff under a General 

Collaborative Agreement (MOA 2005-003/6764) between the NOAA National Ocean Service’s 

(NOS) National Centers for Coastal Ocean Science (NCCOS) and the EPA Office of Research 

and Development (ORD)/National Health and Environmental Effects Research Laboratory 

(NHEERL). Funding was provided primarily by the NOAA/NCCOS Center for Coastal 

Environmental Health and Biomolecular Research (CCEHBR) to support sampling design, field 

work, and sample processing; EPA/NHEERL-Gulf Ecology Division for water-column nutrient 

analysis; and EPA/NHEERL/AED for field sampling. Field work was conducted on the NOAA 

Ship Nancy Foster Cruise NF-08-09-CCEHBR by scientists from NOAA/NCCOS/CCEHBR and 

EPA/NHEERL-Atlantic Ecology Division. Several institutions participated in the processing of 

samples. These included Barry Vittor and Associates (Mobile, AL) for the analysis of benthic 

samples and determination of sediment grain size and TOC; NOAA/NCCOS/CCEHBR for 

sediment toxicity testing and analysis of chemical contaminants in sediments and fish tissues; 

and B&B Laboratories (College Station, TX) for analysis of nutrients and chlorophyll in water 

samples. 
iv
v

Table of Contents

1.0 Introduction ................................................................................................................. 1

2.0 Methods....................................................................................................................... 3

2.1 Sampling Design and Field Collections................................................................... 3

2.2 Water Quality Analysis............................................................................................ 6

2.3 Sediment TOC and Grain Size Analysis.................................................................. 6

2.4 Chemical Contaminant Analysis.............................................................................. 6

2.4.1 Laboratory Sample Preparation ........................................................................ 6

2.4.2 Inorganic Sample Digestion and Analysis........................................................ 6

2.4.3 Organic Extraction and Analysis...................................................................... 7

2.5 Benthic Community Analysis .................................................................................. 7

2.6 Sediment Toxicity Testing ....................................................................................... 8

2.7 Data Analysis ........................................................................................................... 8

3.0 Results and Discussion.............................................................................................. 12

3.1 Depth and Water Quality........................................................................................ 12

3.1.1 Depth............................................................................................................... 12

3.1.2 General Water Characteristics ........................................................................ 12

3.1.3 Nutrients and Chlorophyll............................................................................... 17

3.2 Sediment Quality.................................................................................................... 21

3.2.1 Grain Size and TOC........................................................................................ 21

3.2.2 Chemical Contaminants in Sediments............................................................ 24

3.2.3 Sediment Toxicity........................................................................................... 30

3.3 Chemical Contaminants in Fish Tissues ................................................................ 30

3.4 Status of Benthic Communities.............................................................................. 35

3.4.1 Taxonomic Composition................................................................................. 35

3.4.2 Abundance and Dominant Taxa...................................................................... 38

3.4.3 Diversity.......................................................................................................... 38

3.4.4 Patterns of biogeographic distribution............................................................ 42

3.4.5 Non-indigenous Species.................................................................................. 46

3.5 Potential Linkage of Biological Condition to Stressor Impacts............................. 46

4.0 Literature Cited.......................................................................................................... 48

5.0 Appendices................................................................................................................ 54
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List of Figures

Figure 1. Map showing location of Stellwagen Bank National Marine Sanctuary (SBNMS) in the 

Gulf of Maine.................................................................................................................................. 1

Figure 2. Map of SBNMS study area location and sampling sites. ............................................... 5

Figure 3. Percent area (and 95% confidence intervals) of SBNMS waters vs. selected waterquality characteristics.................................................................................................................... 15

Figure 4. Percent area (and 95% confidence intervals) of SBNMS waters vs. nutrient, 

chlorophyll, and TSS concentrations. ........................................................................................... 16

Figure 5. Bottom-water concentrations of dissolved inorganic nitrogen (DIN).......................... 19

Figure 6. Relationship of bottom-water dissolved nitrogen (DIN and its constituent components) 

to depth and bottom salinity.......................................................................................................... 20

Figure 7. Distribution of percentages of gravel, sand, and silt-clay in surficial sediments.......... 21

Figure 8. Percent gravel, sand, and silt-clay content of sediments.............................................. 22

Figure 9. (A) Percent area (and 95% confidence intervals) represented by varying levels of siltclay content of sediment (mg/g), and (B) percent area having TOC content within specified 

ranges. ........................................................................................................................................... 23

Figure 10. (A) Percent area (and 95% confidence intervals) represented by varying levels of 

TOC content of sediment (mg/g), and (B) percent area having TOC content within specified 

ranges. ........................................................................................................................................... 23

Figure 11. Plot of mean ERM quotient versus sediment % silt-clay. ........................................... 25

Figure 12. Plot of mean ERM quotient versus TOC content of sediment. ................................... 25

Figure 13. Mean ERM quotients (mean ERM-Q) calculated based on measured contaminant 

concentrations in sediments. ......................................................................................................... 29

Figure 14. Relative percent composition of major taxonomic groups expressed as percent of 

total taxa and percent of abundance.............................................................................................. 36

Figure 15. Percent area (and 95% confidence intervals) of SBNMS study area vs. benthic 

infaunal taxonomic richness (A), density (B), and H' diversity (C) ............................................. 41

Figure 16. Dendrogram resulting from hierarchical cluster analysis............................................ 43

Figure 17. Ordination plot derived from non-metric multidimensional scaling (NMDS)............ 44

Figure 18. Plot of mean density (#/m2) versus sediment % silt-clay. ........................................... 45

Figure 19. Plot of mean density (#/m2) versus TOC content of sediment. ................................... 45

Figure 20. Plot of mean # of taxa (per 0.04 m2) versus TOC content of sediment....................... 46
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List of Tables

Table 1. Thresholds used for classifying samples relative to various environmental indicators... 9

Table 2. ERM and ERL guideline values in sediments (Long et al. 1995). ................................ 11

Table 3. Risk-based EPA advisory guidelines for recreational fishers (USEPA 2000a)............. 12

Table 4. Summary of depth and water-column characteristics for near-bottom (lower 3 m) and 

near-surface (0.5 - 4 m) waters. .................................................................................................... 14

Table 5. Summary of sediment characteristics. ........................................................................... 23

Table 6. Summary of chemical contaminant concentrations in sediments. ................................ 27

Table 7. Listing of fish specimens retained for tissue contaminant analysis and the stations 

where they were collected............................................................................................................. 30

Table 8. Listing of stations where concentrations of contaminants in fish tissues exceeded 

corresponding risk-based human-health guidelines...................................................................... 32

Table 9. Summary of contaminant concentrations (wet weight) measured in fish tissues.......... 33

Table 10. Summary of major taxonomic groups of benthic infauna and corresponding numbers of 

identifiable taxa based on 60 0.04-m

2 grab samples..................................................................... 37

Table 11. Mean, range, and selected distributional properties of key benthic variables. ............ 39

Table 12. Fifty most abundant benthic taxa................................................................................. 40
viii

List of Appendices

Appendix A. Locations (latitude, longitude), depth, and sediment characteristics of sampling 

stations. ......................................................................................................................................... 55

Appendix B. Near-bottom water characteristics by station. ........................................................ 56

Appendix C. Near-surface water characteristics by station......................................................... 57

Appendix D. Summary by station of mean ERM quotients and the number of contaminants that 

exceeded corresponding ERL or ERM values. ............................................................................. 58

Appendix E. Summary by station of benthic macroinfaunal (>0.5mm) characteristics. ............. 59
ix

List of Acronyms

ASE Accelerated Solvent Extraction

CCMA Center for Coastal Monitoring and Assessment

CDF Cumulative Distribution Function

Chl a Chlorophyll a

CRM Certified Reference Material

CTD Conductivity-Temperature-Depth

CV Coefficient of Variation

CVAA Cold Vapor Atomic Absorption

CWA Clean Water Act

DDT Dichlorodiphenyltrichloroethane

DIN Dissolved Inorganic Nitrogen

DIP Dissolved Inorganic Phosphate

DO Dissolved Oxygen

DQO Data Quality Objectives

EAM Ecosystem Approach to Management

EC50 Effective Concentration that reduces light output by 50% relative to controls

EI Electron-impact Ionization

EMAP Environmental Monitoring and Assessment Program

EPA Environmental Protection Agency

ERL Effects-Range Low

ERM Effects-Range Median

ERM-Q Effects-Range Median Quotient

GC/MS Gas Chromatography/Mass Spectrometry

GFAA Gas Flame Atomic Absorption

GMCC Gulf of Maine Coastal Current

GRTS Generalized Random Tessellation Stratified

ICP-MS Inductively Coupled Plasma-Mass Spectrometry

LCM Laboratory Control Materials

MAB Mid-Atlantic Bight

MBDS Massachusetts Bay Disposal Site

MDL Method Detection Limit

MIT Massachusetts Institute of Technology

MITIS Marine Invader Tracking Information System

MWRA Massachusetts Water Resources Authority

NAS National Aquatic Species database

NCA National Coastal Assessment

NCCOS National Centers for Coastal Ocean Science

NCI Negative Chemical Ionization

NEMESIS National Exotic Marine and Estuarine Species Information System

NMDS Non-metric Multidimensional Scaling

NMS National Marine Sanctuaries

NMSP National Marine Sanctuary Program

NOAA National Oceanic and Atmospheric Administration

NS&T National Status and Trends program
x

PAH Polycyclic Aromatic Hydrocarbon

PBDE Polybrominated Diphenyl Ether

PCB Polychlorinated Biphenyl

RPD Relative Percent Difference

SAB South Atlantic Bight

SBE Sea-Bird Electronics

SBNMS Stellwagen Bank National Marine Sanctuary

SEC Size Exclusion Chromatography

SQG Sediment Quality Guideline

SRM Standard Reference Material

TOC Total Organic Carbon

TSS Total Suspended Solids

UPGMA Unweighted Pair Group Method using Arithmetic mean 

USGS U.S. Geological Survey
xi

Executive Summary

In June 2008, the NOAA National Ocean Service (NOS), in conjunction with the EPA National 

Health and Environmental Effects Laboratory (NHEERL), conducted an assessment of the status 

of ecological condition of soft-bottom habitat and overlying waters within the boundaries of 

Stellwagen Bank National Marine Sanctuary (SBNMS). The sanctuary lies approximately 20 

nautical miles east of Boston, MA in the southwest Gulf of Maine between Cape Ann and Cape 

Cod and encompassing 638 square nautical miles (2,181 km2). A total of 30 stations were 

targeted for sampling using standard methods and indicators applied in prior NOAA coastal 

studies and EPA’s Environmental Monitoring and Assessment Program (EMAP) and National 

Coastal Assessment (NCA). A key feature adopted from these studies was the incorporation of a 

random probabilistic sampling design. Such a design provides a basis for making unbiased 

statistical estimates of the spatial extent of ecological condition relative to various measured 

indicators and corresponding thresholds of concern. Indicators included multiple measures of 

water quality, sediment quality, and biological condition (benthic fauna, fish tissue contaminant 

levels).

Depths ranged from 31 – 137 m throughout the study area. About 76 % of the area had 

sediments composed of sands (< 20 % silt-clay), 17 % of the area was composed of intermediate 

muddy sands (20 – 80 % silt-clay), and 7 % of the sampled area consisted of mud (> 80 % siltclay). About 70 % of the area (represented by 21 sites) had sediment total organic carbon (TOC)

concentrations < 5 mg/g and all but one site (located in Stellwagen Basin) had levels of TOC < 

20 mg/g, which is well below the range potentially harmful to benthic fauna (> 50 mg/g).

Surface salinities ranged from 30.6 – 31.5 psu, with the majority of the study region 

(approximately 80 % of the area) having surface salinities between 30.8 and 31.4 psu. Bottom 

salinities varied between 32.1 and 32.5 psu, with bottom salinities at all sites having values 

above the range of surface salinities. Surface-water temperatures varied between 12.1 and 16.8

oC, while near-bottom waters ranged in temperature from 4.4 – 6.2 oC. An index of density 

stratification (Δσt) indicated that the waters of SBNMS were stratified at the time of sampling. 

Values of Δσt at 29 of the 30 sites sampled in this study (96.7 % of the study area) varied from 

2.1 – 3.2, which is within the range considered to be indicative of strong vertical stratification 

(Δσt > 2) and typical of the western Gulf of Maine in summer.

Levels of dissolved oxygen (DO) were confined to a fairly narrow range in surface (8.8 – 10.4

mg/L) and bottom (8.5 – 9.6 mg/L) waters throughout the survey area. These levels are within 

the range considered indicative of good water quality (> 5 mg/L) with respect to DO. None of 

these waters had DO at low levels (< 2 mg/L) potentially harmful to benthic fauna and fish.

Total suspended solids (TSS) in surface waters ranged from 2.4 – 9.1 mg/L, with slightly higher 

values observed in bottom waters (3.4 – 15.1 mg/L). Most sites (90 % of the area sampled) had 

concentrations of bottom-water TSS < 9.1 mg/L.

Dissolved inorganic nitrogen (DIN: nitrogen as nitrate + nitrite + ammonium) in surface waters 

of SBNMS ranged from 0.03 mg/L to 0.56 mg/L and averaged 0.09 mg/L. Ninety percent of the 

study area surface waters had DIN concentrations < 0.07 mg/L. Bottom-water concentrations of 
xii

DIN tended to be higher than surface concentrations. For example, about 50% of bottom waters 

had DIN > 0.55 mg/L (near the maximum surface-water concentration of 0.56 mg/L) and the 

average concentration was 0.51 mg/L (range of 0.06 – 0.74 mg/L). Bottom-water DIN levels 

were higher at deeper sites in the sanctuary compared to shallower sites. 

Concentrations of dissolved inorganic phosphorus (DIP) in surface waters ranged between 0.02 

mg/L and 0.12 mg/L, averaging 0.03 mg/L. Ninety percent of the study area surface waters had 

DIP concentrations < 0.04 mg/L. While the range of bottom-water concentrations of DIP (0.02 

mg/L to 0.14 mg/L) were similar to those measured in surface waters, the mean (0.11 mg/L) and 

estimated percentiles were higher. Half of the study area had bottom-water DIP concentrations 

that were greater than the maximum surface DIN concentration (0.12 mg/L). 

DIN:DIP ratios in surface waters ranged from 1.98 to 10.57 (mean of 3.73), which are strongly 

indicative of nitrogen limitation (DIN:DIP < 16). 

Surface-water concentrations of chlorophyll a, an indicator of phytoplankton biomass and 

abundance, ranged from 0.31 μg/L to 1.65 μg/L and averaged 0.57 μg/L. Bottom-water 

concentrations of chlorophyll a were similar to concentrations in surface waters, ranging 

between 0.07 μg/L and 1.12 μg/L and averaging 0.36 μg/L.

Bottom sediments of SBNMS appeared to be relatively uncontaminated. No contaminants were 

found in excess of their corresponding Effects-Range Median (ERM) sediment quality guideline 

values. The entire survey region was rated in good condition (no chemicals above corresponding 

ERM values and < 5 chemicals above corresponding Effects-Range Low (ERL) values). Arsenic 

was one of only three chemicals that exceeded their corresponding ERL guidelines. The ERL 

exceedances for arsenic occurred at eleven sites, representing an estimated 36.7 % of the survey 

area. The concentration of arsenic at most sites (28 sites, 93% area) was within the range typical 

of uncontaminated near-shore marine sediments (5 – 15 μg/g dry weight total arsenic) and 

reflects its natural presence at low to moderate concentrations in crustal rocks of the region. 

Arsenic concentrations greater than 15 μg/g dry weight were found at two sites (stations 3 and 

20) in the northern part of the sanctuary. Concentrations of lead and mercury in excess of the 

corresponding ERLs were observed at only one site (station 1) which was located in a deep, silty 

area of Stellwagen Basin approximately 4 nautical miles southeast of the Massachusetts Bay 

Disposal Site

Concentrations of a suite of metals, pesticides, and PCBs were measured in edible tissues (fillets) 

of 26 fish specimens (representing five distinct species) collected at 16 of the 30 stations and 

compared to risk-based EPA advisory guidelines for recreational fishers. Two of the 16 stations 

where fish were collected and retained for analysis had chemical contaminants in tissues above 

the corresponding upper human-health endpoints. The exceedances at these sites were for 

methylmercury (station 3, measured as total mercury and assumed to be all methylmercury) and 

total PCB (station 17). Stations 3 and 17 were located in a deep area adjacent to Gloucester 

Basin in the northern part of the sanctuary and in the southwest portion of the sanctuary in 

Stellwagen Basin, respectively. Lower human-health endpoints also were exceeded at one of the 

above sites and at an additional six sites, one of which had multiple exceedances. The 

exceedances of lower human-health guidelines were for methylmercury (measured as total 
xiii

mercury, as above) and inorganic arsenic. Thus, two of the 16 sites would be rated as “poor” 

with respect to contaminants in fish tissues according to EPA advisory guidelines, six would be 

rated as “fair”, and the remaining eight sites would be rated as “good”. The status with respect to 

fish tissue contamination of the remaining 14 sites where no fish were collected could not be 

determined.

Benthic taxonomic richness was relatively high in SBNMS assemblages, ranging from 10 – 45

per 0.04-m

2 grab and averaging 30 taxa/grab. Diversity (Shannon H′ (log2)) averaged 3.6

overall, varying between 2.8 and 4.5 throughout the study area, and tended to be lowest among 

deeper, depositional sites in Stellwagen and Gloucester Basins. A total of 330 taxa were 

identified in the 60 grabs collected throughout the study area, of which 160 were identified to 

species level. Polychaetes, crustaceans, and molluscs were the dominant taxa both by percent 

abundance (69 %, 15 %, and 8 %, respectively) and percent of taxa (38 %, 33 %, and 20 %, 

respectively). Densities ranged from 612 – 15,500 ind/m

2 and averaged 6,723 ind/m2

.

The 10 dominant (most abundant) taxa, in decreasing order of abundance, included the syllid 

polychaete (Family Syllidae) Exogone verugera; maldanid polychaetes (Maldanidae); sabellid 

polychaetes (Sabellidae); the sabellid polychaete genus Chone; the polychaetes Axiothella 

mucosa (Maldanidae), Prionospio steenstrupi (Spionidae), and Parapionosyllis longicirrata

(Syllidae); the gammarid amphipod genus Unciola; the polychaete Exogone hebes; and tubificid 

oligochaetes (Tubificidae). Shallow, sandy sites on Stellwagen Bank were dominated by 

maldanid and syllid polychaetes (mean densities of 2,129 ind/m2 and 2,014 ind/m2 for families 

Maldanidae and Syllidae, respectively). Densities and numbers of taxa were lowest in the 

deeper, depositional areas of Stellwagen and Gloucester Basins. Infaunal assemblages in the 

remainder of the sanctuary were characterized by high diversity and richness (number of taxa).

A small number of species collected as part of the 2008 SBNMS survey (i.e., Harmothoe 

imbricata) are considered to be cryptogenic (Ruiz et al. 2000). The only non-indigenous species 

identified in the present study was the gammarid amphipod Microdeutopus gryllotalpa, found at 

a single station (station 21). This species was listed in the SBNMS Final Management Plan and 

Environmental Assessment as a known invasive to the Gulf of Maine region, but had not yet 

been documented in SBNMS.

This study found no evidence of biological impacts linked to measured stressors. In fact, no 

indications of poor sediment or water quality relative to published evaluation thresholds were 

observed. These results suggest that waters and sediments of SBNMS are in good condition, 

with lower-end values of biological attributes representing parts of a normal reference range 

controlled by natural factors. Some influence of habitat type on infaunal density, diversity, and 

taxonomic richness was observed, with the shallower, sandy areas of Stellwagen Bank and the 

deeper, depositional regions of Stellwagen and Gloucester Basins emerging as distinct habitats, 

as described above.

It is possible that for some of these sites the lower values of benthic variables reflect symptoms 

of disturbance induced by other unmeasured stressors. In efforts to be consistent with the 

underlying concepts and protocols of earlier EMAP and NCA programs, the indicators in this 

study included measures of stressors, such as chemical contaminants and symptoms of 
xiv

eutrophication, which are often associated with adverse biological impacts in shallower estuarine 

and inland ecosystems. However, there may be other sources of human-induced stress in these 

offshore systems, particularly those causing physical disruption of the seafloor (e.g., commercial 

bottom trawling, cable placement, minerals extraction), that pose greater risks to living resources 

and which have not been captured adequately. Future monitoring efforts in these offshore areas 

should include indicators of such alternative sources of disturbance.
1.0 Introduction 

The National Oceanic and Atmospheric Administration (NOAA) and the Environmental 

Protection Agency (EPA) each perform a broad range of research and monitoring activities 

designed to assess the status of coastal ecosystems and the potential effects of natural and human 

impacts. Authority to conduct such work is given by several legislative mandates including the 

Clean Water Act (CWA) of 1977 (33 U.S.C. §§ 1251 et seq.), National Coastal Monitoring Act 

of 1992 (Title V of the Marine Protection, Research, and Sanctuaries Act, 33 U.S.C. §§ 2801-

2805), and the National Marine Sanctuary Act of 2000. To the extent possible, the two agencies 

have sought to coordinate related activities through partnerships with states and other institutions 

to prevent duplication of effort and to bring together complementary resources to fulfill common 

research and management goals. Accordingly, in June 2008, NOAA and EPA conducted a joint 

survey of ecological conditions in Stellwagen Bank National Marine Sanctuary (SBNMS). The 

sanctuary is located in the southwest part of the Gulf of Maine, located approximately 20 

nautical miles east of Boston and encompassing 638 square nautical miles (2,181 km2) of coastal 

ocean waters between Cape Ann and Cape Cod (Figure 1). 

Figure 1. Map showing location of Stellwagen Bank National Marine Sanctuary (SBNMS) in the Gulf of 

Maine. 
2

The present survey is part of a series of studies being conducted by NOAA and EPA to assess the 

condition of aquatic resources throughout coastal-ocean waters of the U.S. using multiple 

indicators of ecological condition. The protocols and design of these studies are similar to those 

used in EPA’s Environmental Monitoring and Assessment Program (EMAP) and subsequent 

National Coastal Assessment (NCA), both of which have focused mainly on estuarine and inland 

waters. The offshore series extends these prior efforts onto the continental shelf, from 

approximately one nautical mile of the shoreline seaward to the shelf break (~100-m depth 

contour). Where applicable, sampling has included NOAA’s National Marine Sanctuaries 

(NMS) to provide a basis for comparing conditions in these protected areas to surrounding nonsanctuary waters. To date such surveys have been conducted throughout the western U.S. 

continental shelf, from the Straits of Juan de Fuca, WA to the U.S./Mexican border (Nelson et al. 

2008); shelf waters of the South Atlantic Bight (SAB) from Cape Hatteras, NC to West Palm 

Beach, FL (Cooksey et al. 2010); shelf waters of the mid-Atlantic Bight (MAB) from Cape 

Hatteras to Cape Cod, MA (Balthis et al. 2009); the continental shelf off southern Florida, from 

West Palm Beach in the Atlantic Ocean to Anclote Key in the Gulf of Mexico (see Cooksey and 

Hyland 2007 for cruise report); and the continental shelf along northeastern Gulf of Mexico (see 

Cooksey et al. 2010 for cruise report). Plans are underway to continue these surveys throughout 

the remaining portions of the Gulf of Mexico west of the Mississippi Delta and the New England 

coast north of Cape Cod. 

The purpose of the present study was to assess the current status of ecological condition and 

stressor impacts in SBNMS and to provide this information as a framework for evaluating future 

changes due to natural or human-induced disturbances. To address this objective, the study 

incorporated standard methods and indicators applied in previous coastal EMAP/NCA projects 

(U.S. EPA 2001a, 2004, 2008) including multiple measures of water quality, sediment quality, 

and biological condition (benthic community health and fish tissue contamination). Synoptic 

sampling of the various indicators provided an integrative weight-of-evidence approach to 

assessing condition at each station and a basis for examining potential associations between the 

presence of stressors and biological responses. Another key feature was the incorporation of a 

probabilistic sampling design with stations (30 in total) positioned randomly throughout the 

study area. The probabilistic sampling design provided a basis for making unbiased statistical 

estimates of the spatial extent of condition relative to the various measured indicators and 

corresponding thresholds of concern. Other surveys in the current coastal-ocean series have 

applied stratified random sampling designs, with stations stratified by NMS vs. non-sanctuary 

status. However, since the present study was restricted to coastal ocean waters within the 

sanctuary boundaries, the assessment of condition relative to these various indicators did not 

include sanctuary vs. non-sanctuary comparisons.

Because the protocols and indicators are consistent with those used in previous EMAP/NCA 

estuarine surveys, comparisons can be made between conditions in offshore waters and those 

observed in neighboring estuarine habitats, thus providing a more holistic account of ecological 

conditions and processes throughout the inshore and offshore resources of the region. Such 

information should provide valuable input for future National Coastal Condition Reports, which 

historically have included limited coverage in offshore areas (e.g., U.S. EPA 2001a, 2004, 2008).
3

Results of this study should also provide valuable support to evolving interests within the U.S. 

and other parts of the world to move toward an ecosystem approach to management (EAM) of 

coastal resources (Murawski 2007; Marine Ecosystems and Management 2007). While the focus 

of the present study is on indicators of ecological condition, some human-dimension indicators 

have been included as well (e.g., fish contaminant levels relative to human-health guidelines, 

water clarity, marine debris, foul odors, oil slicks), which can be used to help address common 

public concerns such as “Are the fish safe to eat?” or “Is the water clean enough to swim in?” 

Humans are considered as both sources and receptors of ecosystem impacts in the EAM process.

This report attempts to describe the status of ecological condition in SBNMS with respect to the 

parameters measured in this study. A number of other publications are available which describe 

the sanctuary setting in general, its geology, oceanography, biological resources and habitat, and 

its commercial, recreational, and historical context. The Stellwagen Bank National Marine 

Sanctuary Final Management Plan and Environmental Assessment (U.S. Department of 

Commerce 2010) is one excellent source of information. In addition, an ecological 

characterization of SBNMS was conducted by the National Centers for Coastal Ocean Science 

(NCCOS), Center for Coastal Monitoring and Assessment (CCMA) in partnership with the 

National Marine Sanctuary Program (NMSP) in 2006, which describes physical, contaminant, 

and biological patterns of the SBNMS region (NCCOS 2006). These reports, together with other 

sources of information in the peer-reviewed literature (some of which are cited later in this 

report), provide a description of the processes influencing conditions in SBNMS and which place 

it in the larger context of the Gulf of Maine ecosystem.

2.0 Methods

2.1 Sampling Design and Field Collections

The sampling frame for this study was based on a generalized random-tessellation stratified 

(GRTS) design. The GRTS design represents a unified strategy for selecting spatially balanced 

probability samples of natural resources, in which sampling sites are more or less evenly 

dispersed over the extent of the resource (Stevens & Olsen 2004). Sampling was conducted from 

June 17 – 21, 2008 at 30 stations located within the boundaries of SBNMS (Figure 2, Appendix 

A).

Vertical water-column profiles of conductivity/salinity, temperature, depth, dissolved oxygen, 

and pH were conducted at each station using a Sea-Bird Electronics (SBE) ConductivityTemperature-Depth (CTD) profiler, equipped with supplemental dissolved oxygen and pH 

sensors. The CTD was an SBE 9Plus with an 11Plus deck unit that provided real-time data 

recording of the vertical profile. The CTD was incorporated into a frame that included a rosette 

of 12 Nisken bottles used to collect water samples at discrete depths (near-surface, near-bottom). 

Water samples were analyzed for nutrients, total suspended solids (TSS), and chlorophyll a. 

The CTD was lowered into the water until completely submerged and held just beneath the 

surface for three minutes while the water pump was allowed to purge any air from the system. 

The unit was then lowered to within one meter of the bottom at a rate of approximately 1 m s-1

. 
4

Four Nisken bottles were fired at approximately 1 m below the surface and another four at nearbottom (approximately 1 m off the bottom).

Sediment samples were collected using a 0.04-m

2 Young-modified Van Veen grab sampler. 

Two replicate grab samples were retained for analysis of benthic infaunal composition, sieved 

onboard through a 0.5-mm screen, and preserved in 10% buffered formalin with rose bengal 

stain. The upper 2 – 3 cm of sediment from additional grabs (typically 1 or 2) was combined to 

yield a sediment composite, which was then homogenized and sub-sampled for analysis of 

metals, organic contaminants (pesticides, PCBs, PAHs, PBDEs), grain size (% silt-clay), and 

total organic carbon (TOC). Sediment samples (other than infauna) were kept frozen onboard 

the ship and later transferred to the respective analytical laboratories for analysis.

Hook-and-line fishing was attempted at all 30 stations. Targeted species included members of 

the orders Pleuronectiformes (flatfishes) and Gadiformes (cod, hake, haddock) , family Sparidae 

(porgies, scup), and the genera Centropristis (sea basses) and Sebastes (rockfishes). Specimens 

from three (Pleuronectiformes, Gadiformes, Sebastes) of the five groups listed above were 

collected from 18 of the 30 stations. Edible tissue (fillets) of 26 specimens from 16 of these 

stations was analyzed for metals, pesticides, PAHs, PCBs, and PBDEs.
5 

Figure 2. Map of SBNMS study area location and sampling sites. 
6

2.2 Water Quality Analysis

Readings of temperature, conductivity/salinity, dissolved oxygen, depth, and pH were recorded 

directly from the CTD unit during its descent and ascent through the water column. An index of 

density stratification (Δσt) was calculated as the difference between the computed bottom and 

surface density (σt) values, where σt is the density of a parcel of water with a given salinity and 

temperature relative to atmospheric pressure (Fofonoff and Millard 1983). Dissolved inorganic 

nutrients, including nitrate (NO3

-

), nitrite (NO2

-

), orthophosphate (HPO4

2-

), silicate (HSiO3

-

), and 

ammonium (NH4

+

); chlorophyll a; and total suspended solids (TSS) were sampled at discrete 

water depths (near surface, mid-water, and near-bottom) and analyzed following standard 

methods (U.S. EPA 1997; U.S. EPA 1995). Only surface and bottom values for these various 

indicators are presented in this report. Data for all depths are included in the study database and 

are available on request to the authors.

2.3 Sediment TOC and Grain Size Analysis

Samples for grain size analysis were homogenized and diluted to a suspended slurry with the aid 

of a chemical dispersant and the suspension was passed through a 63μm sieve. The fine fraction 

passing through the sieve (< 63μm) and the coarse fraction retained on the sieve (> 63μm) were 

separately dried and weighed (see U.S. EPA 1995). Total organic carbon (TOC) was determined 

by combusting pre-acidified samples at high temperature and measuring the volume of carbon 

dioxide gas produced (U.S. EPA 1995).

2.4 Chemical Contaminant Analysis

2.4.1 Laboratory Sample Preparation

Sediment samples were kept frozen at approximately - 40 oC prior to analysis. Samples were 

thawed in closed containers in a 4 oC cooler for approximately 24 hours. Prior to extraction, 

samples were homogenized thoroughly by hand. Fish tissue samples were frozen upon receipt in 

the laboratory and stored at - 40 oC until analysis. Fish were removed from the freezer and 

stored overnight at 4 oC and allowed to thaw partially. The fish were filleted (skin-on) and 

homogenized well using a ProScientific homogenizer in 500 mL Teflon containers. The 

homogenized tissue sample was split into organic (pre-cleaned glass container) and inorganic 

(pre-cleaned polypropylene container) aliquots and stored at - 40 oC until extraction or digestion. 

A percent dry-weight determination was made gravimetrically on an aliquot of the wet sediment 

and tissues.

2.4.2 Inorganic Sample Digestion and Analysis

Dried sediment was ground with a mortar and pestle and transferred to a 20 mL plastic screw-top 

container. A 0.25-g sub-sample of the ground material was transferred to a Teflon-lined 

digestion vessel and digested in 5 mL of concentrated nitric acid using microwave digestion. 

The sample was brought to a fixed volume of 50 mL in a volumetric flask with deionized water 

and stored in a 50-mL polypropylene centrifuge tube until instrumental analysis of Li, Be, Al, 

Fe, Mg, Ni, Cu, Zn, Cd, and Ag. A second 0.25-g sub-sample was transferred to a Teflon-lined 
7

digestion vessel and digested in 5 mL of concentrated nitric acid and 1 mL of concentrated 

hydrofluoric acid in a microwave digestion unit. The sample was then evaporated on a hot plate 

at 225 °C to near dryness and 1 mL of nitric acid was added. The sample was brought to a fixed 

volume of 50 mL in a volumetric flask with deionized water and stored in a 50 mL 

polypropylene centrifuge tube until instrumental analysis for V, Cr, Co, As, Sn, Sb, Ba, Tl, Pb, 

and U. Selenium was analyzed by hot plate digestion using a third 0.25-g sub-sample and 5 mL 

of concentrated nitric acid. Each sample was brought to a fixed volume of 50 mL in a 

volumetric flask with deionized water and stored in a 50 mL polypropylene centrifuge tube until 

instrumental analysis. Additionally, two to three grams wet tissue were microwave-digested in 

Teflon-lined digestion vessels using 10 mL of concentrated nitric acid along with 2 mL of 

hydrogen peroxide. Digested samples were brought to a fixed volume with deionized water in 

graduated polypropylene centrifuge tubes and stored until analysis. Finally, a separate inorganic 

aliquot was used for mercury analysis for both sediments and tissues. Approximately 0.5 g of 

wet sediment or tissue was analyzed on a Milestone DMA-80 Direct Mercury Analyzer. 

All remaining elemental analyses were performed using Inductively Coupled Plasma Mass

Spectrometry (ICP-MS) except for silver, which was determined using Graphite Furnace Atomic

Absorption (GFAA) spectroscopy. Data quality was controlled by using a series of blanks,

control solutions (Trace Metals in Drinking Water), and standard reference materials including 

NRC MESS-3 (Marine Sediments) and NIST 1566b (freeze-dried mussel tissue).

2.4.3 Organic Extraction and Analysis

An aliquot (10 g sediment or 5 g tissue wet weight) was extracted with anhydrous sodium sulfate 

using Accelerated Solvent Extraction (ASE) in either 1:1 methylene chloride:acetone (sediments) 

or 100% dichlormethane (tissues) (Schantz et al. 1997). Following extraction, samples were 

dried and cleaned using Gel Permeation Chromatography and Solid Phase Extraction to remove 

lipids and then solvent-exchanged into hexane for analysis. Samples were analyzed for PAHs, 

PBDEs, PCBs (by congener), and a suite of chlorinated pesticides using appropriate GC/MS 

technology. Data quality was assured by using a series of spiked blanks, reagent blanks, and 

appropriate standard reference materials including NIST 1944 (sediments) and NIST 1974b 

(mussel tissue). 

2.5 Benthic Community Analysis

Identification and enumeration of benthic fauna was performed by Barry A. Vittor & Associates, 

Inc., Mobile, Alabama. Only skilled taxonomists conducted organism identification. A 

minimum of 10% of samples were rechecked by other qualified taxonomists for accuracy in 

identification and enumeration. Species lists from different labs were cross-checked, with 

external experts consulted for difficult identifications. Judged accuracy rates were well above 

standard levels for sorting and taxonomy (quality control reworks all > 95 %).

Characteristics of benthic communities were assessed using standard measures of total faunal 

abundance (density/m2

), individual species abundances, species richness (number of taxa), and 

diversity (Shannon H′; Shannon 1948, Hayek and Buzas 1997). H′ was calculated using base-2 

logarithms. Total faunal abundance was used to rank dominant taxa. Taxa were grouped 
8

according to higher taxonomic classifications to determine relative percentages (by abundance 

and number of taxa) of major groups of organisms (i.e., polychaetes, crustaceans, molluscs, 

echinoderms, other taxa). The full list of identified taxa was examined to evaluate the incidence 

of non-indigenous species vs. native species or ones with indeterminate status relative to 

invasiveness. Spatial patterns in benthic faunal distributions were also examined using a 

combination of hierarchical cluster analysis and non-metric multidimensional scaling (Clarke & 

Warwick 2001). 

2.6 Sediment Toxicity Testing

Microtox® assays were conducted using the standardized solid-phase test protocols (Microbics 

Corporation 1992) and a Microtox Model 500 analyzer (Strategic Diagnostics Inc., Newark, DE). 

In this assay, sediment was homogenized and a 7.0 – 7.1 g sediment sample was used to make a 

series of sediment dilutions with 3.5% NaCl diluent, which were incubated for 10 minutes at 15 

oC. Luminescent bacteria (Vibrio fisheri) were then added to the test concentrations. The liquid 

phase was filtered from the sediment phase and bacterial post-exposure light output was 

measured using Microtox Omni Software. An EC50 value (the sediment concentration that 

reduces light output by 50% relative to the controls) was calculated for each sample. Triplicate 

samples were analyzed simultaneously. Sediment samples were classified as either toxic or 

nontoxic using criteria developed by Ringwood et al. (1997; Table 1 herein).

2.7 Data Analysis

The probabilistic sampling design used in this study allows calculation of estimates of the 

percent area of the resource that corresponds to specified values of a given parameter under 

consideration. Estimated cumulative distribution functions (CDFs), point estimates, and 95% 

confidence intervals were developed for water quality, sediment, and biological parameters 

measured in this study using formulas described in the EMAP statistical methods manual (DiazRamos 1996). Calculation of CDFs was facilitated using algorithms (spsurvey package; Kincaid 

2008) developed for R, a language and environment for statistical computing and graphics (R 

Development Core Team 2008).

Measured parameters were compared to established thresholds of concern, where available 

(Tables 1–3), and the corresponding percentiles of the estimated CDFs were reported. Where no 

such recommended levels of concern exist (e.g., benthic metrics), common distributional 

properties are reported (e.g., lower or upper percentiles).
9

Table 1. Thresholds used for classifying samples relative to various environmental indicators.

Indicator Threshold Reference

Water Quality 

Salinity (psu) < 5 = Oligohaline

5 – 18 = Mesohaline

>18 – 30 = Polyhaline

> 30 = Euhaline

Carriker 1967 

Δ σt > 2 = strong vertical stratification Nelson et al. 2008

DO (mg/L) < 2 = Low (Poor) 

2 – 5 = Moderate (Fair)

> 5 = High (Good)

USEPA 2008; 

Diaz and Rosenberg 

1995

DIN/DIP > 16 = phosphorus limited

< 16 = nitrogen limited

Geider and La Roche 

2002

Sediment Quality 

Silt-Clay Content (%) > 80 = Mud 

20 – 80 = Muddy Sand 

< 20 = Sand

USEPA 2008

TOC Content (mg/g) > 50 = High (Poor)

20 – 50 = Moderate (Fair)

< 20 = Low (Good)

USEPA 2008

> 36 = High (Poor) Hyland et al. 2005

Overall chemical 

contamination of 

sediments

≥ 1 ERM value exceeded = High (Poor); 

≥ 5 ERL values exceeded = Moderate (Fair); 

No ERMs exceeded and < 5 ERLs exceeded = Low 

(Good) 

USEPA 2008

Individual chemical 

contaminant 

concentrations in 

sediments

> ERM = High probability of bioeffects

< ERL = Low probability of bioeffects

Long et al. 1995; Table 

2 herein

Sediment toxicity 

using Microtox® assay

Silt-clay < 20 %: Toxic if EC50 < 0.5 %

Silt-clay > 20 %: Toxic if EC50 < 0.2 % 

Ringwood et al. 1997
10

Table 1 (continued).

Indicator Threshold Reference

Biological Condition

Reduced benthic 

taxonomic richness, 

diversity, or abundance

< lower 10th percentile of all values for corresponding 

variable

Nelson et al. 2008

Chemical Contaminants in 

Fish Tissues

≥ 1 chemical exceeded Human Health upper limit = 

High (Poor) 

≥ 1 chemical within Human Health risk range = 

Moderate (Fair) 

All chemicals below Human Health lower risk limit = 

Low (Good)

USEPA 2008

Individual chemical 

contaminants in fish 

tissues

Non-cancer (chronic systemic effects) endpoints 

based on consumption of four 8-ounce meals per 

month (general adult population).

Cancer risk endpoints (1 in 100,000 risk level) based 

on consumption of four 8-ounce meals per month 

(general adult population).

USEPA 2000a; Table 3 

herein
11

Table 2. ERM and ERL guideline values in sediments (Long et al. 1995).

Chemical ERL ERM

Metals (μg/g)

Arsenic 8.2 70

Cadmium 1.2 9.6

Chromium 81 370

Copper 34 270

Lead 46.7 218

Mercury 0.15 0.71

Nickel 20.9 51.6

Silver 1 3.7

Zinc 150 410

Organics (ng/g)

Acenaphthene 16 500

Acenaphthylene 44 640

Anthracene 85.3 1100

Fluorene 19 540

2-Methylnaphthalene 70 670

Naphthalene 160 2100

Phenanthrene 240 1500

Benzo[a]anthracene 261 1600

Benzo[a]pyrene 430 1600

Chrysene 384 2800

Dibenz[a,h]Anthracene 63.4 260

Fluoranthene 600 5100

Pyrene 665 2600

Low molecular weight PAHs 552 3160

High molecular weight PAHS 1700 9600

Total PAHs 4020 44800

4,4-DDE 2.2 27

Total DDT 1.58 46.1

Total PCBs 22.7 180
12

Table 3. Risk-based EPA advisory guidelines for recreational fishers (USEPA 2000a).

EPA Advisory Guidelines 

Fish Tissue Concentration Range

(wet weight) a

Health

Endpoint

Metals (μg/g)

Arsenic (inorganic)b 0.35 – 0.70 non-cancer

Cadmium 0.35 – 0.70 non-cancer

Mercury (methylmercury)c 0.12 – 0.23 non-cancer

Selenium 5.9 – 12.0 non-cancer

Organics (ng/g)

Chlordane 590 – 1200 non-cancer

DDT (total) 59 – 120 non-cancer

Dieldrin 59 – 120 non-cancer

Endosulfan 7000 – 14000 non-cancer

Endrin 350 – 700 non-cancer

Heptachlor epoxide 15 – 31 non-cancer

Hexachlorobenzene 940 – 1900 non-cancer

Lindane 350 – 700 non-cancer

Mirex 230 – 470 non-cancer

Toxaphene 290 – 590 non-cancer

PAHs (benzo[a]pyrene) 1.6 – 3.2 cancerd

PCB (total) 23 – 47 non-cancer

a Range of concentrations associated with non-cancer and cancer health endpoint risk for consumption of four 8-oz meals per 

month. b Inorganic arsenic, the form considered toxic, estimated as 2% of total arsenic.

c Because most mercury present in fish and shellfish tissue is present primarily as methylmercury and because of the relatively 

high cost of analyzing for methylmercury, the conservative assumption was made that all mercury is present as methylmercury 

(U.S. EPA, 2000a). d A non-cancer concentration range for PAHs does not exist.

3.0 Results and Discussion

3.1 Depth and Water Quality

3.1.1 Depth

Bottom depths for the 30 stations sampled in coastal shelf waters of the SBNMS ranged from 31

m to 137 m (Table 4, Figure 3). The shallowest sites were located on top of Stellwagen Bank 

proper, while the deeper sites were in deep basins in the northern part of the sanctuary or in 

Stellwagen Basin. The mean depth of all sites sampled was 71 m.

3.1.2 General Water Characteristics: Temperature, Salinity, Water-Column 

Stratification, DO, pH, TSS

Temperatures of surface water (upper 2 m) ranged from 12.1 oC to 16.8 oC (Table 4). Fifty 

percent of the area sampled had surface temperatures < 16 oC, and only 10 % of the area had 

temperatures greater than 16.7 oC (CDF 90th percentile, Table 4). Bottom-water temperatures 

(lower 2 – 10 m of the water column, depending on station depth) were notably colder, ranging 

from 4.4 oC to 6.2 oC, with 50 % of the area < 5.1 oC and only 10 % exceeding 5.9 oC.
13

Surface salinities varied within a narrow range between 30.6 psu and 31.5 psu. The mean and 

50th percentile (based on area) were 31.1 psu, with 10 % of the area having surface salinities 

between 30.6 psu and 30.8 psu. Bottom salinities varied between 32.1 and 32.5 psu, with a mean 

and median of 32.3 psu. 

Some evidence of density stratification was observed among the stations sampled in this study. 

Computed values of Δσt indicate that coastal shelf waters of the SBNMS at the time of this 

sampling were stratified, with 90 % of the survey area having values of Δσt > 2.3. Values of Δσt

at 29 of the 30 sites sampled in this study (96.7 % of the study area) ranged from 2.1 to 3.2, 

which is within the range considered to be indicative of strong vertical stratification (Δσt > 2; 

Nelson et al. 2008). These values are similar to summertime values reported for the western 

Gulf of Maine (Clark et al. 2006).

DO levels indicated that SBNMS waters were well-oxygenated. Measured DO concentrations 

occupied a fairly narrow range for both surface and bottom waters, with surface DO 

concentrations varying between 8.8 mg/L and 10.4 mg/L and bottom water concentrations 

between 8.5 mg/L and 9.6 mg/L. None of these waters had DO at low levels (< 2 mg/L) 

potentially harmful to benthic fauna and fish (Table 4, Figure 3). By comparison, other coastal 

and estuarine waters in the region had similar DO levels, although occupying a wider range of 

values. For example, reported ranges of bottom DO concentrations were 3.0 – 9.6 mg/L among 

53 sites in Cape Cod Bay and 5.6 – 10.9 mg/L among 31 sites in Massachusetts Bay (including 

sites in Boston Inner Harbor) (NCA 2006).

The range of pH values was 7.9 – 8.0 for surface waters and 7.6 – 7.8 for bottom waters, which 

falls within the normal range for seawater of 7.5 – 8.5 (Pinet 2006).

Total suspended solids (TSS) ranged from 2.4 – 9.1mg/L in surface waters. Fifty percent of the 

area had TSS values < 6.3 mg/L, and 90 % of the area had surface TSS values < 8.7 mg/L. TSS 

concentrations in bottom waters were similar to those of surface waters. The area-weighted 50th

and 90th percentiles were 6.5 mg/L and 9.1 mg/L, respectively. Concentrations of TSS in surface 

waters of Cape Cod Bay and Massachusetts Bay were slightly lower, varying from 0.02 – 4.60 

mg/L and 0.50 to 8.70, respectively (NCA 2006).

The full range of values across all SBNMS stations, for the various water-quality variables 

discussed above, is displayed as CDF plots in Figures Figure 3 and Figure 4. The mean values 

by station (average of multiple CTD measurements for near-surface and near-bottom waters for 

each station) appear in Appendices B and C.
14

Table 4. Summary of depth and water-column characteristics for near-bottom (lower 3 m) and near-surface (0.5 - 4 m) waters.

Near-bottom water Near-surface water

Mean Range CDF

10th pctl

CDF

50th pctl

CDF

90th pctl

Mean Range CDF

10th pctl

CDF

50th pctl

CDF

90th pctl

Depth (m) 71 31 - 137 34 65 93 — — — — —

Δσt 2.7 1.6 - 3.2 2.3 2.7 3 — — — — —

Temperature (oC) 5.2 4.4 - 6.2 4.6 5.1 5.9 15.8 12.1 - 16.8 15.1 16 16.7

Salinity (psu) 32.3 32.1 - 32.5 32.2 32.3 32.5 31.1 30.6 - 31.5 30.8 31.1 31.4

DO (mg/L) 9.2 8.5 - 9.6 8.7 9.2 9.5 9.3 8.8 - 10.4 9 9.2 9.5

pH 7.7 7.6 - 7.8 7.6 7.7 7.8 8 7.9 - 8 7.9 8 8

DIN (mg/L) 0.51 0.06 - 0.74 0.32 0.55 0.68 0.09 0.04 - 0.56 0.05 0.05 0.07

DIP (mg/L) 0.11 0.02 - 0.14 0.09 0.12 0.13 0.03 0.02 - 0.12 0.02 0.03 0.04

DIN/DIP 8.16 5.81 - 9.57 6.30 8.35 9.15 3.73 1.98 - 10.57 2.29 3.08 4.93

Chl a (μg/L) 0.36 0.07 - 1.12 0.07 0.24 1 0.57 0.31 - 1.65 0.34 0.51 0.77

TSS (mg/L) 7 3.4 - 15.1 5 6.5 9.1 6.6 2.4 - 9.1 4.9 6.3 8.7
15

Figure 3. Percent area (and 95% confidence intervals) of SBNMS waters vs. selected water-quality 

characteristics.
16

Figure 4. Percent area (and 95% confidence intervals) of SBNMS waters vs. nutrient, chlorophyll, and 

TSS concentrations.
17

3.1.3 Nutrients and Chlorophyll

The concentration of dissolved inorganic nitrogen (DIN: nitrogen as nitrate + nitrite +

ammonium) in surface waters ranged from 0.03 mg/L to 0.56 mg/L and averaged 0.09 mg/L 

(Table 4, Figure 4). Ninety percent of the study area surface waters had DIN concentrations <

0.07 mg/L. Bottom-water concentrations of DIN tended to be higher than surface 

concentrations. For example, about 50% of bottom waters had DIN > 0.55 mg/L (near the 

maximum surface-water concentration of 0.56 mg/L) and the average concentration was 0.51

mg/L (range of 0.06 – 0.74 mg/L). Reported surface-water concentrations of DIN in Cape Cod 

Bay and Massachusetts Bay (NCA 2006) range from 0 – 0.06 mg/L and 0 – 0.29 mg/L, 

respectively.

While there are no published water-quality guidelines for DIN in offshore waters, Figure 5 shows 

the spatial distribution of DIN in bottom waters relative to evaluation cutpoints established for 

neighboring estuaries (USEPA 2008). The figure depicts a clear pattern of higher bottom-water 

DIN levels at deeper sites in comparison to shallower sites. Although for estuaries the criteria 

corresponding to high nutrient levels are used as an indication of eutrophication associated with 

terrestrial input of nitrogen, the concentrations observed here reflect the naturally nutrient-rich

waters of the Gulf of Maine (and Stellwagen Bank). The principal source of nutrients that 

support the high offshore primary production is generally thought to be the influx into the Gulf 

of Maine of nutrient-rich deep Slope Water through the Northeast Channel (Townsend et al. 

2006). In SBNMS, nutrient-rich bottom water upwells to the top of Stellwagen Bank and mixes 

with sunlight, causing suitable conditions for phytoplankton production (Clark et al. 2006) and 

contributing to the high productivity of sanctuary waters.

This association between bottom-water DIN and depth (as well as salinity) is also depicted in 

Figure 6. DIN was positively correlated with depth (R2=0.4398, p<0.0001) and salinity 

(R2

=0.6416, p<0.0001). These observations are consistent with the patterns of seasonal 

stratification that occur in the western Gulf of Maine and Massachusetts Bay. The strong 

stratification of the water column in summer acts as a partial barrier to exchange between the 

surface waters and deeper bottom waters (Geyer et al. 1992). As the seasonal thermocline 

develops, surface layers are isolated from the deep-water nutrient source and nutrient exhaustion 

occurs in surface waters (Townsend et al. 2006).

Concentrations of dissolved inorganic phosphorus (DIP) in surface waters ranged between 0.02 

mg/L and 0.12 mg/L, averaging 0.03 mg/L (Table 4). Ninety percent of the study area surface 

waters had DIP concentrations < 0.04 mg/L. While the range of bottom-water concentrations of 

DIP (0.02 mg/L to 0.14 mg/L) were similar to those measured in surface waters, the mean (0.11 

mg/L) and estimated percentiles were higher (Table 4). Half of the study area had bottom-water 

DIP concentrations that were greater than the maximum surface DIN concentration (0.12 mg/L). 

In comparison, reported surface-water DIP concentrations in Cape Cod Bay and Massachusetts 

Bay (NCA 2006) range from 0 – 0.02 mg/L and 0 – 0.09 mg/L, respectively.

The ratio of DIN to DIP was calculated as an index of nutrient limitation. A DIN:DIP ratio > 16 

is considered to be indicative of phosphorus limitation, while values of DIN:DIP < 16 suggest 

that nitrogen is the limiting factor for primary production (Geider and La Roche 2002). DIN:DIP 
18

ratios (Table 4) ranged from 1.98 to 10.57 (mean of 3.73) in surface waters, and from 5.81 to 

9.57 (mean of 8.16) in bottom waters, which are strongly indicative of nitrogen limitation.

Surface-water concentrations of chlorophyll a, an indicator of phytoplankton biomass and 

abundance, ranged from 0.31 μg/L to 1.65 μg/L and averaged 0.57 μg/L (Table 4). Bottomwater concentrations of chlorophyll a were similar to concentrations in surface waters, ranging 

between 0.07 μg/L and 1.12 μg/L and averaging 0.36 μg/L. In comparison, surface-water 

chlorophyll a concentrations in Cape Cod Bay and Massachusetts Bay (NCA 2006) ranged from 

0.04 – 3.20 μg/L and 0.40 – 12.80 μg/L, respectively.
19 

Figure 5. Bottom-water concentrations of dissolved inorganic nitrogen (DIN). 
20

Figure 6. Relationship of bottom-water dissolved nitrogen (DIN and its constituent components) to depth 

and bottom salinity.
21

3.2 Sediment Quality

3.2.1 Grain Size and TOC

A large proportion of the survey area (76 % area) consisted of bottom sediments composed of 

sand and/or gravel (< 20 % silt-clay content). Five sites (17 % area) had sediments composed of 

intermediate muddy sands (20 – 80 % silt-clay), and two sites (7 % area) had sediments 

classified as muds (> 80 % silt-clay). These intermediate and muddy sites were located mainly 

in depositional areas, either in Stellwagen Basin or in the deeper parts of the sanctuary adjacent 

to Gloucester Basin (Figure 8). Results are summarized in Table 5 and Figure 7, Figure 8, and 

Figure 9.

TOC content of sediments in general was low, ranging from 0.2 – 25.7 mg/g and averaging 4.8 

mg/g throughout the sanctuary (Table 5). Nearly all of the study area (29 of 30 sites, 97 % area) 

had sediment TOC concentrations < 20 mg/g. Of those 29 sites, 21 (70 % area) had sediment 

TOC < 5 mg/g. Sediments at only one site (in Stellwagen Basin) had TOC concentration 

between 20 and 25 mg/g. All sites (100% of the area) had concentrations < 50 mg/g, below 

levels associated with a high incidence of effects on benthic fauna (Figure 10).

Sediments in other coastal and estuarine areas of the region showed similar distributions of 

percent fines (silt-clay) and TOC. For example, sediments in the deeper basin (i.e., depositional 

area) of Cape Cod Bay tended to be higher in percent silt-clay and TOC content. The proportion 

of silt-clay and TOC content of sediments also were higher in estuarine areas of Massachusetts 

Bay (Boston Inner Harbor, Broad Sound, Gloucester Harbor; NCA 2006).

Figure 7. Distribution of percentages of gravel, sand, and silt-clay in surficial sediments.
22 

Figure 8. Percent gravel, sand, and silt-clay content of sediments. 
23

Table 5. Summary of sediment characteristics.

Parameter Mean Range

CDF

10th pctl

CDF

50th pctl

CDF

90th pctl

TOC (mg/g) 4.8 0.2 – 25.7 0.3 2.8 10.2

% Silt-Clay 20 0.1 – 97.6 0.4 12.8 62.6

Mean ERM-Q 0.018 0.003 – 0.071 0.003 0.014 0.033

Figure 9. (A) Percent area (and 95% confidence intervals) represented by varying levels of silt-clay 

content of sediment (mg/g), and (B) percent area having TOC content within specified ranges.

Figure 10. (A) Percent area (and 95% confidence intervals) represented by varying levels of TOC content 

of sediment (mg/g), and (B) percent area having TOC content within specified ranges.
24

3.2.2 Chemical Contaminants in Sediments

The biological significance of chemical contamination of sediments was evaluated by comparing 

measured contaminant concentrations to sediment quality guidelines (SQGs) developed by Long 

et al. (1995). Effects-Range Low (ERL) values represent lower bioeffect limits, below which 

adverse effects of contaminants on sediment-dwelling organisms are not likely to occur (the ERL 

corresponds to an expected incidence of toxicity of about 10%). Effects-Range Median (ERM) 

values are mid-range concentrations above which adverse biological effects are more likely to 

occur (the ERM is the concentration corresponding to an expected incidence of toxicity of about 

50%). Any site having one or more chemicals in excess of their corresponding ERM values (see 

Table 2) was rated as having poor sediment quality; any site with five or more chemicals 

between the corresponding ERL and ERM values was rated as fair; any site with no ERMs 

exceeded and < 5 ERLs exceeded was rated as having good sediment quality (sensu U.S. EPA 

2008). Overall sediment contamination from multiple chemicals also was expressed through the 

use of mean ERM quotients (sensu Long et al. 1998; Hyland et al. 1999, 2003). The mean ERM 

quotient (mean ERM-Q) is the mean of the ratios of individual chemical concentrations in a 

sample relative to corresponding published ERM values (using all chemicals in Table 2 except 

nickel, low- and high-molecular-weight PAHs, and total PAHs). A useful feature of this method 

is that overall contamination in a sample from mixtures of multiple chemicals present at varying 

concentrations can be expressed as a single number that can be compared to values calculated the 

same way for other samples (either from other locations or sampling occasions).

The overall mean, range, and area-weighted percentiles of mean ERM-Qs are shown in Table 5. 

None of the stations had mean ERM-Qs high enough to suggest significant risks of adverse 

effects on benthic fauna. Hyland et al. (2003) reported the highest incidence of impaired benthic 

assemblages (85% of samples) in Virginian Province estuaries at mean ERM-Qs above a critical 

point of 0.473 and a low incidence of effects (9% of samples) at mean ERM-Qs ≤ 0.022. 

Although in the present study we are dealing with offshore benthic fauna, none of the stations 

had mean ERM-Qs in this upper bioeffect range (which are the most applicable guidelines 

known to us for comparison). Of the 30 sites sampled in this study, 22 (73.3% area) had mean 

ERM-Qs in the low (< 0.022) range reported by Hyland et al. (2003). The remaining 8 sites 

(26.7% area) had mean ERM-Qs in the moderate (0.022 – 0.098) range. Six of these eight sites 

corresponded to the mud/muddy-sand sites noted in the previous section and all eight were 

located either in Stellwagen Basin or adjacent to Gloucester Basin (Figure 13). No sites had 

mean ERM-Qs in either the high (0.098 – 0.473) or very high (> 0.473) range.

Compared to SBNMS, mean ERM quotients among 53 sites in Cape Cod Bay (NCA 2006) were 

similar, ranging from 0.001 – 0.104 (mean of 0.030). Mean ERM-Qs were higher in the deeper, 

depositional area of Cape Cod Bay, which also contained higher proportions of fine-grained 

sediments. In Massachusetts Bay, mean ERM-Qs were higher in some places and tended to be 

highest (> 0.100) in the more silty estuarine portions (Gloucester Harbor, Salem Sound, Broad 

Sound, Boston Harbor). The highest mean ERM-Qs occurred in Boston Inner Harbor, with 

values as high as 1.800 (NCA 2006).

Similar spatial patterns of contaminant levels were described by Hartwell et al. (2006), who 

found highest concentrations of metals and organic contaminants in and around Boston Harbor, 
25

intermediate concentrations in the middle and deeper areas of Massachusetts and Cape Cod 

Bays, and lowest on Stellwagen Bank.

In SBNMS, the more fine-grained, organically-enriched sediments were associated with higher 

levels of chemical contaminants (Figure 11 and Figure 12). The regression fit of mean ERM 

quotient to sediment % silt-clay was significant, with R2 = 0.57 (p < 0.001). The goodness-of-fit 

for sediment TOC was also significant, with R2 = 0.94 (p < 0.001). Hence, with few exceptions, 

sediment TOC and silt-clay content appeared to be good predictors of overall sediment 

contaminant levels throughout the sanctuary.

Figure 11. Plot of mean ERM quotient versus sediment % silt-clay.

Figure 12. Plot of mean ERM quotient versus TOC content of sediment.
26

No contaminants were found in excess of their corresponding ERMs (Table 6). Only three 

chemicals, arsenic, lead, and mercury, exceeded their corresponding ERL guidelines. Thus, all 

stations (representing 100% of the survey area) would be ranked as having good sediment quality 

with respect to chemical contaminants based on the EPA’s NCA guidelines (no ERM values 

exceeded and < 5 ERL values exceeded, USEPA 2008). The ERL exceedances for arsenic 

occurred at eleven sites, representing an estimated 36.7 % of the survey area. The concentration 

of arsenic at most sites (28 sites, 93% area) was within the range typical of uncontaminated nearshore marine sediments (5 – 15 μg/g dry weight total arsenic) reported by Neff (1997) and 

reflects its natural presence at low to moderate concentrations in crustal rocks of the region. 

Arsenic concentrations greater than 15 μg/g dry weight were found at two sites (stations 3 and 

20) in the northern part of the sanctuary. Concentrations of lead and mercury in excess of the 

corresponding ERLs were observed at only one site (station 1) which was located in a deep, silty 

area of Stellwagen Basin approximately 4 nautical miles southeast of the Massachusetts Bay 

Disposal Site (MBDS, Figure 13).

Circulation in the Gulf of Maine is characterized by a cyclonic (counter-clockwise) gyre over the 

deep central basin (Ingham et al. 1992, Lynch et al. 1996, Lynch et al. 1997, Cook and Auster 

2007). Within the context of this overall mean circulation pattern the western Gulf of Maine 

Coastal Current (GMCC) flows southwestward along the coast. This coastal current branches 

near Cape Ann, with the main branch continuing southward over Stellwagen Bank and east of 

Cape Cod and a weak branch proceeding southwestward into Massachusetts Bay (Lynch et al. 

1996, Butman and Bothner 1997). The mean current through Massachusetts Bay flows 

southward through the bay, along the western shore, and easterly out of the bay north of Race 

Point. The deep basins of Massachusetts Bay are long-term sinks for fine-grained sediments, and 

contaminants discharged into Boston Harbor are sequestered in the sediments of Boston Harbor, 

Stellwagen Basin, and Cape Cod Bay (Butman and Bothner 1997). Tracer studies using osmium 

isotopes and silver have shown that sewage discharged into Boston Harbor has affected 

sediments in Cape Cod Bay, over 70km away (Ravizza and Bothner 1996). The distribution of 

sediment contaminant concentrations observed in the present study likely are the result of these 

overall patterns of circulation, transport, and deposition of fine-grained sediments in the deep 

basins of the sanctuary (i.e., Stellwagen Basin and Gloucester Basin).
27

Table 6. Summary of chemical contaminant concentrations in sediments ('N.D.' = not detected; '-' = no corresponding ERL or ERM available).

Concentration > ERL, < ERM Concentration > ERM

Analyte Mean (Std. Dev.) Range # Stations % Area # Stations % Area

Metals (% dry)

Aluminum 1.289 (1.080) 0.302 - 4.53 - - - -

Iron 1.517 (1.375) 0.3 - 5.68 - - - -

Trace Metals (μg/g dry mass)

Antimony 0.155 (0.362) 0 - 1.12 - - - -

Arsenic 7.210 (6.079) 1.54 - 29 11 36.7 0 0

Cadmium 0.046 (0.033) 0.009 - 0.146 0 0 0 0

Chromium 22.705 (13.857) 5.3 - 61.4 0 0 0 0

Copper 4.517 (4.172) 0.741 - 19.1 0 0 0 0

Lead 18.702 (9.969) 5.03 - 48.9 1 3.3 0 0

Manganese 417.703(287.002) 93.1 - 1330 - - - -

Mercury 0.023 (0.033) 0.001 - 0.161 1 3.3 0 0

Nickel 8.252 (7.033) 1 - 28.5 - - - -

Selenium 0.290 (0.289) 0 - 1.2 - - - -

Silver N.D. N.D. N.D. 0 0 0 0

Tin 1.877 (1.582) 0.428 - 7.67 - - - -

Zinc 26.272 (21.755) 4.4 - 94.1 0 0 0 0

PAHs (ng/g dry)

Acenaphthene 0.369 (1.207) 0 - 5.5882 0 0 0 0

Acenaphthylene 4.667 (8.118) 0 - 36.645 0 0 0 0

Anthracene 6.920 (10.740) 0 - 48.914 0 0 0 0

Benz[a]anthracene 11.675 (17.889) 0 - 81.36 0 0 0 0

Benzo[a]pyrene 14.342 (20.401) 0 - 92.762 0 0 0 0

Benzo[b]fluoranthene 20.207 (27.319) 0 - 122.97 - - - -

Benzo[g,h,i]perylene 12.215 (16.695) 0 - 76.363 - - - -

Benzo[k]fluoranthene 7.240 (10.098) 0 - 45.911 - - - -

Biphenyl 0.144 (0.789) 0 - 4.3212 - - - -

Chrysene 14.284 (21.073) 0 - 98.486 0 0 0 0

Dibenz[a,h]anthracene 2.529 (4.038) 0 - 16.851 0 0 0 0

Dibenzothiophene 1.234 (2.500) 0 - 10.965 - - - -

Fluoranthene 25.395 (36.230) 0 - 162.18 0 0 0 0

Fluorene 1.788 (3.283) 0 - 14.313 0 0 0 0

Indeno[1,2,3-c,d]pyrene 12.417 (18.010) 0 - 83.659 - - - -

Naphthalene 6.096 (11.793) 0 - 51.544 0 0 0 0

1-Methylnaphthalene 1.388 (2.968) 0 - 12.215 - - - -
28

Table 6 (continued).

Concentration > ERL, < ERM Concentration > ERM

Analyte Mean (Std. Dev.) Range # Stations % Area # Stations % Area

2-Methylnaphthalene 2.669 (5.033) 0 - 20.283 0 0 0 0

2,6-Dimethylnaphthalene 1.491 (2.951) 0 - 10.165 - - - -

2,3,5-Trimethylnaphthalene 0.145 (0.792) 0 - 4.3401 - - - -

Phenanthrene 15.479 (21.679) 0 - 97.48 0 0 0 0

1-Methylphenanthrene 3.064 (4.601) 0 - 21.055 - - - -

Pyrene 22.991 (33.973) 0 - 155.14 0 0 0 0

Low Molecular Weight PAHs 45.310 (73.540) 0 - 327.2532 0 0 0 0

High Molecular Weight PAHs 121.771 (173.971) 0 - 791.285 0 0 0 0

Total PAHsa 177.758 (261.897) 0 - 1186.7372 0 0 0 0

PCBs (ng/g dry)

Total PCBsb 0.174 (0.291) 0 - 1.25 0 0 0 0

Pesticides (ng/g dry)

2,4'-DDD (o,p'-DDD) N.D. N.D. N.D. - - - -

2,4'-DDE (o,p'-DDE) 0.012 (0.047) 0 - 0.232 - - - -

2,4'-DDT (o,p'-DDT) N.D. N.D. N.D. - - - -

4,4'-DDD (p,p'-DDD) 0.015 (0.080) 0 - 0.438 - - - -

4,4'-DDE (p,p'-DDE) N.D. N.D. N.D. 0 0 0 0

4,4'-DDT (p,p'-DDT) N.D. N.D. N.D. - - - -

Aldrin N.D. N.D. N.D. - - - -

alpha-Chlordane N.D. N.D. N.D. - - - -

Dieldrin N.D. N.D. N.D. - - - -

Endosulfan I N.D. N.D. N.D. - - - -

Endosulfan II (beta-Endosulfan) N.D. N.D. N.D. - - - -

Endosulfan sulfate N.D. N.D. N.D. - - - -

Endrin

gamma-HCH (g-BHC, lindane) 0.006 (0.033) 0 - 0.183 - - - -

Heptachlor N.D. N.D. N.D. - - - -

Heptachlor epoxide N.D. N.D. N.D. - - - -

Hexachlorobenzene (HCB) N.D. N.D. N.D. - - - -

Mirex N.D. N.D. N.D. - - - -

Total DDTsc 0.026 (0.091) 0 - 0.438 0 0 0 0

trans-Nonachlor N.D. N.D. N.D. - - - -

a Sum of 23 measured PAHs.

b Sum of 21 measured PCB congeners. c Sum of 2,4′-DDD, 4,4′-DDD, 2,4′-DDE, 4,4′-DDE, 2,4′-DDT, and 4,4′-DDT.
29 

Figure 13. Mean ERM quotients (mean ERM-Q) calculated based on measured contaminant 

concentrations in sediments. 
30

3.2.3 Sediment Toxicity

None of the 30 samples tested using the Microtox® assay were found to be toxic, based on the criteria 

listed in Table 1 (Ringwood et al. 1997). One site had an EC50 just above the toxicity threshold for 

sediments with silt-clay > 20 % (station 29, EC50 = 0.2065 %, silt-clay = 82.64 %). This site was located 

in the northern part of the sanctuary (Gloucester Basin) at 130 m depth.

3.3 Chemical Contaminants in Fish Tissues

Collection of fish specimens by hook-and-line fishing was successful at 18 of the 30 stations 

sampled in this study. Of these specimens, 26 individuals representing five distinct species

collected at 16 stations were used for tissue contaminant analysis. Species retained for analysis 

and the corresponding stations where they were collected are displayed in Table 7.

Table 7. Listing of fish specimens retained for tissue contaminant analysis and the stations where they 

were collected.

Station Common Name Scientific Name Specimen No.

03 Haddock Melanogrammus aeglefinus 1

Acadian Redfish Sebastes fasciatus 1

04 Atlantic Cod Gadus morhua 1

Haddock M. aeglefinus 1

06 Red Hake Urophycis chuss 1

2

07 Red Hake U. chuss 1

11 Silver Hake Merluccius bilinearis 1

12 Haddock M. aeglefinus 1

13 Red Hake U. chuss1 1

2

15 Atlantic Cod G. morhua 1

Haddock M. aeglefinus 1

17 Silver Hake M. bilinearis 1

Red Hake U. chuss 1

2

20 Red Hake U. chuss 1

21 Red Hake U. chuss 1

22 Haddock M. aeglefinus2 1

2

24 Red Hake U. chuss 1

25 Haddock M. aeglefinus 1

Red Hake U. chuss3 1

2

26 Red Hake U. chuss 1

29 Acadian Redfish S. fasciatus 1

1 Two specimens were selected randomly from 6 available. 2 Two specimens were selected randomly from 4 available. 3 Two specimens were selected randomly from 3 available.
31

Concentrations of a suite of metals, pesticides, and PCBs were measured in edible tissues (fillets) 

of each of the fish specimens listed in Table 7 and compared to risk-based EPA advisory 

guidelines for recreational fishers (Table 3). The guidelines selected for this analysis were 

endpoints associated with an average consumption rate of four 8-oz fish meals per month (from 

USEPA 2000a), which is consistent with the comparison basis used currently in the National 

Coastal Condition Report (USEPA 2008) and by States for setting fish advisories. A station was 

rated as “good” if all chemical contaminants listed in Table 3 had concentrations below the 

corresponding lower endpoints, “fair” if at least one contaminant fell within the corresponding 

lower and upper endpoints, and “poor” if at least one contaminant occurred at a concentration 

above the upper endpoint (USEPA 2008).

Two of the 16 stations where fish were collected and retained for analysis had chemical 

contaminants in tissues above the corresponding upper human-health endpoints (Table 8). At 

station 03, the deepest site sampled in this study (137m) and located in the region of the 

sanctuary north of Stellwagen Bank adjacent to Gloucester Basin (Creed Basin), an Acadian 

redfish (Sebastes fasciatus) had methylmercury concentrations (measured as mercury and 

assumed to be all methylmercury, sensu U.S. EPA 2000a) of 0.371 μg/g wet weight, which is in 

excess of the upper human-health endpoint of 0.23 μg/g. Another specimen analyzed from this 

station (haddock, Melanogrammus aeglefinus) exceeded the lower methylmercury endpoint of 

0.12 μg/g. The other upper human-health endpoint exceedance occurred at station 17, where a 

silver hake (Merluccius bilinearis) was found to contain 51.125 ng/g of total PCBs in edible 

tissue. Exceedances of lower guidelines (but not upper guidelines), besides the one noted above, 

occurred for methylmercury (stations 03, 04, 12, 22, and 25) and inorganic arsenic (stations 13, 

20, and 25). Multiple lower-guideline exceedances were noted at station 25 (M. aeglefinus, 

methylmercury; U. chuss, inorganic arsenic and methylmercury). The foregoing results are 

summarized in Table 8. Overall mean fish tissue contaminant concentrations, ranges, and 

numbers of human-health advisory guideline exceedances, summarized by contaminant and 

irrespective of fish species, are listed in Table 9. With respect to risk-based EPA advisory 

guidelines, two sites would be classified as “poor”, six sites as “fair”, and the remaining eight 

sites (where fish were collected) would be classified as “good”. The status of the 14 sites where 

no fish were collected is unknown.
32

Table 8. Listing of stations where concentrations of contaminants in fish tissues exceeded corresponding 

risk-based human-health guidelines.

Station Fish species Analyte Concentration

(wet weight)

Exceeded 

lower 

endpoint 1

Exceeded 

upper 

endpoint 1

03 Melanogrammus aeglefinus Methylmercury 2 0.151 μg/g 1 0

Sebastes fasciatus Methylmercury 0.371 μg/g 0 1

04 Gadus morhua Methylmercury 0.145 μg/g 1 0

12 M. aeglefinus Methylmercury 0.202 μg/g 1 0

13 Urophycis chuss Inorganic Arsenic 3 0.382 μg/g 1 0

17 Merluccius bilinearis Total PCBs 51.125 ng/g 0 1

20 U. chuss Inorganic Arsenic 0.368 μg/g 1 0

22 M. aeglefinus Methylmercury 0.185 μg/g 1 0

25 M. aeglefinus Methylmercury 0.188 μg/g 1 0

U. chuss Inorganic Arsenic 0.640 μg/g 1 0

Methylmercury 0.122 μg/g 1 0

1 Risk-based EPA advisory guidelines for recreational fishers (USEPA 2000a) listed in Table 3. 2 Measured as total mercury and assumed to be all methylmercury.

3 Estimated as 2% of total arsenic.
33

Table 9. Summary of contaminant concentrations (wet weight) measured in fish tissues. A total of 26 

fish from 16 stations were analyzed. All measured contaminants are included. Concentrations are 

compared to human-health guidelines where available (from US EPA 2000a, also see Table 3 herein). 

('N.D.' = Not detected; 'N.M.' = Not measured; '-' = no corresponding guideline available).

Analyte Mean Range

No. of fish exceeding 

health endpoints

> Lower

&

< Upper > Upper

Metals (μg/g wet weight)

Aluminum 12.538 8.697 - 28.069 - -

Arsenic 10.976 1.272 - 31.984 - -

Arsenic (Inorganic)a 0.220 0.025 - 0.640 3 0

Barium 0.049 0.015 - 0.218 - -

Beryllium N.D. 0.000 - 0.000 - -

Cadmium 0.001 0.000 - 0.005 0 0

Chromium 0.109 0.065 - 0.334 - -

Cobalt N.D. 0.000 - 0.000 - -

Copper 0.319 0.209 - 1.060 - -

Methylmercury (estimated)b 0.101 0.024 - 0.371 6 1

Iron 6.972 2.665 - 19.924 - -

Lead 0.012 0.000 - 0.086 - -

Lithium 0.011 0.000 - 0.026 - -

Manganese 0.503 0.164 - 2.965 - -

Nickel 0.064 0.000 - 1.181 - -

Selenium 0.542 0.282 - 1.035 0 0

Silver N.D. 0.000 - 0.000 - -

Thallium N.D. 0.000 - 0.000 - -

Tin 0.001 0.000 - 0.033 - -

Uranium N.D. 0.000 - 0.000 - -

Vanadium 0.214 0.058 - 0.671 - -

Zinc 4.160 3.066 - 9.514 - -

PAHs (ng/g wet weight)

Acenaphthene 0.123 0.000 - 0.748 - -

Acenaphthylene 0.003 0.000 - 0.055 - -

Anthracene 0.011 0.000 - 0.162 - -

Benz[a]anthracene N.D. 0.000 - 0.000 - -

Benzo[a]pyrene N.D. 0.000 - 0.000 0 0

Benzo[b]fluoranthene N.D. 0.000 - 0.000 - -

Benzo[e]pyrene N.D. 0.000 - 0.000 - -

Benzo[g,h,i]perylene N.D. 0.000 - 0.000 - -

Benzo[j,k]fluoranthene N.D. 0.000 - 0.000 - -

Biphenyl 0.140 0.000 - 2.068 - -

Chrysene+Triphenylene N.D. 0.000 - 0.000 - -

Dibenz[a,h]anthracene N.D. 0.000 - 0.000 - -

Dibenzothiophene N.D. 0.000 - 0.000 - -

Flouranthene N.D. 0.000 - 0.000 - -

Flourene N.D. 0.000 - 0.000 - -

Indeno[1,2,3-c,d]pyrene N.D. 0.000 - 0.000 - -

Napthalene 0.035 0.000 - 0.221 - -

1-Methylnaphthalene 0.017 0.000 - 0.158 - -

2-Methylnaphthalene 0.076 0.000 - 1.642 - -

2,6-Dimethylnaphthalene N.D. 0.000 - 0.000 - -
34

Table 9 (continued).

Analyte Mean Range

No. of fish exceeding 

health endpoints

> Lower

&

< Upper > Upper

1,6,7-Trimethylnaphthalene N.D. 0.000 - 0.000 - -

Perylene N.D. 0.000 - 0.000 - -

Phenanthrene 0.059 0.000 - 1.535 - -

1-Methylphenanthrene 0.017 0.000 - 0.158 - -

Pyrene N.D. 0.000 - 0.000 - -

Total PAH 0.470 0.000 - 4.154 - -

PBDEs (ng/g wet weight)

PBDE 100 0.040 0.000 - 0.722 - -

PBDE 138 N.D. 0.000 - 0.000 - -

PBDE 153 N.D. 0.000 - 0.000 - -

PBDE 154 N.D. 0.000 - 0.000 - -

PBDE 17 N.D. 0.000 - 0.000 - -

PBDE 183 N.D. 0.000 - 0.000 - -

PBDE 190 N.D. 0.000 - 0.000 - -

PBDE 28 N.D. 0.000 - 0.000 - -

PBDE 47 0.239 0.000 - 2.657 - -

PBDE 66 N.D. 0.000 - 0.000 - -

PBDE 71 N.D. 0.000 - 0.000 - -

PBDE 85 N.D. 0.000 - 0.000 - -

PBDE 99 0.020 0.000 - 0.529 - -

PCBs (ng/g wet weight)

Total PCBsc 5.746 0.437 - 51.125 0 1

Pesticides (ng/g wet weight)

2,4' - DDD (o,p' - DDD) N.D. 0.000 - 0.000 - -

2,4' - DDE (o,p' - DDE) 0.095 0.000 - 0.362 - -

2,4' - DDT (o,p' - DDT) 0.028 0.000 - 0.735 - -

4,4' - DDD (p,p' - DDD) 0.228 0.000 - 2.293 - -

4,4' - DDE (p,p' - DDE) 0.849 0.000 - 8.292 - -

4,4' - DDT (p,p' - DDT) 0.096 0.000 - 2.486 - -

Aldrin N.D. 0.000 - 0.000 - -

Chlorpyrifos N.D. 0.000 - 0.000 - -

cis-Chlordane (alpha-Chlordane) N.D. 0.000 - 0.000 - -

Dieldrin 0.066 0.000 - 0.990 0 0

Endosulfan N.M. N.M. 0 0

Endosulfan I N.D. 0.000 - 0.000 - -

Endosulfan II N.D. 0.000 - 0.000 - -

Endosulfan sulfate N.D. 0.000 - 0.000 - -

Endrin N.M. N.M. - -

Heptachlor N.D. 0.000 - 0.000 - -

Heptachlor epoxide N.D. 0.000 - 0.000 0 0

Hexachlorobenzene 0.037 0.000 - 0.495 0 0

Lindane 0.009 0.000 - 0.231 0 0

Mirex N.D. 0.000 - 0.000 0 0

Total DDT 1.295 0.000 - 14.058 0 0

Total Chlordane N.D. 0 0

Toxaphene N.M. - -

trans-Nonachlor N.D. 0.000 - 0.000 - -

a Estimated as 2% of the measured total arsenic. b Measured as total mercury and assumed to be all methylmercury. c Sum of 79 measured PCB congeners.
35

3.4 Status of Benthic Communities

Macrobenthic infauna (those retained on a 0.5-mm sieve) were sampled at a total of 30 stations 

throughout the sanctuary. Two grabs (0.04 m2 each) were collected at each station, resulting in a 

total of 60 grabs. Measures of taxonomic diversity and abundance were calculated separately for 

each of the 60 grabs and averaged by station where indicated in Table 11 (e.g., mean # taxa/0.04 

m

2

, mean H′/0.04 m2). The resulting data were used to assess the status of benthic community 

characteristics (taxonomic composition, diversity, abundance, and dominant taxa), the incidence 

of non-indigenous species, and potential linkages to ecosystem stressors throughout sanctuary 

waters.

3.4.1 Taxonomic Composition

A total of 330 taxa were identified throughout the study area, of which 160 were identified to the 

species level. Polychaetes were the dominant taxa (Figure 14, Table 10), both by percent of taxa 

(38 %) and percent abundance (69 %). Crustaceans and molluscs were the second and third 

dominant taxa, respectively, both by percent of taxa (33 % crustaceans, 20 % mollusks) and 

percent abundance (15 % crustaceans, 8 % mollusks). Collectively, these three groups 

represented 91 % of total taxa and 92 % of total faunal abundance. Crustaceans were 

represented primarily by amphipods (70 identifiable taxa, 21.2 % of the total number of taxa), 

followed by isopods (16 taxa, 4.8 % of total taxa), cumaceans (11 taxa, 3.3 % of total taxa), and 

tanaidaceans and ostracods (5 taxa each, 3 % of total taxa both groups combined; Table 10). 

Molluscs were represented mainly by bivalves (45 taxa, 13.6 % of total taxa), followed by 

gastropods (19 taxa, 5.8 % of total taxa).
36

Figure 14. Relative percent composition of major taxonomic groups expressed as percent of total taxa 

and percent of abundance.
37

Table 10. Summary of major taxonomic groups of benthic infauna and corresponding numbers of 

identifiable taxa based on 60 0.04-m2 grab samples.

Taxonomic Group Number identifiable taxa % Total identifiable taxa

Phylum Cnidaria

Class Anthozoa* 1 0.3

Class Hydrozoa* 1 0.3

Phylum Platyhelminthes* 1 0.3

Phylum Nemertea* 2 0.6

Phylum Sipuncula* 2 0.6

Phylum Mollusca

Class Aplacophora 1 0.3

Class Bivalvia 45 13.6

Class Gastropoda 19 5.8

Class Polyplacophora 1 0.3

Class Scaphopoda 1 0.3

Phylum Annelida

Class Clitellata

Subclass Oligochaeta* 2 0.6

Class Polychaeta 124 37.6

Phylum Arthropoda

Subphylum Chelicerata* 1 0.3

Subphylum Crustacea

Class Malacostraca

Order Amphipoda 70 21.2

Order Cumacea 11 3.3

Order Decapoda 1 0.3

Order Isopoda 16 4.8

Order Mysida 1 0.3

Order Tanaidacea 5 1.5

Class Ostracoda 5 1.5

Phylum Phoronida* 1 0.3

Phylum Brachiopoda* 1 0.3

Phylum Echinodermata

Class Asteroidea 3 0.9

Class Echinoidea 2 0.6

Class Holothuroidea 4 1.2

Class Ophiurida 5 1.5

Phylum Ectoprocta* 1 0.3

Phylum Chordata* 2 0.6

Phylum Porifera* 1 0.3

Total 330 100

* Taxonomic groups followed by an asterisk were assigned to the group ‘Other’ in Figure 11.
38

3.4.2 Abundance and Dominant Taxa

A total of 16,136 individuals were collected across the 30 stations (60, 0.04 m2 grabs) sampled 

for benthos. Densities ranged from 612 – 15,500 ind/m

2 and averaged 6,723 ind/m2 (Table 11, 

Appendix E). On an area-weighted basis, 50 % of the survey area had mean densities >5,650

ind/m and 10 % of the area (upper 10th percentile) had mean densities > 12,688 ind/m

2 (Table 9, 

Figure 15).

The 50 most abundant taxa collected throughout SBNMS are listed in Table 12. The top 10 

dominants, in decreasing order of abundance, included the syllid (Family Syllidae) polychaete 

Exogone verugera; maldanid polychaetes (Maldanidae); sabellid polychaetes (Sabellidae); the 

sabellid polychaete genus Chone; the polychaetes Axiothella mucosa (Maldanidae), Prionospio 

steenstrupi (Spionidae), and Parapionosyllis longicirrata (Syllidae); the gammarid amphipod 

genus Unciola; the polychaete Exogone hebes; and tubificid oligochaetes (Tubificidae).

3.4.3 Diversity

A total of 330 taxa were identified (160 to species) in 60 grabs collected throughout the study 

area. Taxonomic richness, expressed as the mean number of taxa present in replicate 0.04 m2

grabs at a station, ranged from 10 to 45 taxa/grab, with an overall mean and median of 30

taxa/grab (Table 11). Area-weighted percentiles also are given in Table 11, and the full 

distribution of area-weighted estimates is illustrated in Figure 15.
39

Table 11. Mean, range, and selected distributional properties of key benthic variables. The benthic measures represent 60 0.04-m2 grabs collected 

at 30 sites (2 replicate grabs at each station).

Overall 

Mean

Overall 

Range

Area-based Percentilesa Frequency-based percentilesb

CDF

10th pctl

CDF

50th pctl

CDF

90th pctl 10th 25th 50th 75th 90th

Mean # Taxa/0.04 m2 30 10 - 45 18 30 40 19 23 30 36 43

Total # Taxa/0.08 m2 46 15 - 72 27 48 63 28 35 48 56 66

Mean Density (#/m2) 6,723 612 – 15,500 1,900 5,650 12,688 1,938 3,612 5,694 9,012 12,806

Mean H′/0.04 m2 3.6 2.8 - 4.5 3.0 3.5 4.2 3.0 3.3 3.5 3.9 4.2

a Value of benthic variable corresponding to the designated cumulative % area of the estimated CDF.

b Corresponding lower 10th percentile, lower quartile, median, upper quartile, and upper 10th percentile of all values for each benthic variable.

Mean # taxa, mean density, and mean H′ represent the average of each of those measures calculated separately for the two grabs. 

Total # taxa is the total number of taxa in both replicate grabs combined (0.08 m2

).
40

Table 12. Fifty most abundant benthic taxa. Mean density (#/m2), and percent frequency of occurrence 

are based on 60 0.04-m2 grabs. Classification: Native = native species; Crypto = cryptogenic species (of 

uncertain origin); Indeter = indeterminate taxon (not identified to a level that would allow determination 

of origin).

taxon group Classification mean_density pct_freq

Exogone verugera Polychaeta Native 311.3 47.4

Maldanidae Polychaeta Indeter 292.1 60.0

Sabellidae Polychaeta Indeter 266.8 32.6

Chone spp. Polychaeta Native 255.0 30.5

Axiothella mucosa Polychaeta Native 209.2 23.2

Prionospio steenstrupi Polychaeta Native 166.1 31.6

Parapionosyllis longicirrata Polychaeta Native 113.7 16.8

Unciola spp. Crustacea Native 103.7 23.2

Exogone hebes Polychaeta Native 103.4 31.6

Tubificidae Other Indeter 82.1 38.9

Ampharetidae Polychaeta Indeter 78.4 47.4

Unciola inermis Crustacea Native 69.2 12.6

Aricidea spp. Polychaeta Native 67.4 41.1

Anobothrus gracilis Polychaeta Native 66.8 38.9

Cirratulidae Polychaeta Indeter 66.1 51.6

Serpulidae Polychaeta Indeter 54.7 7.4

Polygordius spp. Polychaeta Native 54.7 18.9

Sphaerosyllis spp. Polychaeta Native 54.5 20.0

Enchytraeidae Other Indeter 54.5 11.6

Sipuncula Other Indeter 54.2 28.4

Eudorella hispida Crustacea Native 53.2 27.4

Cirrophorus spp. Polychaeta Native 51.6 25.3

Ericthonius fasciatus Crustacea Native 48.9 16.8

Leptochelia spp. Crustacea Native 43.2 16.8

Ascidiacea Other Indeter 41.1 27.4

Thyasira gouldii Mollusca Native 39.5 26.3

Ninoe nigripes Polychaeta Native 38.7 21.1

Spionidae Polychaeta Indeter 37.6 30.5

Levinsenia gracilis Polychaeta Native 35.3 23.2

Nephtyidae Polychaeta Indeter 34.2 37.9

Glyceridae Polychaeta Indeter 32.1 26.3

Portlandia frigida Mollusca Native 31.1 18.9

Hemipodus borealis Polychaeta Native 29.5 22.1

Aoridae Crustacea Indeter 27.9 13.7

Nucula delphinodonta Mollusca Native 26.3 26.3

Protodorvillea kefersteini Polychaeta Native 25.5 13.7

Astarte crenata subequilatera Mollusca Native 25.5 17.9

Terebellidae Polychaeta Indeter 25.3 29.5

Cerastoderma pinnulatum Mollusca Native 24.7 20.0

Spio spp. Polychaeta Indeter 23.9 25.3

Bivalvia Mollusca Indeter 23.4 30.5

Ampelisca spp. Crustacea Indeter 20.0 15.8

Galathowenia oculata Polychaeta Native 19.7 25.3

Actiniaria Other Indeter 19.2 11.6

Mediomastus californiensis Polychaeta Native 19.2 7.4

Astarte spp. Mollusca Native 18.7 15.8

Mediomastus spp. Polychaeta Native 18.4 18.9

Crenella decussata Mollusca Native 17.9 27.4

Aglaophamus circinata Polychaeta Native 17.4 27.4

Mayerella limicola Crustacea Native 17.4 16.8
41

Figure 15. Percent area (and 95% confidence intervals) of SBNMS study area vs. benthic infaunal 

taxonomic richness (A), density (B), and H' diversity (C)
42

3.4.4 Patterns of biogeographic distribution

Benthic ecological community data were analyzed for patterns in faunal distributions using 

hierarchical cluster analysis of Bray-Curtis dissimilarities (unweighted pair-group method with 

arithmetic mean, or UPGMA) and non-metric multidimensional scaling (NMDS) in R (R 

Development Core Team 2008). Analyses were performed on double-square root-transformed 

abundances, with taxonomic classifications held at the Family level. Reasons for using familylevel data were two-fold: first, analysis of families often reveals broad-scale patterns in benthic 

distributions (Clarke & Warwick 2001); second, many of the specimens collected (in particular, 

polychaete worms) were fragmented with no identifiable posterior end, which would be needed 

to identify beyond family. Consequently, many polychaetes (the dominant taxonomic group)

were identified only to Family level.

From the cluster analysis, three main site groups emerge (Figure 16). Site Group A represents 

what may be termed a ‘top-of-bank’ assemblage, having shallow depths (31m – 55m, mean of 

40m) and sandy sediments (65% - 97% sand, mean = 84%). Sediments at these sites also had 

very low silt-clay (0.4 – 5% silt-clay, mean = 1.8%) and TOC (0.2 – 0.7 mg/g, mean=0.4 mg/g) 

content. The seven stations comprising this site group were characterized by relatively high 

densities (overall mean density = 8,330 ind/m

2

) and dominated by maldanid and syllid 

polychaetes (mean densities of 2,129 ind/m

2 and 2,014 ind/m2 for families Maldanidae and 

Syllidae, respectively). These two polychaete families represent 50% cumulative density of all 

taxa found at Site Group A stations. Other taxa in this site group, in decreasing order of 

abundance, were gammarid amphipod crustaceans (Family Aoridae), tubificid oligochaetes 

(Family Tubificidae), and other polychaete worms (Families Paraonidae, Polygordiidae, 

Glyceridae, and Serpulidae). Taken together, the taxa listed above made up nearly 80% 

cumulative density of taxa found in Site Group A.

The next site group (Site Group B, Figure 16) appears to represent sites in depositional 

environments of Stellwagen Basin and Gloucester Basin. These sites tended to be of 

intermediate or deep depths (61m – 130m, mean of 85m), with relatively high sediment silt-clay

(36% - 98% silt-clay, mean = 66%) and TOC (7.7 – 25.7 mg/g) content. Densities of benthic 

infauna were relatively low at these sites (overall mean density = 1,735 ind/m2

). The top 

dominants included a number of polychaete families (i.e., Lumbrineridae, Spionidae, 

Ampharetidae, Paraonidae), bivalve molluscs (Thyasiridae), and other polychaete worms 

(Maldanidae, Cirratulidae, Trichobranchidae, Cossuridae, and Orbiinidae). Along with other 

bivalve molluscs (Periplomatidae) and gammarid amphipod crustaceans (Phoxocephalidae), 

these taxa made up 80% cumulative density of taxa in Site Group B.
43

Figure 16. Dendrogram resulting from hierarchical cluster analysis.

The number of taxa among stations in Site Group A (mean of 24.7 taxa/grab) was greater than 

that of Site Group B (mean of 17.4 taxa/grab), though mean Shannon diversity (H′) was slightly 

lower (3.27 vs. 3.44, respectively). This likely is due to a less even distribution of taxonomic 

abundance in Site Group A compared to Site Group B (mean Pielou’s evenness, J′ = 0.70 and 

0.83, respectively), where the infaunal assemblages of Site Group A are dominated by a few taxa 

as described above.

The same site groups emerge from NMDS analysis of the same community dataset (Figure 17). 

Adding vectors of abiotic variables such as depth and % silt-clay to the plot helps to illustrate the 

influence of these factors on the distributions of benthic taxa as discussed above. While Site 

Groups A and B are described in the previous two paragraphs, the stations labeled as Site Group 

C in Figure 16 appear to be representative of habitats that are intermediate along the gradients of 

sediment type and depth. Most sites were of intermediate depth (mean depth = 79 m), with 

sediment silt-clay content < 30 %, and TOC from 2 – 7 mg/g. Mean infaunal density among 

these sites (7,484/m2) was intermediate between that of Site Groups A and B, though only 

slightly less than Site Group A. Because of the range of habitat types represented by stations in 

Site Group C, mean taxonomic diversity (3.71) and richness (35.4 taxa/grab) were higher than 

either Site Group A or B. Taxa were slightly more equitably distributed (mean J′ = 0.72) than 

Site Group A, but considerably less so than Site Group B.
44

Figure 17. Ordination plot derived from non-metric multidimensional scaling (NMDS).

In their assessment of the benthic community of Boston Harbor, Massachusetts/Cape Cod Bay, 

and Stellwagen Bank, Hartwell et al. (2006) described three major habitat zones: Boston Harbor 

(muddy, shallow, low salinity); Stellwagen Bank (coarse sand, low TOC); and the deeper, openwater areas of Massachusetts Bay, Cape Cod Bay, and Stellwagen Basin (fine sand, deep, higher 

TOC). Our analysis appears to resolve further the latter habitat zone into the deep, silty, high 

TOC areas (Site Group B) and Site Group C (intermediate silt-clay, TOC, and depth). As noted 

in their assessment (Hartwell et al. 2006), the Massachusetts Water Resources Authority 

(MWRA) concluded in their benthic community analysis (Maciolek 2005) that the largest

differences among community groups was related primarily to grain size.

In the present study, overall mean infaunal densities tended to be lower at sites with higher 

percent silt-clay content (Figure 18; R2

= 0.19, p = 0.017). These sites also had lower numbers of 

taxa and higher concentrations of TOC (Figure 19; R2 = 0.21, p < 0.011).
45

Figure 18. Plot of mean density (#/m2

) versus sediment % silt-clay.

Figure 19. Plot of mean density (#/m2) versus TOC content of sediment.

Though numbers of taxa were lower at sites having very high % silt-clay and high TOC sediment 

content, there also were fewer taxa present at sites where organic carbon was scarce (and, 

perhaps, limiting). The observed pattern of species richness (Figure 20) appears to reflect 

general conceptual models of benthic response to organic enrichment (Pearson and Rosenberg 

1978, Hyland et al. 2005), with low numbers of taxa at stations with sediments low in organic 

carbon, higher numbers of taxa with increasing TOC, and then declining numbers of taxa at 

highly organically-enriched sites.
46

Figure 20. Plot of mean # of taxa (per 0.04 m2) versus TOC content of sediment.

3.4.5 Non-indigenous Species

The list of taxa collected in SBNMS was examined for the occurrence of non-native and exotic 

species by searching NISbase, a distributed database on non-indigenous species that queries a 

number of different information systems. Databases that are part of NISbase include the U.S. 

Geological Survey (USGS) National Aquatic Species Database (NAS, U.S. Geological Survey 

2004), the Smithsonian National Exotic Marine and Estuarine Species Information System 

(NEMESIS, Fofonoff et al. 2003), the Massachusetts Institute of Technology Sea Grant Program 

Marine Invader Tracking Information System (MITIS, MIT 2008), and the NOAA National 

Benthic Inventory (NBI 2004), among others. A small number of species collected as part of the 

2008 SBNMS survey (i.e., Harmothoe imbricata) are considered to be cryptogenic (Ruiz et al. 

2000). The only non-indigenous species identified in the present study was the gammarid 

amphipod Microdeutopus gryllotalpa, found at a single station (station 21). This species was 

listed in the SBNMS Final Management Plan and Environmental Assessment (U.S. Department 

of Commerce 2010, Table 4) as a known invasive to the Gulf of Maine region, but had not been 

documented yet in SBNMS. A number of specimens collected in this study were only identified 

to higher taxonomic level (e.g., Phylum Bryozoa (=Ectoprocta), Porifera; Order Actiniaria; Class 

Ascidiacea, Hydrozoa; Family Mysidae; Genus Caprella, Molgula). Hence, it was not possible 

to determine definitively whether additional known invasives from these groups were present in 

samples from SBNMS.

3.5 Potential Linkage of Biological Condition to Stressor Impacts

Multi-metric benthic indices are commonly used to summarize and classify benthic habitat 

conditions along the continuum from non-degraded to degraded (see review by Diaz et al. 2004) 

and have been developed for a variety of estuarine applications (Engle et al. 1994, Weisberg et 

al. 1997, Van Dolah et al. 1999, Llansó et al. 2002a, 2002b, Hale and Heltshe 2008). A desired 

characteristic of these indices is the ability to discriminate between impaired versus unimpaired 
47

benthic condition, based on key biological attributes (e.g., numbers of species, diversity, 

abundance, biomass, relative proportion of pollution-sensitive or pollution-tolerant species), 

while taking into account natural controlling factors. Such indices have been developed for 

estuaries of the mid-Atlantic states and Chesapeake Bay (Weisberg et al. 1997, Llansó et al. 

2002a, 2002b) and nearshore Gulf of Maine (Hale and Heltshe 2008). An index is being 

developed for near-coastal NJ (to 3 km; Strobel et al. 2008), but no such index exists that would 

be directly applicable to the offshore waters of SBNMS.

In the absence of a benthic index, we attempted to assess potential stressor impacts in the present 

study by evaluating linkages between reduced values of biological attributes (numbers of taxa, 

diversity, and abundance) and synoptically measured indicators of poor sediment or water 

quality. Using the lower 10th percentile as a basis for defining ‘low’ values, we looked for cooccurrences of low values of biological attributes with indications of poor sediment or water 

quality defined as follows (sensu U.S. EPA 2000b for dissolved oxygen, U.S. EPA 2004 for 

other indicators): ≥ 1 chemical in excess of ERMs (from Long et al. 1995), TOC > 50 mg/g, and 

DO in near-bottom water < 2.0 mg/L.

We found no association of low values of biological attributes (as defined above) with indicators 

of poor sediment or water quality. In fact, no indications of poor sediment or water quality were 

observed based on these criteria. The highest observed TOC concentration was 25.7 mg/g 

(Appendix A), well below 50 mg/g as well as the more conservative bioeffect threshold of 35 

mg/g TOC published in Hyland et al. (2005). DO concentrations in bottom waters were at least 

8.5 mg/L (Appendix B) and no ERM exceedances were observed (Appendix D). These results 

suggest that sediments and overlying waters of SBNMS are in good condition, with lower-end 

values of biological attributes (Appendix E) representing parts of a normal reference range 

controlled by natural factors.
48

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Environmental Protection Agency, Office of Water, Washington, DC. 383 pp.

Available from: http://www.epa.gov/waterscience/fish/advice/volume2/.
53

U.S. EPA. 2000b. Ambient Aquatic Life Water Quality Criteria for Dissolved Oxygen 

(Saltwater): Cape Cod to Cape Hatteras. EPA-822-R-00-012. Office of Water and Office of 

Research and Development, Washington, DC. 49 pp. Available at

http://www.epa.gov/waterscience/criteria/dissolved/.

U.S. EPA. 2001a. National Coastal Condition Report. EPA-620/R-01/005. Office of Research 

and Development and Office of Water, Washington, DC. 204 pp. Available at: 

http://www.epa.gov/nccr/.

U.S. EPA. 2001b. Environmental Monitoring and Assessment Program (EMAP). National 

Coastal Assessment Quality Assurance Project Plan, 2001–2004. EPA/620/R-01/002. Office of 

Research and Development, National Health and Environmental Effects Research Laboratory, 

Gulf Ecology Division, Gulf Breeze, FL. 198 pp.

U.S. EPA. 2006. Test Methods for Evaluating Solid Waste, Physical/Chemical Methods (SW846). Online at http://www.epa.gov/waste/hazard/testmethods/.

U.S. EPA. 2004. National Coastal Condition Report II. EPA-620/R-03/002. U.S. Environmental 

Protection Agency, Office of Research and Development and Office of Water, Washington, D.C. 

286 pp. Available at: http://www.epa.gov/nccr/.

U.S. EPA. 2008. National Coastal Condition Report III. EPA/842-R-08-002. Office of Research 

and Development/Office of Water, Washington, D.C. 301 pp. Available at: 

http://www.epa.gov/nccr/.

Van Dolah, R. F., J. L. Hyland, A. F. Holland, J. S. Rosen, and T. R. Snoots. 1999. A benthic 

index of biological integrity for assessing habitat quality in estuaries of the southeastern USA. 

Marine Environmental Research 48: 269-283.

Weisberg, S. B., J. A. Ranasinghe, D. M. Dauer, L. C. Schaffner, R. J. Diaz, and J. B. Frithsen. 

1997. An estuarine benthic index of biotic integrity (B-IBI) for Chesapeake Bay. Estuaries

20:149-158.
54

5.0 Appendices
55

Appendix A. Locations (latitude, longitude), depth, and sediment characteristics of sampling stations.

Station Latitude Longitude

Depth

(m)

Gravel

(%)

Sand

(%)

Silt-Clay

(%)

TOC

(mg/g)

01 42.36902 -70.52692 93 0.0 2.4 97.6 25.7

02 42.40162 -70.34907 42 32.9 66.7 0.4 0.2

03 42.53540 -70.35034 137 8.1 17.6 74.3 15.7

04 42.66465 -70.21794 90 20.7 66.1 13.2 4.0

05 42.43304 -70.50733 55 34.2 63.7 2.1 3.6

06 42.31778 -70.29494 34 9.5 89.7 0.8 0.3

07 42.58792 -70.42620 85 34.1 47.6 18.3 6.5

08 42.25497 -70.26070 33 5.5 93.9 0.6 0.2

09 42.20325 -70.44878 65 0.0 48.7 51.3 8.6

10 42.37727 -70.40142 42 0.0 97.2 2.8 0.4

11 42.63309 -70.46301 50 14.5 85.4 0.1 1.0

12 42.44634 -70.13119 84 21.2 65.7 13.1 3.6

13 42.26046 -70.42533 75 10.3 53.8 35.9 7.7

14 42.63698 -70.32280 89 16.9 64.8 18.4 5.4

15 42.64134 -70.24021 83 25.8 43.8 30.4 4.2

16 42.41108 -70.25529 59 39.1 60.6 0.3 2.2

17 42.19279 -70.48567 61 0.6 36.8 62.6 10.2

18 42.54229 -70.56082 65 10.8 71.6 17.6 3.9

19 42.25418 -70.32759 54 1.0 97.9 1.1 1.6

20 42.50134 -70.44600 82 37.8 57.7 4.5 6.4

21 42.13129 -70.28621 65 0.6 86.6 12.8 2.8

22 42.55612 -70.24165 95 17.4 65.5 17.1 2.8

23 42.44507 -70.32237 68 19.9 79.4 0.6 1.2

24 42.26105 -70.11768 93 10.4 88.8 0.8 2.8

25 42.45865 -70.36629 83 0.3 80.5 19.2 3.9

26 42.18791 -70.11456 55 7.9 87.1 5.0 0.7

29 42.51436 -70.39874 130 0.0 17.4 82.6 15.8

ALT02 42.62745 -70.37403 85 14.2 71.9 13.9 2.4

ALT07 42.29310 -70.29426 31 34.4 65.0 0.7 0.5

ALT25 42.29822 -70.23617 40 12.3 85.6 2.1 0.4
56

Appendix B. Near-bottom water characteristics by station.

Station Temp.

(oC)

Salinity

(psu)

DO

(mg/L)

pH DIP

(mg/L)

DIN

(mg/L)

Nitrate+

Nitrite

(μg/L)

Ammonium

(μg/L)

N/P Silicate

(μg/L)

Chlorophyll a

(μg/L)

TSS

(mg/L)

01 4.4 32.4 8.5 7.6 0.142 0.682 653.9 27.8 8.19 953.6 0.21 6.9

02 5.6 32.2 9.4 7.7 0.089 0.357 309.4 47.9 8.27 577.8 0.56 15.1

03 4.6 32.5 9.1 7.7 0.127 0.744 739.8 4.1 9.26 794.9 0.09 5.8

04 4.9 32.5 9.0 7.7 0.127 0.683 673.1 10.4 8.71 773.1 0.08 8.7

05 5.5 32.2 9.3 7.7 0.086 0.333 277.0 55.7 8.49 388.5 1.10 6.2

06 6.1 32.2 9.6 7.8 0.095 0.341 320.9 20.5 6.48 295.8 1.07 8.7

07 5.1 32.4 9.2 7.7 0.123 0.590 570.7 19.1 8.03 766.0 0.26 5.2

08 5.9 32.2 9.5 7.8 0.100 0.324 282.6 41.2 6.65 367.2 0.87 7.0

09 4.7 32.4 8.8 7.7 0.126 0.632 586.7 45.2 9.15 689.9 0.23 6.3

10 6.1 32.1 9.5 7.8 0.095 0.284 243.4 40.3 6.30 357.8 1.12 5.9

11 5.8 32.2 9.5 7.8 0.108 0.445 394.2 50.4 8.22 415.0 0.42 5.2

12 4.8 32.5 9.2 7.7 0.128 0.677 667.3 9.4 8.52 658.1 0.07 6.0

13 4.4 32.4 8.5 7.6 0.135 0.674 637.7 36.1 8.78 892.3 0.25 7.4

14 5.0 32.4 9.1 7.7 0.121 0.648 628.6 19.5 8.96 883.7 0.11 5.2

15 5.0 32.5 9.1 7.7 0.122 0.664 657.0 6.6 8.65 687.7 0.07 9.1

16 5.5 32.3 9.5 7.7 0.101 0.461 429.9 31.6 8.35 502.5 0.29 8.6

17 4.8 32.3 9.0 7.7 0.115 0.575 538.7 36.1 9.01 824.5 0.26 6.7

18 5.9 32.1 9.4 7.8 0.099 0.352 311.2 40.6 7.14 610.8 0.35 8.0

19 4.6 32.3 8.7 7.7 0.129 0.621 551.3 70.0 9.57 701.2 0.24 7.3

20 5.1 32.3 9.1 7.7 0.023 0.057 45.3 11.8 5.81 106.6 0.25 6.0

21 5.0 32.2 9.1 7.6 0.121 0.457 392.3 65.0 7.96 600.6 0.33 5.0

22 4.7 32.5 9.1 7.7 0.117 0.700 698.0 2.0 9.38 696.3 0.07 9.3

23 5.3 32.3 9.4 7.7 0.105 0.495 458.2 37.2 8.73 491.1 0.21 6.7

24 5.0 32.4 9.2 7.7 0.118 0.590 561.0 29.0 8.70 559.5 0.15 5.8

25 5.3 32.3 9.3 7.7 0.117 0.507 467.0 39.6 8.08 601.3 0.34 7.0

26 5.1 32.4 9.2 7.7 0.116 0.553 515.8 37.6 8.65 517.9 0.22 6.3

29 4.6 32.5 9.0 7.7 0.126 0.728 723.3 4.5 9.13 733.2 0.09 9.7

ALT02 5.2 32.4 9.1 7.7 0.117 0.551 524.0 26.9 8.24 711.8 0.16 4.8

ALT07 6.2 32.2 9.5 7.8 0.096 0.316 292.2 23.5 6.06 317.7 1.00 3.4

ALT25 5.8 32.3 9.4 7.8 0.103 0.391 355.8 35.6 7.29 328.9 0.47 6.9
57

Appendix C. Near-surface water characteristics by station.

Station Temp.

(oC)

Salinity

(psu)

DO

(mg/L)

pH DIP

(mg/L)

DIN

(mg/L)

Nitrate+

Nitrite

(μg/L)

Ammonium

(μg/L)

N/P Silicate

(μg/L)

Chlorophyll a

(μg/L)

TSS

(mg/L)

01 15.4 31.2 9.5 8.0 0.028 0.035 34.0 0.6 1.98 162.3 0.77 6.6

02 16.8 30.9 9.0 8.0 0.028 0.056 50.5 5.0 3.84 394.4 0.56 5.5

03 16.0 31.2 9.2 8.0 0.031 0.051 51.2 0.2 2.67 68.9 0.54 7.2

04 15.8 31.4 9.0 8.0 0.034 0.055 53.1 1.6 2.70 218.0 0.63 8.7

05 16.8 31.0 9.2 8.0 0.030 0.056 46.7 9.1 4.08 205.0 0.54 6.4

06 16.0 31.0 9.2 8.0 0.029 0.049 47.0 1.5 2.86 68.1 0.58 7.4

07 16.7 30.8 9.3 8.0 0.026 0.060 57.6 2.8 4.02 179.0 0.38 6.3

08 15.3 31.4 9.3 8.0 0.039 0.074 59.4 14.3 4.34 37.4 0.56 6.3

09 16.1 31.1 9.2 8.0 0.030 0.056 56.3 0.2 2.93 15.0 0.31 5.7

10 16.8 31.3 9.0 8.0 0.025 0.055 50.5 5.0 4.14 222.7 0.37 5.8

11 16.6 30.8 9.2 8.0 0.032 0.058 57.5 0.9 3.02 279.9 0.40 5.1

12 15.8 31.4 9.0 8.0 0.035 0.050 49.9 0.5 2.30 40.7 0.37 8.8

13 16.2 31.0 9.0 8.0 0.025 0.057 48.0 8.9 4.93 66.9 0.47 6.3

14 16.0 31.4 9.2 8.0 0.033 0.076 53.0 22.5 6.14 301.1 0.34 5.0

15 16.5 31.3 8.8 8.0 0.031 0.049 49.1 0.3 2.55 4.4 0.38 9.1

16 15.9 31.1 9.1 8.0 0.025 0.053 47.4 5.8 4.14 46.3 0.59 8.4

17 16.2 30.9 9.3 8.0 0.022 0.047 44.1 2.7 3.76 192.4 0.71 5.8

18 12.1 31.3 10.4 8.0 0.046 0.059 59.4 0.1 2.03 270.5 1.65 8.3

19 16.4 31.0 9.2 8.0 0.024 0.051 49.0 1.6 3.54 1.2 0.32 6.4

20 16.1 31.1 9.3 8.0 0.103 0.555 496.7 58.2 10.57 663.3 0.45 6.3

21 15.5 30.6 9.7 7.9 0.024 0.050 50.0 0.2 3.28 77.6 1.26 2.4

22 15.4 31.4 9.3 8.0 0.026 0.052 46.8 5.5 3.99 14.1 0.39 9.0

23 16.4 31.0 8.9 8.0 0.028 0.051 50.6 0.0 2.82 91.7 0.75 7.6

24 14.6 31.4 9.5 7.9 0.034 0.048 47.3 0.8 2.29 40.6 0.48 5.7

25 15.4 31.2 9.5 7.9 0.027 0.050 47.0 2.8 3.26 193.0 0.61 5.0

26 15.5 31.1 9.3 7.9 0.033 0.057 54.5 2.2 2.92 18.1 0.64 6.9

29 16.4 31.0 9.0 8.0 0.026 0.051 50.7 0.1 3.08 38.0 0.36 7.6

ALT02 16.5 31.3 9.2 8.0 0.119 0.563 535.4 27.2 8.22 719.9 0.40 4.8

ALT07 15.1 31.2 9.3 8.0 0.034 0.046 40.5 5.7 2.80 64.0 0.78 5.2

ALT25 15.1 31.2 9.3 8.0 0.031 0.047 44.9 2.2 2.68 31.9 0.59 7.0
58

Appendix D. Summary by station of mean ERM quotients and the number of contaminants that exceeded 

corresponding ERL or ERM values (from Long et al. 1995).

Station # of ERLs

Exceeded

# of ERMs

Exceeded

Mean

ERM-Q

01 3 0 0.071

02 0 0 0.004

03 1 0 0.044

04 0 0 0.014

05 0 0 0.015

06 0 0 0.004

07 1 0 0.022

08 0 0 0.003

09 0 0 0.032

10 0 0 0.003

11 0 0 0.007

12 1 0 0.016

13 1 0 0.033

14 1 0 0.018

15 0 0 0.014

16 1 0 0.014

17 0 0 0.032

18 0 0 0.021

19 0 0 0.009

20 1 0 0.031

21 0 0 0.011

22 1 0 0.014

23 1 0 0.012

24 0 0 0.009

25 0 0 0.016

26 0 0 0.005

29 1 0 0.042

ALT02 0 0 0.010

ALT07 0 0 0.003

ALT25 0 0 0.003
59

Appendix E. Summary by station of benthic macroinfaunal (>0.5mm) characteristics. Two replicate 

benthic grabs (0.04m2 each) were processed from each station. H′ derived using base 2 logarithms. 

(*Values within lower 25th percentile of all values of a specific benthic variable; **values within lower 

10th percentile.)

Station Mean # Taxa

per Grab

Total # Taxa Mean Density

(# / m2)

Mean H′

per Grab

01 10** 15** 613** 3.0**

02 27 39 15,500 2.9**

03 29 45 5,263 3.7

04 33 53 5,738 3.7

05 23* 40 3,175* 3.3*

06 24 32* 5,650 3.5

07 46 70 11,788 4.0

08 25 37 7,988 3.3*

09 21* 36 1,563** 3.7

10 20* 29* 3,075* 3.2*

11 32 52 8,063 3.6

12 41 63 10,250 3.1*

13 19** 29* 1,900** 3.5

14 37 56 6,975 3.9

15 36 54 8,700 3.3*

16 38 58 12,250 4.0

17 20* 33* 1,975* 3.6

18 46 72 9,013 4.2

19 30 49 3,688 4.2

20 36 59 4,625 4.1

21 38 63 13,350 3.3*

22 31 48 6,075 2.8**

23 34 51 12,925 3.4

24 46 71 5,375 4.5

25 31 48 3,613 3.7

26 28 35* 8,888 3.3*

29 18** 24** 2,625* 3.4

ALT02 36 56 3,850 4.2

ALT07 20* 27** 4,525 3.3*

ALT25 32 47 12,688 3.5


United States Department of Commerce

Gary F. Locke 

Secretary

National Oceanic and Atmospheric Administration 

Jane Lubchenco 

Administrator 

National Ocean Service 

David Kennedy 

Assistant Administrator (Acting)

=