2000 overview

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2000 
Outfall monitoring overview 
Massachusetts Water Resources Authority 
Environmental Quality Department 
Report ENQUAD 2001-10

Citation: 
Werme C, Hunt CD. 2001. 2000 Outfall monitoring overview. Boston:
Massachusetts Water Resources Authority. Report ENQUAD 2001-10. 92 p.

2000 
Outfall Monitoring Overview 
submitted to 
Massachusetts Water Resources Authority 
Environmental Quality Department 
100 First Avenue 
Charlestown Navy Yard 
Boston, MA 02129 
prepared by 
Christine Werme 
Norwell, MA 02061 
and 
Carlton D. Hunt 
Battelle 
397 Washington Street 
Duxbury, MA 02332 
November 12, 2001

Executive Summary 
Since its creation in 1985, the Massachusetts Water Resources Authority (MWRA) has worked
to minimize the effects of discharging sewage effluent to the marine environment. The MWRA
program includes source reduction to prevent pollutants from entering the sewage system,
improved treatment, and effective dilution. One aspect of the program, moving the treated
wastewater outfall from Boston Harbor to Massachusetts Bay, which was accomplished in 2000,
has raised some environmental concerns. To address these concerns, MWRA implemented an
extensive monitoring program to measure the health of Boston Harbor and the bays. Further, the
joint federal and state permit for the new outfall requires extensive monitoring of the effluent,
water column, sea floor, and fish and shellfish. The permit links the monitoring program to a
contingency plan, which identifies corrective actions for unexpected effects of the outfall. 
This document, an annual outfall monitoring overview, presents a scientific summary of
monitoring data collected through 2000 and includes information relevant to the contingency
plan. These data include information on effluent quality, baseline conditions, special studies,
and the first results of outfall monitoring. The report also includes a report on the Gerry E.
Studds Stellwagen Bank National Marine Sanctuary. 
Most MWRA studies began in 1992, resulting in a relatively long period in which to conduct
baseline studies. This long period as allowed MWRA to document greater natural variability
than would have been observed in briefer baseline monitoring. These results will allow a more
informed interpretation of results following the diversion of effluent to the bay. 
The first information following start-up of the new outfall provided initial assurances that actual
plume behavior matched the model predictions. They also indicated that ammonia and salinity
were sensitive indicators of the presence of the plume. Other studies that were conducted by the
end of 2000 included a water-column survey, a sediment-contaminant survey, and a nutrient-
cycling study. Chlorophyll concentrations were already elevated throughout the region when the
outfall was commissioned. Subsequently, the winter/spring contingency plan threshold for
chlorophyll was exceeded. The high value was independent of the outfall and reflected the
conditions of the wider region. Preliminary information shows that chlorophyll levels were
lower than the thresholds for the spring of 2001. 
To date, there are no indications that the outfall affects the water quality or biology of the
sanctuary. Water-column sampling has indicated that the stations within the sanctuary are
healthy and similar to other farfield stations. Monitoring also showed no increase in indicator
bacteria at offshore stations following outfall start-up.

2000 OUTFALL MONITORING OVERVIEW III 
Table of Contents 
EXECUTIVE SUMMARY ................................................................................................. I 
TABLE OF CONTENTS................................................................................................. III 
LIST OF FIGURES ........................................................................................................ VI 
LIST OF TABLES ........................................................................................................ VIII 
1. INTRODUCTION......................................................................................................... 1 
Background ....................................................................................................................................1 
Outfall Permit.................................................................................................................................3 
Monitoring Program......................................................................................................................4 
Contingency Plan ...........................................................................................................................5 
Data Management..........................................................................................................................8 
Reporting ........................................................................................................................................9 
Outfall Monitoring Overview .......................................................................................................9 
2. EFFLUENT ............................................................................................................... 11 
Background ..................................................................................................................................11 
Pollution Prevention and Wastewater Treatment.......................................................................11 
Environmental Concerns ............................................................................................................11 
Monitoring Design .......................................................................................................................13 
Results ...........................................................................................................................................16 
Contingency Plan Thresholds .....................................................................................................18

2000 OUTFALL MONITORING OVERVIEW IV 
3. WATER COLUMN BASELINE ................................................................................. 21 
Background ..................................................................................................................................21 
Circulation and Water Properties ...............................................................................................21 
Environmental Concerns ............................................................................................................23 
Monitoring Design .......................................................................................................................24 
Results ...........................................................................................................................................27 
Physical Conditions....................................................................................................................27 
Water Quality .............................................................................................................................28 
Phytoplankton Communities ......................................................................................................32 
Zooplankton Communities.........................................................................................................35 
Contingency Plan Thresholds .....................................................................................................36 
4. SEA FLOOR BASELINE .......................................................................................... 39 
Background ..................................................................................................................................39 
Bottom Characteristics and Sediment Transport........................................................................39 
Environmental Concerns ............................................................................................................39 
Monitoring Design .......................................................................................................................41 
Results ...........................................................................................................................................44 
Sediment Contaminants..............................................................................................................44 
Sediment Profile Imaging...........................................................................................................45 
Soft-bottom Communities ..........................................................................................................47 
Hard-bottom Communities.........................................................................................................50 
Contingency Plan Thresholds .....................................................................................................51 
5. FISH AND SHELLFISH BASELINE ......................................................................... 54 
Background ..................................................................................................................................54 
Fisheries......................................................................................................................................54 
Environmental Concerns ............................................................................................................54 
Monitoring Design .......................................................................................................................56 
Results ...........................................................................................................................................57 
Winter Flounder .........................................................................................................................57 
Lobster........................................................................................................................................59 
Blue Mussel................................................................................................................................61

2000 OUTFALL MONITORING OVERVIEW V 
Contingency Plan Thresholds .....................................................................................................62 
6. OUTFALL MONITORING ......................................................................................... 63 
Plume Observations .....................................................................................................................63 
Water-Column Observations......................................................................................................65 
Sediment Contaminants ..............................................................................................................68 
Benthic Flux..................................................................................................................................69 
Contingency Plan Threshold Results .........................................................................................69 
Dissolved Oxygen Percent Saturation........................................................................................69 
Nearfield Chlorophyll Autumn 2000 .........................................................................................70 
7. SPECIAL STUDIES .................................................................................................. 75 
Background ..................................................................................................................................75 
Water Quality in Boston Harbor................................................................................................75 
Massachusetts Bay Bacteria Monitoring ...................................................................................77 
Nutrient Flux ................................................................................................................................79 
Marine Mammal Observations...................................................................................................80 
8. STELLWAGEN BANK NATIONAL MARINE SANCTUARY .................................... 83 
REFERENCES.............................................................................................................. 88 
LIST OF ACRONYMS................................................................................................... 92

2000 OUTFALL MONITORING OVERVIEW VI 
List of Figures 
Figure 1-1. Map of Massachusetts and Cape Cod bays ...................................................................2 
Figure 2-1. Daily effluent flow in 2000 ........................................................................................14 
Figure 2-2. Annual solids, nitrogen, and metals discharges ..........................................................15 
Figure 2-3. Monthly average TSS and monthly BOD from 1994-2000. Weekly TSS and cBOD
during the period in 2000 that the offshore outfall was discharging. ....................................17 
Figure 2-4. Monthly pH, daily mean chlorine residual, and fecal coliform bacteria data from the
period in 2000 in which the outfall was discharging.............................................................19 
Figure 3-1. General circulation on Georges Bank and in the Gulf of Maine during the summer,
stratified season .....................................................................................................................22 
Figure 3-2. Nearfield sampling stations.........................................................................................24 
Figure 3-3. Farfield sampling stations ...........................................................................................25 
Figure 3-4. Charles River discharge, 1990-2000, and 2000 discharge compared to the historic
mean ......................................................................................................................................26 
Figure 3-5. Surface and bottom temperature and salinity, 1992-2000 .........................................27 
Figure 3-6. Survey mean dissolved inorganic nitrogen and ammonia in the nearfield, 1992-2000 
...............................................................................................................................................29 
Figure 3-7. Survey areal mean chlorophyll concentrations in the nearfield, 1992-2000..............30 
Figure 3-8. Satellite data show an increasing trend in fall chlorophyll levels in Massachusetts
Bay, Cape Cod Bay, south of Cape Cod, and in the Gulf of Maine .....................................31 
Figure 3-9. Survey mean dissolved oxygen concentrations and percent saturation in the nearfield,
1992-2000..............................................................................................................................32 
Figure 3-10. Survey mean phytoplankton abundance....................................................................33 
Figure 3-11. Model results indicate that A. tamarense blooms originate to the north of
Massachusetts Bay.................................................................................................................34 
Figure 3-12. Survey mean zooplankton abundance.......................................................................35 
Figure 4-1. Locations of nearfield soft-bottom stations ................................................................40 
Figure 4-2. Locations of farfield soft-bottom stations ...................................................................41 
Figure 4-3. Locations of hard-bottom transects.............................................................................42 
Figure 4-4. There is a gradient of decreasing C. perfringens spores with distance from Deer
Island and a decrease at Deer Island since the mid 1990s.....................................................44 
Figure 4-5. Typical sediment profile image...................................................................................45 
Figure 4-6. Apparent color RPD layer depth for all data from nearfield stations .........................46 
Figure 4-7. Community parameters for soft-bottom communities ................................................48 
Figure 4-8. Patterns of species abundance in Massachusetts Bay ................................................49 
Figure 4-9. Hard-bottom survey photograph .................................................................................51 
Figure 5-1. Sampling areas for fish and shellfish monitoring .......................................................55 
Figure 5-2. Prevalence of centrotubular hydropic vacuolation (CHV)..........................................57 
Figure 5-3. Concentrations of representative contaminants in flounder fillets and livers .............58 
Figure 5-4. Concentrations of representative contaminants in lobster meat and hepatopancreas .60

2000 OUTFALL MONITORING OVERVIEW VII 
Figure 5-5. Concentrations of representative contaminants in mussels .......................................61 
Figure 6-1. Outfall discharge photographed in June 2001............................................................63 
Figure 6-2. Horizontal contour of NH4 at the pycnocline. ............................................................64 
Figure 6-3. Model predictions for effluent dilutions from Deer Island and Massachusetts Bay
outfalls; measured ammonia concentrations from pre-discharge and post-discharge...........66 
Figure 6-4. Seasonal chlorophyll levels, 1992-winter/spring 2001 ..............................................67 
Figure 6-5. Clostridium perfringens spore density at special contaminant study stations ............68 
Figure 6-6. Patterns of percent saturation in bottom water dissolved oxygen for the nearfield
(left) and Stellwagen Basin (right). . ....................................................................................70 
Figure 7-1. Ammonia levels in waters in the vicinity of the Deer Island and Nut Island outfalls 76 
Figure 7-2. Secchi disk depths in waters in the vicinity of the Deer Island and Nut Island outfalls 
...............................................................................................................................................77 
Figure 7-3. Locations of bacteria monitoring stations ...................................................................78 
Figure 7-4. Whale sightings during 2000 .....................................................................................81 
Figure 8-1. Survey mean dissolved inorganic nitrogen in the nearfield and at the boundary in the
Stellwagen Bank National Marine Sanctuary........................................................................84 
Figure 8-2. Survey mean areal chlorophyll levels in the nearfield and at the boundary in the
Stellwagen Bank National Marine Sanctuary........................................................................85 
Figure 8-3. Survey mean dissolved oxygen concentrations and percent saturation in Stellwagen
Basin, 1992-2000...................................................................................................................86

2000 OUTFALL MONITORING OVERVIEW VIII 
List of Tables 
Table 1-1. Roster of panel and committee members .......................................................................4 
Table 1-2. Summary of the monitoring program .............................................................................6 
Table 1-3. Summary of contingency plan threshold parameters .....................................................7 
Table 1-4. List of monitoring reports submitted to OMSAP ...........................................................9 
Table 2-1. Reporting requirements of the outfall permit ...............................................................13 
Table 2-2. Contingency plan threshold values and 2000 for effluent monitoring .........................18 
Table 3-1. Contingency plan threshold values for water column monitoring ...............................37 
Table 4-1. Contingency plan baseline and threshold values for sea floor monitoring ..................52 
Table 5-1. Contingency plan baseline and threshold values for fish and shellfish monitoring .....62 
Table 6-1. Contingency plan thresholds and threshold testing results for 2000 ambient discharge
monitoring ............................................................................................................................71 
Table 7-1. Fecal coliform bacteria counts from the Boston Harbor outfall location and
Massachusetts Bay. ...............................................................................................................79 
Table 7-2. Enterococcus bacteria counts from the Boston Harbor outfall location and from
Massachusetts Bay.................................................................................................................79 
Table 8-1. Issues of concern for the Stellwagen Bank National Marine Sanctuary .....................83

2000 OUTFALL MONITORING OVERVIEW 2 
1. Introduction 
Background 
Since its creation in 1985, the Massachusetts Water Resources Authority
(MWRA) has worked to end long-standing violations of the Clean Water
Act that resulted from the discharge of sewage sludge and primary-treated
effluent into Boston Harbor. Sludge discharges ended in 1991, and
MWRA has taken several steps to minimize effects of wastewater
discharge. These efforts include source reduction to prevent pollutants
from entering the waste stream, improved treatment before discharge, and
better dilution once the effluent enters the marine environment. 
Source reduction has included projects to lessen household hazardous
waste disposal and minimize mercury discharges from hospitals and
dentists. An ongoing industrial pretreatment/pollution prevention program
ensures that toxic contaminants are removed before they reach the sewer
system. In addition, best management practices are employed at sewer
facilities to mitigate accidental discharge of pollutants. Operator training
programs and process control and maintenance tracking systems are also
in place. 
Improved treatment began in 1995, when a new primary treatment plant at
Deer Island was brought on line, and disinfection facilities were
completed. The first and second batteries of secondary treatment began
operation in 1997 and 1998. Also during 1998, discharge from the Nut
Island Treatment Plant into Quincy Bay ended. All sewage is now
conveyed to Deer Island for treatment. A final battery of secondary
treatment was completed in 2000 and became operational in 2001. 
Better dilution has been achieved by diverting the effluent discharge from
Boston Harbor to a new outfall and diffuser system, located 9.5 miles
offshore in Massachusetts Bay (Figure 1-1). The outfall location was
selected because it had a water depth and current patterns that would
promote effective dilution, it was the least likely to affect sensitive
resources, and it was feasible to construct an outfall tunnel to the location.
The new outfall began operation on September 6, 2000.

2000 OUTFALL MONITORING OVERVIEW 4 
Cape Cod Bay
Marine Sanctuary
Stellwagen Bank
National Marine
Sanctuary 
S t e l l
w
a
g
e
n
B a
n
k 
Barrier beaches
Former Mass Bay Disposal Site,
or Foul Area (FA)
Shipping Lane
Industrial discharges
Legend
Average ocean current direction
State Ocean
Sanctuary
Federal Marine
Sanctuary
State Area of Critical
Environmental Concern
Former Industrial Waste Site (IWS)
Present Mass. Bay Disposal Site (MBDS)
FA
IWS
MBDS
Cape Cod Bay
Area of
Critical
Environmental
Concern
(Right Whale
Sanctuary)
Cape Cod Bay
Ocean Sanctuary
North Essex
Ocean Sanctuary
South Essex
Ocean Sanctuary
New MWRA outfall site
Sewage treatment plant
outfalls 
Figure 1-1. Map of Massachusetts and Cape Cod bays 
The outfall tunnel is bored through bedrock. It has a diffuser system made
up of 55 risers, each with 8 ports, along its final 1.25 miles. Discharge
from the diffuser heads is at the sea floor, at water depths of about 100 feet
(MWRA 1997a). Initial dilution at the outfall is about 5 times that of the
Boston Harbor outfall, which was shallower, in 50 feet of water. The
offshore location of the new outfall diffuser ensures that within a tidal
cycle, even shoreward currents will not transport effluent to beaches or
shellfish beds near Boston, the North Shore, the South Shore, or Cape
Cod. 
MWRA’s goals are to make it safe to swim in the harbor, safe to eat fish
caught there, to protect marine resources, and to ensure that the harbor
becomes and remains a resource that people can aesthetically enjoy,
without degrading the offshore environment. For many of the components

2000 OUTFALL MONITORING OVERVIEW 5 
of MWRA’s work, there has been little or no argument that the project
benefits the marine environment and the people of the region. One aspect
of the project, moving the effluent outfall from the harbor to
Massachusetts Bay, has raised some concerns. The concerns have been
recognized by MWRA and by the joint permit for the outfall issued by the
U.S. Environmental Protection Agency (EPA) and the Massachusetts
Department of Environmental Protection (MADEP). 
Outfall Permit 
Discharges from the new outfall are regulated by a permit issued by EPA
and MADEP under the National Pollutant Discharge Elimination System
(NPDES). The permit, first drafted in May of 1999 and finalized in July
2000, limits discharges of pollutants and requires reporting on the
treatment plant operation and maintenance. It requires MWRA to
continue an ongoing pollution prevention program that encompasses all
users of the system—industrial, commercial, and residential and to
implement best management practices aimed at preventing accidental
discharge of pollutants to the sewer system. 
The permit requires MWRA to monitor the effluent and the ambient
receiving waters for compliance with permit limits and in accordance with
the monitoring plan (MWRA 1991, 1997a) developed in response to the
EPA Supplemental Environmental Impact Statement (SEIS, EPA 1988).
The permit requires MWRA to update, maintain, and run the three-
dimensional Bays Eutrophication Model, and measure the dilution at the
discharge. MWRA must implement a contingency plan (MWRA 1997b,
2001), which identifies relevant environmental quality parameters and
thresholds, which, if exceeded, would require a response. 
EPA and MADEP have established an independent panel of scientists to
review monitoring data and provide advice on key scientific issues related
to the permit. This panel is called the Outfall Monitoring Scientific
Advisory Panel (OMSAP, Table 1-1). OMSAP conducts peer reviews of
monitoring reports, evaluates the data, and advises EPA and MADEP on
implications. OMSAP also provides advice concerning any proposed
modifications to the monitoring or contingency plans. 
OMSAP may form specialized focus groups when specific technical issues
require expanded depth or breadth of expertise. For example, the Model
Evaluation Group meets periodically to review MWRA’s water quality
model. Two standing sub-committees also advise OMSAP. The Public
Interest Advisory Committee (PIAC) represents local, non-governmental
organizations and environmental groups and advises OMSAP on values
and uses of the harbor and the bays. The Inter-agency Advisory

2000 OUTFALL MONITORING OVERVIEW 6 
Committee (IAAC) represents state and federal agencies and provides
OMSAP with advice concerning environmental regulations.

2000 OUTFALL MONITORING OVERVIEW 7 
Table 1-1. Roster of panel and committee members 
OMSAP as of December 2000 
Andrew Solow, Woods Hole Oceanographic Institution (chair) 
Robert Beardsley, Woods Hole Oceanographic Institution 
Norbert Jaworski, retired 
Robert Kenney, University of Rhode Island 
Scott Nixon, University of Rhode Island 
Judy Pederson, MIT Sea Grant 
Michael Shiaris, University of Massachusetts, Boston 
James Shine, Harvard School of Public Health 
Juanita Urban-Rich, University of Massachusetts, Boston 
Catherine Coniaris, New England Interstate Water Pollution Control
Commission (OMSAP assistant) 
IAAC as of December 2000 
Salvatore Testaverde (chair, representative of
National Marine Fisheries Service) 
MA Coastal Zone Management 
Christian Krahforst 
Jan Smith (alternate) 
MA Department of Environmental Protection 
Russell Isaac 
Steven Lipman (alternate) 
MA Division of Marine Fisheries 
Jack Schwartz 
James Fair (alternate) 
National Marine Fisheries Service 
David Dow (alternate) 
Stellwagen Bank National Marine Sanctuary 
Craig MacDonald 
US Army Corps of Engineers 
Thomas Fredette 
US Environmental Protection Agency 
Matthew Liebman 
David Tomey (alternate) 
US Geological Survey 
Michael Bothner 
PIAC as of December 2000 
Polly Foley (chair, representative of Save the
Harbor/Save the Bay) 
Association for the Preservation of Cape Cod 
Maggie Geist 
Bays Legal Fund 
Wayne Bergeron 
The Boston Harbor Association 
Vivian Li 
Joan LeBlanc (alternate) 
Cape Cod Commission 
John Lipman 
Steve Tucker (alternate) 
Center for Coastal Studies 
Peter Borrelli 
Conservation Law Foundation 
Anthony Chatwin 
New England Aquarium 
Marianne Farrington 
Massachusetts Audubon Society 
Robert Buchsbaum 
MWRA Advisory Board 
Joseph Favaloro 
Safer Waters in Massachusetts 
Salvatore Genovese 
Polly Bradley (alternate) 
Save the Harbor/Save the Bay 
Bruce Berman (alternate) 
Stop the Outfall Pipe 
Mary Loebig 
Wastewater Advisory Committee 
Katherine O’Meara 
Monitoring Program 
EPA and MADEP require monitoring to ensure compliance with the
permit, to assess whether the outfall has effects beyond the area identified
in the SEIS as acceptable, and to collect data useful for outfall
management. During 1989-1991, in anticipation of these requirements,
MWRA began to study winter flounder with the Woods Hole
Oceanographic Institution (WHOI), eutrophication issues with the
Bigelow Laboratory for Ocean Sciences, and long-term sediment transport
with the U.S. Geological Survey (USGS). A broader baseline-monitoring
program began in 1992. During the intervening years, both baseline and
discharge ambient monitoring plans have been developed and refined

2000 OUTFALL MONITORING OVERVIEW 8 
(MWRA 1991, 1997a). These plans were developed by MWRA, under
the direction of an Outfall Monitoring Task Force (OMTF), made up of
scientists, regulators, and environmental advocacy groups. The OMTF
was disbanded upon creation of OMSAP in 1998. 
The outfall-monitoring program focuses on critical constituents in
treatment plant effluent, such as nutrients, organic material, toxic
contaminants, pathogens, and solids (Table 1-2). Presence and potential
effects of these constituents are evaluated within the context of four
environmental measurement areas: effluent, water column, sea floor, and
fish and shellfish. This basic program is augmented by special studies that
are conducted in response to specific permit requirements, scientific
questions, and environmental concerns. The monitoring program is
designed to compare environmental quality of the Massachusetts Bay
system, including Boston Harbor and Cape Cod Bay, before and after the
outfall location moved from the harbor to the bay. 
Baseline monitoring was initially planned to last for a minimum of three
years, as the outfall was originally planned for completion in 1995.
Delays in outfall construction have allowed a relatively long period for
baseline studies. Consequently, MWRA has been able to document
greater natural variability and develop a better understanding of the system
than would have been possible in a briefer baseline period. The extended
time has also allowed MWRA to evaluate the response in Boston Harbor
to other parts of the Boston Harbor project, such as improved
pretreatment, ending sludge discharges, and initiation of secondary
treatment of the effluent (Leo et al. 1995, Pawlowski et al. 1996, Rex and
Connor 1997, Rex 2000). Finally, the extended period has meant that the
discharges to Massachusetts Bay, when they did begin, had the benefit of
nearly complete implementation of secondary treatment. 
The monitoring plan is a “living document.” That is, every effort is made
to incorporate new scientific information and improved understanding
resulting from the monitoring program into appropriate thresholds.
MWRA’s NPDES permit requires an annual list of proposed changes to
the monitoring plan. 
Contingency Plan 
The original MWRA contingency plan (MWRA 1997b and available at
www.mwra.com) describes how, if monitoring results indicate a possible
environmental problem, MWRA and the regulatory agencies will respond
to determine the cause of the problem and to specify the corrective actions
that should be taken if the problem appears to be related to the discharge.
The contingency plan identifies the parameters that represent
environmentally significant components of the effluent or the ecosystem

2000 OUTFALL MONITORING OVERVIEW 9 
that, if specific levels are exceeded, indicate a potential for environmental
risk (Table 1-3). These levels are called thresholds. The plan provides a
process for evaluating parameters that exceed thresholds and formulating
appropriate responses. 
Table 1-2. Summary of the monitoring program 
Task Objective Sampling Locations 
And Schedule 
Analyses 
Effluent 
Monthly Toxicity 
Weekly Nutrients 
Daily Organic material (cBOD) 
Several times monthly Toxic contaminants 
3x/day Bacterial indicators, total
chlorine residual 
Effluent sampling Characterize wastewater
discharge from Deer Island
Treatment Plant 
Daily Solids 
Water Column 
Nearfield surveys Collect water quality data near
outfall location 
17 surveys/year 
21 stations 
Farfield surveys Collect water quality data
throughout Massachusetts and
Cape Cod bays 
6 surveys/year 
26 stations 
Temperature 
Salinity 
Dissolved oxygen 
Nutrients 
Solids 
Chlorophyll 
Water clarity 
Photosynthesis 
Respiration 
Plankton 
Marine mammal observations 
Plume-track surveys Track locations and
characteristics of discharge
plume, measure dilution of
discharge 
2 surveys planned for 2001 Rhodamine dye 
Salinity 
Temperature 
Currents 
Nutrients 
Solids 
Selected metals 
Bacterial indicators 
Mooring (USGS) Provides continuous
oceanographic data near
outfall location 
Continuous monitoring 
Two locations 
3 depths 
Currents 
Temperature 
Salinity 
Water clarity 
Chlorophyll 
Remote sensing Provides oceanographic data
on a regional scale through
satellite imagery 
Available daily (cloud-cover
permitting) 
Surface temperature 
Chlorophyll 
Sea Floor 
Soft-bottom studies Evaluate sediment quality and
benthos in Boston Harbor and
Massachusetts Bay 
1 survey/year 
20 nearfield stations 
11 farfield stations 
Sediment chemistry 
Sediment profile imagery 
Community composition 
Hard-bottom studies Characterize marine benthic
communities in rock and
cobble areas 
1 survey/year 
21 stations on 6 transects 
Topography 
Substrate 
Community composition 
Fish and Shellfish 
Winter flounder Determine contaminant body
burden and population health 
1 survey/year 
5 locations 
Tissue contaminant
concentrations 
Physical abnormalities,
including liver histopathology 
American lobster Determine contaminant body
burden 
1 survey/year 
3 locations 
Tissue contaminant
concentrations 
Physical abnormalities 
Blue mussel Evaluate biological condition
and potential contaminant
bioaccumulation 
1 survey/year 
4 locations 
Tissue contaminant
concentrations

2000 OUTFALL MONITORING OVERVIEW 10 
Threshold values, the measurements selected as indicators of the need for
action, are based on permit limits, state water quality standards, and expert
opinion. To alert MWRA to any changes, most parameters have “caution”
as well as “warning” thresholds. Exceeding thresholds could indicate a
need for increased attention or study. If a threshold, is exceeded, MWRA,
with guidance from OMSAP and the regulatory agencies, may expand the
monitoring to track effluent quality and environmental conditions. The
data are examined to determine whether it is likely that an unacceptable
effect resulting from the outfall has occurred. 
Exceeding warning levels could, in some circumstances, indicate a need
for a response to avoid potential adverse environmental effects. If a
threshold is exceeded at a warning level, the response includes early
notification to EPA and MADEP and, if the outfall has contributed to
adverse environmental effects, the quick development of a response plan.
Response plans include a schedule for implementing actions, such as
additional monitoring, making adjustments in plant operations, or
undertaking an engineering feasibility study regarding specific potential
corrective activities. 
Table 1-3. Summary of contingency plan threshold parameters 
Monitoring 
Area 
Parameter 
pH 
Fecal coliform bacteria 
Residual chlorine 
Total suspended solids 
Biological oxygen demand 
Toxicity 
PCBs 
Plant performance 
Effluent 
Total nitrogen load 
Floatables, Oil and grease 
Dissolved oxygen concentration 
Dissolved oxygen percent saturation 
Dissolved oxygen depletion rate 
Chlorophyll 
Nuisance and noxious algae 
Water Column 
Effluent dilution 
Benthic community structure 
Sediment oxygen 
Sea Floor 
Sediment toxic metal and organic chemicals 
Mercury, PCBs, and lipid-normalized toxic
compounds in mussels and flounder and lobster
meat 
Lead in mussels 
Fish and Shellfish 
Liver disease in flounder

2000 OUTFALL MONITORING OVERVIEW 11 
Like the monitoring plan, every effort is made to incorporate new
scientific information and improved understanding resulting from the
monitoring program into appropriate thresholds. A process for modifying
the contingency plan is set forth in MWRA’s NPDES permit. 
In November 2000, MWRA requested several modifications to the
contingency plan. After review by OMSAP and regulatory comment and
public comment, a revised contingency plan was issued in May 2001.
Several changes were made to the plan: 

 Adding the benthic opportunist thresholds and making those
thresholds more stringent than had been suggested in the ambient
monitoring plan. 

 Removing the zooplankton threshold but requiring MWRA to
report annually on appreciable changes to the zooplankton
community and on ongoing special zooplankton studies. 

 Removing the floatables threshold but requiring MWRA to carry
out sampling studies to develop a new threshold. 
Other changes were made on an interim basis and will be submitted by
MWRA for agency review and public comment in November 2001.
Those interim changes include 

 Calculation of background conditions for the dissolved oxygen
percent saturation and concentration thresholds. 

 Change in the nearfield Alexandrium (red tide) cell count threshold
from the 95 th percentile of the seasonal mean to 100 cells/L in any
sample. In addition, MWRA and the Woods Hole Oceanographic
Institution are deriving an improved threshold for “new evidence”
of paralytic shellfish poisoning toxin in shellfish. 
Data Management 
The outfall-monitoring program has generated extensive data sets
documenting baseline environmental conditions. Data quality is
maintained through program-wide quality assurance and quality control
procedures. After validation, data from field surveys and laboratory
analyses are loaded into a centralized project database. Data handling
procedures are automated to the maximum extent possible to reduce
errors, ensure comparability, and minimize reporting time. Data that are
outside the expected ranges are flagged for review. Data reported by the
laboratory as suspect (for example, because the sample bottle was cracked
in transit) are marked as such and not used in interpretation, although they
are retained in the database and included in raw data reports. Any
corrections are documented. Each data report notes any special data
quality considerations associated with the data set.

2000 OUTFALL MONITORING OVERVIEW 12 
As discharge and monitoring results become available, they are compared
with contingency plan thresholds. Computer programs calculate each
threshold parameter value from the data, compare it to the threshold, and
notify the project staff if any caution or warning levels are exceeded. 
Reporting 
MWRA’s NPDES permit requires extensive reporting on the monitoring
program, including a variety of reports submitted to OMSAP for review
and regular reports on effluent quality (Table 1-4). Changes to the
monitoring program or contingency plan must be reviewed by regulators
and published in the Environmental Monitor . Data that exceed
contingency plan thresholds and corrective actions must also be reported.
Data that exceed thresholds must be reported within five days after the
results become available, and MWRA must make all reasonable efforts to
report all data within 90 days of each sampling event. 
Reports are posted on MWRA’s web site (www.mwra.com), with copies
placed in repository libraries in Boston and on Cape Cod. OMSAP also
holds public workshops where outfall-monitoring results are presented. 
Table 1-4. List of monitoring reports submitted to OMSAP 
Report Description/Objectives 
Outfall Monitoring Plan 
Phase I—Baseline Studies (MWRA
1991) 
Phase II—Discharge Ambient
Monitoring (MWRA 1997a) 
Discusses goals, strategy, and design of
baseline and discharge monitoring programs. 
Contingency Plan (MWRA 1997b,
2001) 
Describes development of threshold
parameters and values and MWRA’s planned
contingency measures. 
Program Area Synthesis Reports Summarize, interpret, and explain annual
results for effluent, water column, benthos,
and fish and shellfish monitoring areas. 
Toxics and Nutrients Issues Reports Discuss, analyze, and cross-synthesize data
related to toxic and nutrient issues in
Massachusetts and Cape Cod bays. 
Outfall Monitoring Overviews Summarize monitoring data and include
information relevant to the contingency plan. 
Outfall Monitoring Overview 
Among the many reports that MWRA completes, this report, the outfall
monitoring overview, is prepared for each year of the monitoring program
(Gayla et al. 1996, 1997a, 1997b, Werme and Hunt 2000a, 2000b). The
report includes a scientific summary of each year of monitoring.
Overviews for 1995-1999 included only baseline information. With the
outfall operational, this report will include information relevant to the
contingency plan, such as data that exceed thresholds, responses, and

2000 OUTFALL MONITORING OVERVIEW 13 
corrective activities. When data suggest that monitoring activities,
parameters, or thresholds should be changed, the report will summarize
those recommendations. 
This year’s outfall monitoring overview presents monitoring program
results for baseline effluent and field data collected up to the date the
outfall was commissioned, September 6, 2000. The report discusses the
final baseline results and contingency plan thresholds that are based on
those results. The report also gives the first observations of discharge
monitoring (September 6-December 31, 2000), together with the
Contingency Plan report for that period. It also provides a section on data
relevant to the Stellwagen Bank National Marine Sanctuary.

2000 OUTFALL MONITORING OVERVIEW 11 
2. Effluent 
Background 
Pollution Prevention and Wastewater Treatment 
MWRA’s strategy for improving the environmental quality of Boston
Harbor without degrading Massachusetts and Cape Cod bays relies on
reduction of pollutants at their sources, along with effective treatment.
The MWRA Toxic Reduction and Control Program sets and enforces
limits on the types and amounts of pollutants that industries can
discharge into the sewer system. Continuing the source reduction
program and making sure that the treatment plant is working as designed
are the most important actions MWRA can take to ensure that the
relocated outfall does not cause any harm to the environment. 
To mitigate accidental discharge of pollutants to the system, MWRA has
developed best management practice plans for the Deer Island plant, its
headworks facilities, the combined sewer overflow facilities, and the
sludge pelletizing plant. These plans have been implemented. They
include inspections, which are conducted at least once a year by non-
facility staff. 
Environmental Concerns 
Effluent constituents of concern include pathogens, chlorine, solids,
organic matter, nutrients, toxic contaminants, pH, and “floatables.”
Floatables include oil and grease slicks, as well as plastic and other
debris. 
Pathogens, including bacteria, viruses, and protozoa are found in human
and animal waste and can cause disease. Human exposure to water-
borne pathogens can occur through consumption of contaminated
shellfish or through ingestion or physical contact while swimming.
MWRA disinfects the effluent and is required to meet water quality
standards for fecal coliform bacteria, an indicator of the presence of
pathogens. 
Disinfection is accomplished by addition of a form of chlorine, sodium
hypochlorite, which is the active ingredient in bleach. Unfortunately,
while sodium hypochlorite is effective in destroying pathogens, at high
enough concentration, it is also harmful to marine life. Better solids
removal by secondary treatment and the longer time that the effluent is

2000 OUTFALL MONITORING OVERVIEW 12 
exposed to chlorine in the outfall tunnel allow MWRA to minimize the
amount of chlorine added while still achieving effective disinfection. 
Suspended solids, small particles of debris in the water column, decrease
water clarity and consequently affect growth and productivity of algae
and other marine plants. Excess suspended solids also detract from
people’s aesthetic perception of the environment. As noted above,
suspended solids can also interfere with disinfection. 
Organic material, a major constituent of sewage effluent, consumes
oxygen as it decays. Even under natural conditions, oxygen levels
decline in bottom waters during the late summer, so any effluent
component that might further decrease oxygen levels is a concern. Too
much organic material could also disrupt the sea-bottom ecosystem. 
In marine waters, nitrogen is the limiting nutrient that controls growth of
algae and other aquatic plants. Excess nitrogen can be detrimental,
leading to eutrophication and low levels of dissolved oxygen, excess
turbidity, and nuisance algal blooms. Nutrients, particularly dissolved
forms, are the only components of sewage entering the treatment plant
that are not substantially reduced by secondary treatment. 
Some toxic contaminants can accumulate in marine life, potentially
affecting human health if contaminated seafood is consumed. Toxic
contaminants can lower survival and reproduction of marine organisms.
Toxic metals and organic contaminant levels in MWRA wastewater have
dramatically declined since 1989, due to source reduction and secondary
treatment. 
Seawater is noted for its buffering capacity, that is, its ability to
neutralize acids and bases. However, state water quality standards
dictate that effluent discharges not change the pH of the ambient
seawater more than 0.5 standard units. Consequently, the outfall permit
sets both upper and lower values for pH of the effluent. Because of the
pure oxygen used in the activated sludge reactors, the effluent pH tends
to be at the lower, more acidic, limit of the allowable pH range. 
The oil and grease slicks and floating debris that comprise floatables
pose an aesthetic concern. Plastic debris can also be harmful to marine
life, as plastic bags are sometimes mistaken for food and clog the
digestive systems of turtles and mammals. Plastic can also entangle
animals and cause them to drown.

2000 OUTFALL MONITORING OVERVIEW 13 
Monitoring Design 
The main purpose of effluent monitoring is to measure the
concentrations and variability of constituents of the effluent. Effluent
monitoring is designed to assess compliance with NPDES permit limits,
which are based on state and federal water quality standards and criteria,
ambient conditions, and the projected dilution at the outfall (Table 2-1).
Effluent monitoring also provides accurate mass loads of effluent
constituents, so that fate, transport, and risk of contaminants can be
assessed. 
Table 2-1. Reporting requirements of the outfall permit 
Parameter Sample Type Frequency 
Flow, million gallons/day
(MGD) Flow meter Continuous 
Flow Dry Day, MGD Flow meter Continuous 
cBOD 24-hr Composite 1/Day 
TSS 24-hr Composite 1/Day 
pH Grab 1/Day 
Fecal Coliform Bacteria Grab 3/Day 
Total Residual Chlorine Grab 3/Day 
PCB, Aroclors 24-hr Composite 1/Month 
LC50 24-hr Composite 2/Month 
C-NOEC 24-hr Composite 2/Month 
Settleable Solids Grab 1/Day 
Chlorides (Influent only) Grab 1/Day 
Mercury 24-hr Composite 1/Month 
Chlordane 24-hr Composite 1/Month 
4,4 – DDT 24-hr Composite 1/Month 
Dieldrin 24-hr Composite 1/Month 
Heptachlor 24-hr Composite 1/Month 
Ammonia-Nitrogen 24-hr Composite 1/Month 
Total Kjeldahl Nitrogen 24-hr Composite 1/Month 
Total Nitrate 24-hr Composite 1/Month 
Total Nitrite 24-hr Composite 1/Month 
Cyanide, Total Grab 1/Month 
Copper, Total 24-hr Composite 1/Month 
Total Arsenic 24-hr Composite 1/Month 
Hexachlorobenzene 24-hr Composite 1/Month 
Aldrin 24-hr Composite 1/Month 
Heptachlor Epoxide 24-hr Composite 1/Month 
Total PCBs 24-hr Composite 1/Month 
Volatile Organic Compounds Grab 1/Month 
The permit includes numeric limits for suspended solids, fecal coliform
bacteria, pH, chlorine, polychlorinated biphenyls (PCBs), and
carbonaceous biochemical oxygen demand (cBOD). In addition, state
water quality standards establish limits for 158 pollutants, and the permit
prohibits any discharge that would cause or contribute to exceeding of

2000 OUTFALL MONITORING OVERVIEW 14 
any of those limits. The permit also prohibits discharge of nutrients in
amounts that would cause eutrophication. The permit requires MWRA
to test the toxicity of the effluent as a whole on sensitive organisms and
establishes strict limits based on the tests. Allowable concentrations of
contaminants were based on the predicted dilution at the new outfall.
Actual dilution is being measured now that the outfall is discharging.
Preliminary results suggest that dilution is as great as had been predicted. 
Most parameters require 24-hour composite samples, and some must
meet daily, weekly, or monthly limits. Flow is measured continuously.
Nutrient measurements include total Kjeldahl nitrogen, ammonia, nitrate,
nitrite, total phosphorus, and phosphate. Organic material is monitored
by measuring the cBOD. Monitoring for toxic contaminants includes
analyses for heavy metals of concern, chlorinated pesticides, PCBs,
volatile organic compounds, PAHs, total residual chlorine, and cyanide.
Toxicity is tested using whole effluent samples. Tests for acute toxicity
include 48-hour survival of mysid shrimp ( Americamysis bahia , formerly
known as Mysidopsis bahia ) and inland silverside ( Menidia beryllina ).
Chronic toxicity is assessed through inland silverside growth and
survival and sea urchin ( Arbacia punctulata ) one-hour fertilization tests.
Pathogen monitoring consists of enumeration of fecal coliform bacteria.
Total suspended solids (TSS) and settleable solids are also measured.
Methods for measuring floatables remain under development. 
Figure 2-1. Daily effluent flow in 2000 
Daily Flow in 2000
0
100
200
300
400
500
600
700
800
900
1000
Jan-00
Feb-00
Mar-00
Apr-00
May-00
Jun-00
Jul-00
Aug-00
Sep-00
Oct-00
Nov-00
Dec-00
Date
Flow (MGD)
Daily Flow

2000 OUTFALL MONITORING OVERVIEW 15 
Figure 2-2. Annual solids, nitrogen, and metals discharges 
Total Nitrogen Discharged by MWRA
0
2000
4000
6000
8000
10000
12000
14000
16000
1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000
Year 
Nitrogen ( mtons/yr) 
Total Nitrogen
Warning
Caution
Metals in MWRA Treatment Plant Discharges 1989-2000
0
200
400
600
800
1000
1200
89 90 91 92 93 94 95 96 97 98 99 00
Year
Average pounds per day discharged Silver
Nickel
Chromium
Lead
Copper
Zinc
MWRA Solids Discharges to Boston Harbor
0
20
40
60
80
100
120
140
160
180
88 89 90 91 92 93 94 95 96 97 98 99 00
Year
Tons per day
Sludge
Nut Island
Deer Island

2000 OUTFALL MONITORING OVERVIEW 16 
Results 
Average daily flow of effluent from the Deer Island treatment plant in
2000 was 362 million gallons per day (Figure 2-1), slightly more than
1999, which had been a year of drought. Because of the higher flows,
approximately 85% of the flow received secondary treatment, slightly
less than 1999. With the final battery of secondary treatment
operational, MWRA anticipates that 98% of the flow will receive
secondary treatment. 
Total solids discharged in the effluent remained low, about 32 tons per
day (Figure 2-2). Solids removal has steadily increased over the past 10
years and will continue to improve with the addition of the third battery
of secondary treatment. As a result, monthly average TSS and cBOD
have declined and remained low in 2000, reflecting the implementation
of secondary treatment (Figure 2-3). 
Although secondary treatment effectively removes most contaminants, it
has less effect on nutrients. As a result of implementation of secondary
treatment in 1997 and 1998, nitrogen loads have been reduced to levels
that meet contingency plan thresholds (Figure 2-2). Of the nitrogen
released, 20% is organic nitrogen, 72% is ammonium and 8% is nitrate.
Ammonium levels have increased slightly, due to the secondary
treatment and the addition of “pressate” from the sludge treatment
process. When the final battery of secondary treatment comes on line,
total nitrogen loads should slightly decrease. 
Discharge of toxic compounds in 2000 was similar to 1999. Metals
loads were slightly higher due to the somewhat higher flow, however
metals loads have declined dramatically since 1989 (Figure 2-2).
Organic contaminant loads have also declined. No data are available
from the 1980s, as detection limits achieved by the available analytical
methods were not low enough to detect the toxic compounds of concern
until the mid-1990s. Since 1996, before implementation of secondary
treatment, until 1999-2000, with 87% secondary treatment, PAH
concentrations declined 88%, from 8,250 to 980 ng/l. Likewise, PCB
concentrations declined 79%, from 11 to 2.3 ng/l, and DDT
concentrations declined 78%, from 5 to 1.1 ng/l. 
Overall, many contaminant loads are less than had been predicted in
EPA’s SEIS for the outfall. These differences result from lower than
expected flows, effective industrial pretreatment, and dramatic
improvements to analytical methods since the preparation of the SEIS.
Predictions in the SEIS were based on presumptions of contaminant
concentrations that were reported as “below detection limits.” With
analytical improvements that lowered detection limits, MWRA found
that concentrations of contaminants are lower than had been presumed.

2000 OUTFALL MONITORING OVERVIEW 17 
Loadings of many contaminants are also lower than had been predicted
in a 1997 pilot plant study. That study evaluated high flow and stressed
conditions. The actual treatment plant under ambient conditions
performs better than the test plant. The lower than predicted loads
suggest that potential effects of the outfall may also be less than the
minimal effects predicted in the SEIS. 
Figure 2-3. Monthly average TSS and monthly BOD (measured as cBOD since 1997) from
1994-2000. Weekly TSS and cBOD during the period in 2000 that the offshore outfall was
discharging. 
Monthly Average TSS, Deer Island, 1994-2000
0
10
20
30
40
50
60
70
80
90
100
Jan
Apr
Jul
Oct
Jan
Apr
Jul
Oct
Jan
Apr
Jul
Oct
Jan
Apr
Jul
Oct
Jan
Apr
Jul
Oct
Jan
Apr
Jul
Oct
Jan
Apr
Jul
Oct
Year
TSS (mg/L)
TSS
TSS Limit 1999 Permit
1994 1995 1996 1997 1998 1999 2000
Monthly BOD, Deer Island 1994-2000
0
20
40
60
80
100
120
140
160
Jan
Apr
Jul
Oct
Jan
Apr
Jul
Oct
Jan
Apr
Jul
Oct
Jan
Apr
Jul
Oct
Jan
Apr
Jul
Oct
Jan
Apr
Jul
Oct
Jan
Apr
Jul
Oct
Year
BOD (Monthly Average in mg/L) BOD
cBOD
cBOD Limit 1999 Permit
1994 1995 1996 1997 1998 1999 2000
TSS Weekly Mean
0
10
20
30
40
50
60
Month
TSS (mg/L)
TSS Weekly Mean
TSS Permit Limit (<=45) 
September October November December Jan. 2001
cBOD Weekly Mean
0
10
20
30
40
50
60
70
Month
cBOD (mg/L)
cBOD Weekly Mean
cBOD Permit Limit (<=40)
September October November December Jan. 2001

2000 OUTFALL MONITORING OVERVIEW 18 
Table 2-2. Contingency Plan threshold values and 2000 results for effluent monitoring 
Parameter Caution Level Warning Level 
September 6 –
December 31, 2000
Results 
Fecal coliform bacteria None 
14,000 fecal coliforms/100
ml (monthly 90 th percentile,
weekly geometric mean,
maximum daily geometric
mean, and minimum of 3
consecutive samples) 
Not exceeded 
Chlorine, residual None 631 ug/l daily, 
456 ug/l monthly 
One warning level
exceedance = 900 ug/l;
should not be repeated
with implementation of
feedback for
dechlorination 
Total suspended solids None 45 mg/l weekly 
30 mg/l monthly Not exceeded 
cBOD None 40 mg/l weekly, 
25 mg/l monthly Not exceeded 
Toxicity None 
Acute: effluent LC50<50%
for shrimp and fish 
Chronic: effluent NOEC for
fish survival and growth and
sea urchin fertilization
<1.5% effluent 
Not exceeded 
PCBs Aroclor=0.045 ng/l Not exceeded 
Plant performance 5 violations/year Noncompliance >5% of the
time Not applicable 
pH None <6 or >9 
One warning level
exceedance = 5.8, due to
sampling artifact 
Flow None Flow >436 for annual
average of dry days Not applicable 
Total nitrogen load 12,500 mtons/year 14,000 mtons/year Not applicable 
Oil and Grease None 15 mg/l weekly Not exceeded 
Floatables Threshold revision
pending 
Contingency Plan Thresholds 
Two permit violations were reported after the contingency plan became
effective on September 6, 2000, one for pH level and one for residual
chlorine (Table 2-2, Figure 2-4). Subsequent testing suggested that the
low pH level did not result from plant operations but from a flawed
sampling protocol. During regular plant operations, the effluent “off-
gasses” during transit in the disinfection basins, resulting in an increased
pH. The effluent sampling site and method did not allow for this off-
gassing to occur. Consequently, measured pH values were typically low
by approximately 0.2 standard units. As a result of the violation,
MWRA has improved its sampling technique and worked to ensure that
pH levels are high enough to result in no further violations.

2000 OUTFALL MONITORING OVERVIEW 19 
Figure 2-4. Monthly pH, daily mean chlorine residual, and fecal coliform
bacteria data from the period in 2000 in which the outfall was discharging 
Monthly pH, Maximum and Minimum
5.0
5.5
6.0
6.5
7.0
7.5
8.0
8.5
9.0
9.5
10.0
September October November December
Month
pH (S.U.)
pH Max pH Min
Max permit limit (9) Min permit limit (6)
Fecal Coliform Bacteria, Weekly Geometric Mean
1
10
100
1000
10000
100000
Month
Fecal Coliform (# colonies/100mL)
Fecal coliform geometric mean
Weekly permit limit (14,000)
September October November December Jan.01
Total Chlorine Residual, Daily Mean
0
100
200
300
400
500
600
700
800
900
1000
Month
TCR (ug/L)
TCR Daily Mean (ug/L) Permit Limit
September October November December

2000 OUTFALL MONITORING OVERVIEW 20 
The total chlorine residual (TCR) level was exceeded once while
MWRA was in the start-up phase of commissioning the outfall. After
disinfection, the effluent is dechlorinated by the additions of sodium
bisulfite. Automated TCR sensors now aid in determining how much
sodium bisulfite to use, but the sensors had not yet been installed. The
exceedance occurred during a rainstorm, when flow through the
treatment plant was changing rapidly. These conditions made adding the
appropriate amounts of sodium bisulfate difficult. Since the automated
TCR sensors were installed, the problem has not recurred. Although a
permit violation, the actual chlorine levels were low, 900 ppb, and no
adverse impact resulted. 
No other contingency plan exceedances for effluent occurred. Fecal
coliform bacteria levels remained well below the 14,000 bacteria per 100
ml established by the permit (Figure 2-4). Acute and chronic toxicity
tests results indicated that toxicity of the whole effluent was within
permit limits. Contaminant concentrations were also well below permit
limits.

2000 OUTFALL MONITORING OVERVIEW 21 
3. Water Column Baseline 
Background 
When MWRA’s ocean outfall began operations on September 6, 2000, it
marked the completion of baseline monitoring. This section summarizes
results from water column monitoring through the year 2000. It primarily
discusses baseline data, understanding that September through December
were in the discharge monitoring period. A more detailed discussion of
discharge monitoring, along with a report on contingency plan thresholds,
is in Section 6, Outfall Monitoring. 
Circulation and Water Properties 
Circulation, water properties, and consequently, the biology of
Massachusetts and Cape Cod bays are mainly driven by the larger pattern
of water flow in the Gulf of Maine (Figure 3-1). A general coastal current
flows southwestward and may enter the bays by Cape Ann to the north of
Boston. Water flows back out of the bays to the north of Race Point at the
tip of Cape Cod. During much of the year, a weak counterclockwise
circulation persists within eastern Massachusetts Bay and Cape Cod Bay. 
When the MWRA monitoring program began, scientists assumed that the
water quality and biology of the bays followed an annual cycle typical for
coastal waters. In fact, monitoring has shown that wind, regional
conditions, and other factors greatly influence the pattern. According to
the typical coastal cycle, waters are well mixed, and nutrient levels are
high during November through April. As light levels increase in the early
spring, phytoplankton begin the period of rapid growth known as a spring
bloom. Monitoring has shown that spring blooms do not occur every year.
During the years in which they do, the bloom begins in the shallowest
waters of Cape Cod Bay. Blooms in deeper waters begin two to three
weeks later. Spring phytoplankton blooms are typically followed by an
increase in zooplankton abundance. These zooplankton populations are
food for many animals, including the endangered right whale. 
Later in the spring, the surface waters warm, and the water column
stratifies. Inputs of freshwater from rivers contribute to the stratification,
with lower salinity water remaining at the surface. Stratification
effectively separates the surface and bottom waters, preventing
replenishment of nutrients to the surface and of oxygen to the bottom.
Phytoplankton in the surface waters deplete the available nutrients and
then undergo senescence, sinking to the bottom. Oxygen levels remain
high in the surface waters throughout the year, but oxygen is depleted in

2000 OUTFALL MONITORING OVERVIEW 22 
the bottom waters. Bottom-dwelling animals respire, and bacteria use up
oxygen as they decompose the phytoplankton, so bottom-water oxygen
levels are typically lowest during August through October. 
Figure 3-1. General circulation on Georges Bank and in the Gulf of Maine during
the summer, stratified season. Figure courtesy of Jack Cooke, WHOI graphics. 
In the fall, cooling surface waters and strong winds promote mixing of the
water column. Oxygen is replenished in the bottom waters, and nutrients
brought to the surface can stimulate a fall phytoplankton bloom.
Typically, fall blooms end in the early winter, when declining light levels
limit photosynthesis. Plankton die and decay, replenishing nutrients in the
water column. 
Surface water temperatures show nearly the same pattern each year.
Bottom water temperatures are more variable and are affected by wind
patterns. If strong southerly or southwesterly winds, that is, winds from
the south or southwest, persist during the summer, then upwelling occurs.

2000 OUTFALL MONITORING OVERVIEW 23 
Upwelling leads to colder bottom-water temperatures and also higher
concentrations of dissolved oxygen. Weaker southerly winds result in less
upwelling, with warmer bottom-water temperatures and lower levels of
dissolved oxygen. 
Environmental Concerns 
Water column monitoring focuses on concerns that relocation of the
outfall will introduce effects from organic material, nutrients, and toxic
contaminants in the effluent. Because organic material and toxic
contaminants are effectively removed by secondary treatment, but
nutrients are not, nutrient issues cause the greatest concerns. 
The concern is that excess nutrients, particularly nitrogen, could promote
algal blooms followed by low levels of dissolved oxygen when the
phytoplankton die, sink, and decompose. Another fear is that changes in
the relative levels of nutrients could stimulate growth of undesirable algae.
Three nuisance or noxious species are of particular concern: the
dinoflagellate Alexandrium tamarense , the diatom Pseudo-nitzschia
multiseries , and the colonial flagellate Phaeocystis pouchetii . 
Alexandrium tamarense typically blooms during April to June and can
cause paralytic shellfish poisoning, known as PSP or red tide. The toxin,
when sufficiently concentrated, can be fatal to marine mammals, fish, and
humans. Paralytic shellfish poisoning toxin has been periodically found in
Massachusetts since the 1970s. Pseudo-nitzschia multiseries blooms can
occur at any time of the year. In high concentrations, more than 1 million
cells per liter, it may produce domoic acid, which can cause a condition
known as amnesic shellfish poisoning. Phaeocystis pouchetii blooms
usually occur during the late winter and spring. The species is not toxic,
but individual cells can aggregate in gelatinous colonies that are poor food
for zooplankton. 
Although it is effectively removed by secondary treatment, organic
material from the wastewater effluent remains a concern. Decomposition
of organic matter consumes the oxygen necessary for survival of marine
life. Because of the concern that low levels of dissolved oxygen could
affect animals in the vicinity of the outfall, it has been important during
the baseline-monitoring period to develop an understanding of the natural
fluctuations within the system. Modeling and measurements have shown
that the periods of low oxygen that are typical in bottom waters appear to
correlate with saltier bottom waters. 
Due to source reduction and treatment, toxic contaminants discharged in
the MWRA effluent are present at extremely low concentrations. Most
monitoring for the effects of toxic contaminants will be focused on the
sediments, which are known to be contaminant sinks, and on fish and
shellfish, which could accumulate organic compounds or metals.

2000 OUTFALL MONITORING OVERVIEW 24 
Monitoring Design 
Water column monitoring includes assessments of water quality,
phytoplankton, and zooplankton in Massachusetts and Cape Cod bays.
Baseline monitoring includes four major components: nearfield surveys,
farfield surveys, continuous recording, and remote sensing. Results from
preliminary plume-tracking studies are presented in Section 6, Discharge
Monitoring; detailed studies will occur in 2001. 
Figure 3-2. Nearfield sampling stations

2000 OUTFALL MONITORING OVERVIEW 25 
Figure 3-3. Farfield sampling stations 
Nearfield surveys provide vertical and horizontal profiles of physical,
chemical, and biological characteristics of the water column in the area
around the outfall where effects of the effluent are expected (Figure 3-2).
Farfield surveys assess differences across the bays and seasonal changes
over a large area (Figure 3-3). Five stations mark the boundary of the
monitoring area and are in or near the Stellwagen Bank National Marine
Sanctuary. During 2000, 17 surveys were conducted, including six
surveys of farfield stations. Twelve of those surveys, including five that
sampled farfield stations, were conducted before the Massachusetts Bay
outfall came on line. Samples were taken from 48 stations in Boston
Harbor, Massachusetts Bay, and Cape Cod Bay.

2000 OUTFALL MONITORING OVERVIEW 26 
Parameters measured in water column monitoring include dissolved
inorganic and organic nutrients, particulate forms of nutrients, chlorophyll,
total suspended solids, dissolved oxygen, productivity, respiration,
phytoplankton abundance and species composition, and zooplankton
abundance and species composition. Nutrient measurements include the
major forms of nitrogen, phosphorus, and silica. 
The continuous recording component of the program captures temporal
variations in water quality between nearfield water quality surveys.
Remote sensing captures spatial variations in water quality on a regional
scale. 
Figure 3-4. Charles River discharge, 1990-2000, and 2000 discharge compared to the historic
mean

2000 OUTFALL MONITORING OVERVIEW 27 
Results 
Physical Conditions 
Overall, the weather in Boston in 2000 was typical. After a warm March,
the rest of the year was slightly cooler than average. The spring,
particularly June, was wet, with 4 inches of rain falling on one day, June 6.
July continued to be cool and rainy. The fall was slightly drier than
average, with two 10-day rain-free stretches in October and November. 
Wind stresses were also typical. Downwelling conditions persisted during
the spring. The upwelling conditions typical during the summer were
somewhat less strong than average. Downwelling conditions in October
were stronger than usual. Average wind speeds were typical, and there
were no extreme wind-stress events. 
Figure 3-5. Surface and bottom temperature and salinity, 1992-2000

2000 OUTFALL MONITORING OVERVIEW 28 
Water temperatures followed a typical pattern in the surface and at the
bottom (Figure 3-5), except that bottom waters were warm in June,
following the major storm. There was no dramatic decline in temperatures
in the fall. 
Similar to 1999, which was a drought year, surface and bottom salinities
were typical (Figure 3-5). Conditions resulted in a typical annual pattern
of water stratification in 2000. Stratification was largely controlled by
water temperature rather than salinity through August. The stratification
pattern was broken, not by an intense hurricane season, but by gradual
seasonal changes during late August through mid-September. 
Water Quality 
The nutrient cycles for 2000 were typical for the baseline-monitoring
period. Nitrate concentrations were high during the winter and decreased
sharply between February and March with spring blooms of diatoms and
the flagellate Phaeocystis pouchetii . By April, surface nitrate
concentrations in the nearfield had been depleted. Increased nitrate
concentrations occurred at mid-depth in late August and early September,
as stratification broke down or as a new water mass entered the area. 
Phosphate concentrations also followed a typical pattern, similar to nitrate.
There was also a marked decline in silicate concentrations in February and
March, coincident with the increase in diatoms, which have cell walls
made of silica. By April, however, diatom populations were shrinking,
and silicate concentrations increased, remaining elevated through the
summer. Silicate concentrations declined again during a fall
phytoplankton bloom, but did not reach record low concentrations. 
The sharp drop in nitrate concentrations during the spring of 2000 was
similar to decreases observed in 1992, 1994, and 1996, when spring
blooms rapidly depleted nutrient concentrations. The year was in contrast
to 1998 and 1999, when nutrient levels remained elevated well into the
spring. In 1998, no spring bloom occurred, and concentrations of nitrate
remained high through May. During the fall of 2000, breakdown of
stratified conditions apparently increased nutrient availability, leading to a
fall bloom. Similar situations occurred during 1993, 1995, and 1999. In
other years, when mixing was delayed, surface waters remained depleted
and no blooms occurred. 
From 1997 through 2000, there was a slight increase in concentrations of
dissolved inorganic nitrogen in the nearfield (Figure 3-6). Nitrate
concentrations followed a normal seasonal pattern. However, there was an
increase in ammonia levels in Boston Harbor. Ammonia in the western
nearfield also increased, correlated with increased concentrations in

2000 OUTFALL MONITORING OVERVIEW 29 
Boston Harbor. This apparently resulted from an increase in flow from
the Deer Island treatment plant’s harbor outfalls following diversion of
south system flow to Deer Island and also from the treatment process.
Secondary treatment breaks down organic wastes, decreasing total
nitrogen but increasing ammonia concentrations in the effluent. 
Figure 3-6. Survey mean dissolved inorganic nitrogen and ammonia in the
nearfield, 1992-2000 
Survey Mean DIN 
0
2
4
6
8
10
12 
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001
YEAR
DIN (mM)
Outfall Start-up 
Survey Mean Ammonium
0
1
2
3
4
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001
YEAR
NH4 (mM) 
Outfall Start-up

2000 OUTFALL MONITORING OVERVIEW 30 
Chlorophyll levels increased from 1998 through 2000 (Figure 3-7). The
mean chlorophyll concentration in the nearfield during February through
April 2000 was 5.03 μg/l, greater than any winter/spring mean obtained
during the baseline period. Winter/spring chlorophyll levels for 1992,
1994, 1996, and 1999, when spring blooms also occurred, averaged only
about 2 μg/l. The summer and fall mean chlorophyll levels in the
nearfield were also higher in 2000 than in any other year of the baseline
period. An extended fall bloom resulted in a mean chlorophyll
concentration of 5.69 μg/l. Previous years means had ranged from 1.31
μg/l in 1997 to 5.45 μg/l in 1999. (Quality assurance reviews in 2000
detected analytical errors in chlorophyll measurements during 1998-2000,
and data for those years were reevaluated. Two data quality problems
were identified: a degraded standard, which had been used to calibrate
samples from late September and October 2000, and impurity of the
standard, which may have affected all data from 1998. The data have
been corrected.) 
The high chlorophyll levels occurred not only in the nearfield, but
throughout the region. Boston Harbor, the boundary stations, Cape Cod
Bay, the coastal stations, and the offshore stations also had annual mean
levels that were higher in 2000 than in any baseline year. 
Figure 3-7. Survey areal mean chlorophyll concentrations in the nearfield, 1992-2000 
Nearfield Survey Average Areal Chlorophyll
0
100
200
300
400
500
600
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 
Year 
Chlorophyll (mg/m2) 
Outfall Start-up

2000 OUTFALL MONITORING OVERVIEW 31 
Figure 3-8. Satellite data show an increasing trend in fall chlorophyll levels in Massachusetts
Bay, Cape Cod Bay, south of Cape Cod, and in the Gulf of Maine (J. Yoder, URI, J.O’Reilly,
NOAA). October 2000 is in the discharge-monitoring period (see Section 6). 
Interpretation of MWRA chlorophyll data is aided by results from the Sea-
viewing Wide Field-of-view Sensor (SeaWiFS) Project, which is part of
the National Air and Space Administration (NASA) mission to view earth
from space to better understand it as a system. SeaWiFS provides satellite
images using sensors that detect the subtle changes in ocean color that
signify the presence of phytoplankton. 
SeaWiFS images from the autumns of 1997-2000 depict a region-wide,
steady increase in chlorophyll concentrations (Figure 3-8). The reasons
for this widespread increase are unknown. Some scientists have suggested
that the North Atlantic oscillation, region-wide shifts in water masses, may
be responsible for cyclic variation in nutrient levels. Regardless of the
explanation, the images graphically demonstrate that Massachusetts Bay is
part of a larger system, that increases in fall phytoplankton biomass have
been occurring steadily throughout the late baseline monitoring period,
and that any exceedances of water-column thresholds must be evaluated in
a regional context. 
Dissolved oxygen concentrations in the nearfield were not unusually low
in 2000 (Figure 3-9). The annual minimum percent saturation was less
than 80%, but within the baseline range. Concentrations in bottom waters
were about one percent higher in Stellwagen Basin than in the nearfield.
Rates of decline in dissolved oxygen concentrations were typical for the
period, both in the nearfield and in Stellwagen Basin, although low levels
were reached somewhat earlier than usual. The early decline may have
resulted from the large amount of organic matter produced by the spring
algal blooms.

2000 OUTFALL MONITORING OVERVIEW 32 
Figure 3-9. Survey mean dissolved oxygen concentrations and percent saturation
in the nearfield, 1992-2000 
Phytoplankton Communities 
Phytoplankton abundance in 2000 was variable and low from February
through early March. In late March and April, there was a system-wide
bloom of Phaeocystis pouchetii , the undesirable, although not toxic,
flagellate. Total phytoplankton abundance declined with the end of the
bloom in May, but subsequently increased in June and July. Over the
year, the magnitude and trends in phytoplankton abundance were similar
in the nearfield and the farfield. Although Phaeocystis abundance was the
highest measured in the baseline period, the year was similar to other
years with spring Phaeocystis blooms (Figure 3-10; Libby et al. 2001). 
Nearfield Bottom Water DO
4
5
6
7
8
9
10
11
12
13
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001
DO (mg L -1 )
Mean Caution Warning Background
Year Outfall Start-up 
Nearfield Bottom Water DO %SAT
40
50
60
70
80
90
100
110
120
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001
DO %SAT
Mean Caution Warning Background
Year Outfall Start-up

2000 OUTFALL MONITORING OVERVIEW 33 
Figure 3-10. Survey mean phytoplankton abundance, 1992-2000 
The assemblages of phytoplankton species were also typical for the
baseline period. Except for the Phaeocystis bloom, unidentified
microflagellates and centric diatoms dominated the first part of the year.
Microflagellates, cryptomonads, and the diatom Leptocylindrus danicus 
dominated the latter part of the year. 
Throughout the baseline period, microflagellates have numerically
dominated whole-water samples throughout the year and have been more
abundant during the summer than the winter. Diatoms, including 
Chaetoceras debilis, C. socialis , Thalassiosira nordenskioldii , and T.
rotula are also abundant in the winter. During some years, such as 2000, 
Phaeocystis blooms during the spring. In other years, diatoms, the
dinoflagellate Heterocapsa rotundatum , and cryptomonads dominate
during the spring. During the summer, when microflagellates are at peak
abundance, cryptomonads and the diatoms Skeletonema costatum , 
Leptocylindrus danicus , Rhizosolenia delicatula , Cerataulina pelagica ,
and several small species in the genus Chaetoceros are present.
Crypotomonads, gymnodinoid dinoflagellates, and diatoms, including 
Asterionellopsis glacialis , Rhizosolenia delicatula , Skeletonema costatum , 
Leptocylindrus danicus , L. minimus , are abundant in the fall (Figure 3-7;
Libby et al. 2001). 
Outbursts of single-species blooms have occurred several times
throughout the baseline period. Phaeocystis blooms occurred in 1992,
1994, 1997, and 2000. There was a bloom of the diatom Asterionellopsis
glacialis in the fall of 1993, and there have been periodic summer and fall 
Total Phytoplankton Abundance - Area Mean
0
2
4
6
8
10
12
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001
Year
10 6 Cells/L
BOUNDARY NEARFIELD HARBOR CCB COASTAL 
Outfall Start-up

2000 OUTFALL MONITORING OVERVIEW 34 
outbursts of Ceratium spp. These blooms have been intermittent but
dramatic. 
Occurrence of potentially toxic nuisance species was rare during 2000, as
it has been for most of the baseline period. The dinoflagellate 
Alexandrium tamarense , the cause of PSP or red tide, was recorded only
sporadically through the year, although Maine saw its greatest incidence
of PSP toxicity in more than 10 years, and some toxicity was measured on
the North Shore. The diatoms Pseudo-nitzschia spp. were also recorded
only sporadically and in lower numbers than in 1999. 
A. tamarense has been recorded in trace but not abundant amounts
throughout the baseline period. The frequency of sampling by the general
MWRA program may not be appropriate for monitoring this toxin-
producing species; programs that target A. tamarense during the red-tide
season tend to record higher abundances. 
Consequently, MWRA also evaluates data from a targeted program
directed by Donald M. Anderson at the Woods Hole Oceanographic
Institution. A. tamarense blooms are thought to originate from seedbeds
to the north of Massachusetts Bay and be transported southward by
currents. These blooms only occasionally reach Massachusetts Bay when
northeast winds cause downwelling conditions and press the Maine coastal
current along the shoreline (Figure 3-11, Anderson et al. in press). The
southwest winds and upwelling conditions that predominated during the
summer of 2000 were not conducive to the presence of A. tamarense in
Massachusetts Bay. 
Figure 3-11. Model results indicate that A. tamarense blooms originate to the north of
Massachusetts Bay and are only transported into the bay when winds are from the northeast
(Anderson et al . in press). The first panel depicts initial conditions, with a bloom occurring north
of Massachusetts Bay. The second panel shows conditions five days later if there are northeast
winds. The third panel shows conditions five days later if there are southwest winds.

2000 OUTFALL MONITORING OVERVIEW 35 
Figure 3-12. Survey mean zooplankton abundance, 1992-2000 
Zooplankton Communities 
Abundance of zooplankton was high in 2000 (Libby et al. 2001; Figure 3-
12). Abundance steadily increased from February through July. In the
nearfield, total counts in June were among the highest measured in the
baseline period, partially due to the presence of planktonic bivalve larvae,
which comprised up to 64% of the total individuals at some stations. Total
abundances began to decline in early August. 
Overall, zooplankton assemblages were similar in the nearfield and the
farfield. From February through May, communities were dominated by
juvenile copepods, including the small species Oithona similis , and the
larger species Pseudocalanus spp. and Calanus finmarchicus . Barnacle
larvae were common in April. Bivalve veligers began to be common in
the nearfield in May, and in June they dominated many samples. Copepod
nauplii and copepodites remained common throughout the year. 
The copepods Acartia spp. ( Acartia hudsonica and Acartia tonsa ), which
are typically abundant in Boston Harbor but which were unusually sparse
in 1999, rebounded in 2000. Their decline and rebound gave further
credence to the theory that these species were affected by the high
salinities noted during a drought in 1999. Acartia spp. was once thought
to be responsive to nutrient loading and therefore a good indicator species
for the monitoring program. That relationship has been in doubt for
several years; data from the literature, supported by baseline-monitoring
data have indicated that salinity rather than nutrient loading limits Acartia 
spp. abundance. 
Total Zooplankton - Area Means
0
50,000
100,000
150,000
200,000
250,000
300,000
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001
Year
Individuals/m 3
BOUNDARY NEARFIELD HARBOR CCB COASTAL 
Outfall Start-up

2000 OUTFALL MONITORING OVERVIEW 36 
One major event for zooplankton communities, decimation of Boston
Harbor zooplankton populations by the ctenophore Mnemiopsis leidii ,
occurred in the fall. Ctenophores are gelatinous carnivores that feed
voraciously on copepods and other zooplankton. Normally thought to
occur only south of Cape Cod, Mnemiopsis had never been noticed in the
harbor-and-outfall monitoring program. In 2000, Mnemiopsis became
abundant in the harbor and adjacent coastal regions in October.
Zooplankton populations plummeted, as they have in other coastal areas
when ctenophores are present. Overgrazing of the zooplankton
populations may have contributed to the fall phytoplankton bloom in the
harbor and the coastal area. 
Contingency Plan Thresholds 
Threshold parameters for water-column monitoring include minimum
dissolved oxygen concentrations and percent saturation in nearfield and
Stellwagen Bank bottom waters, dissolved oxygen depletion rate in
nearfield bottom waters, chlorophyll levels, abundance of nuisance algal
species, geographic extent of PSP toxin, and initial dilution (Table 3-1).
Baseline monitoring was completed for the water column thresholds at the
end of August 2000. Those data were used to calculate the threshold
values described in the contingency plan, as revised in May 2001. 
Fall 2000 marked the end of the baseline period, completing the data set
for MWRA to calculate the threshold values that will be used to compare
monitoring results to baseline conditions. Those parameters include
background levels for dissolved oxygen concentrations and percent
saturation in bottom waters of the nearfield and Stellwagen Basin, oxygen
depletion rate, annual and seasonal chlorophyll levels in the nearfield, and
seasonal abundance for the nuisance algae Phaeocystis and Pseudo-
nitzschia . 
In 1997, Outfall Monitoring Task Force recommended deleting bottom
dissolved oxygen saturation as a threshold parameter, because baseline
conditions frequently fell below the thresholds that had been fixed by state
standards, both in the nearfield and in Stellwagen Basin. EPA and
MADEP declined to accept this recommendation but in 2001 suggested
adding the phrase “unless background conditions are lower” to the
descriptions of both dissolved oxygen concentration and dissolved oxygen
saturation, bringing the threshold into closer conformity with the state
standard. MWRA has calculated those background conditions as follows:
5.75 mg/l dissolved oxygen in the nearfield. 6.2 mg/l dissolved oxygen in
Stellwagen Basin, 64.3% saturation in the nearfield, and 66.3% saturation
in Stellwagen Basin.

2000 OUTFALL MONITORING OVERVIEW 37 
Table 3-1. Contingency Plan threshold values for water column monitoring 
Location/ 
Parameter 
Specific
Parameter Baseline Caution Level Warning Level 
Dissolved oxygen
concentration 
Background 5 th
percentile 
5.75 mg/l 
Lower than 6.5
mg/l for any survey
(June-October)
unless background
conditions are
lower 
Lower than 6.0 mg/l
for any survey
(June-October)
unless background
conditions are lower 
Bottom water
nearfield 
Dissolved oxygen
percent saturation 
Background 5 th
percentile 
64.3% 
Lower than 80%
for any survey
(June-October)
unless background
conditions are
lower 
Lower than 75% for
any survey (June-
October) unless
background
conditions are lower 
Dissolved oxygen
concentration 
Background 5 th
percentile 
6.2 mg/l 
Lower than 6.5
mg/l for any survey
(June-October)
unless background
conditions are
lower 
Lower than 6.0 mg/l
for any survey
(June-October)
unless background
conditions are lower 
Bottom water
Stellwagen Basin 
Dissolved oxygen
percent saturation 
Background 5 th
percentile 
66.3% 
Lower than 80%
for any survey
(June-October)
unless background
conditions are
lower 
Lower than 75% for
any survey (June-
October) unless
background
conditions are lower 
Bottom water
nearfield 
DO depletion rate
(June-October) 0.0244 mg/l/d 0.037 mg/l/d 0.049 mg/l/d 
Annual 71 mg/m 2 107 mg/m 2 143 mg/m 2 
Winter/spring 81 mgml 2 182 mg/m 2 None 
Summer 51 mg/m 2 80 mg/m 2 None 
Chlorophyll
nearfield 
Autumn 90 mg/m 2 161 mg/m 2 None 
Winter/spring 470,000 cells/l 2,020,000 cells/l None 
Summer 7.2 cells/l 334 cells/l None 
Nuisance algae
nearfield 
Phaeocystis
pouchetii Autumn 300 cells/l 2,370 cells/l None 
Winter/spring 6,200 cells/l 21,000 cells/l None 
Summer 13,000 cells/l 38,000 cells/l None 
Nuisance algae
nearfield 
Pseudonitzschia Autumn 9,700 cells/l 24,600 cells/l None 
Nuisance algae
nearfield 
Alexandrium
tamarense 
Any nearfield
sample 
Baseline maximum
= 163 cells/l 100 cells/l None 
Farfield PSP toxin extent 
Never observed at
certain southern
Mass. Bay stations 
New incidence None 
Plume* Initial dilution Not applicable None Effluent dilution less
than 70:1 
* 70:1 is the dilution used by EPA as the basis for MWRA’s NPDES permit, to be certified by a dye dilution
study in 2001 
Chlorophyll threshold values are based on areal measurements, integrating
data from 0.5-m depth intervals, rather than on the volume measurements
that are typically used to discuss conditions on a finer scale. Had the
thresholds been in place, fall chlorophyll concentrations for 1999 would
have exceeded the fall caution threshold of 161 mg/m 2 . Likewise, fall

2000 OUTFALL MONITORING OVERVIEW 38 
2000 values exceeded the caution threshold. (Fall 2000 was not part of the
baseline and is discussed further in Section 6, Outfall Monitoring.)
However, both the 1999 and 2000 exceedances are important, because
they reflect a general increase in fall chlorophyll levels that was recorded
since 1998 throughout the region. Preliminary data indicate that the spring
2001 nearfield average chlorophyll concentration was well within the
threshold. 
In 2001, EPA and MADEP established an interim threshold of 100
cells/liter in any sample for Alexandrium tamarense, noting that the
maximum count prior to the outfall startup was 163 cells/l. Paralytic
shellfish poisoning toxicity is not generally observed until cell counts
reach more than 300 cells/l. 
MWRA also uses data from a Massachusetts Department of Marine
Fisheries (DMF) monitoring program, which addresses extent of paralytic
shellfish poison toxicity in the area. The program traditionally has been
conducted from early April through November and has involved sampling
of shellfish, primarily blue mussels, from 16 primary stations and, if
significant toxin is measured at the primary sites, 47 secondary stations.
PSP toxin was not detected in bay waters in 2000.

2000 OUTFALL MONITORING OVERVIEW 39 
4. Sea Floor Baseline 
Background 
This section presents results of sea floor monitoring for the year 2000,
focusing on the completion of the baseline period, which ended on
September 6, 2000. Data from September through December are actually
in the discharge-monitoring period and are discussed in more detail in
Section 6, Outfall Monitoring. 
Bottom Characteristics and Sediment Transport 
The sea floor of Massachusetts and Cape Cod bays was originally shaped
by the glaciers, which sculpted the bottom and deposited debris, forming
knolls, banks, and other features. Within Massachusetts Bay, the sea floor
ranges from mud in depositional basins to coarse sand, gravel, and
bedrock on topographic highs. The area around the new outfall is marked
by drumlins, which are elongated hills about 10 meters high, with crests
covered by gravel and boulders. Long-term sinks for fine-grained
sediments include Boston Harbor, Cape Cod Bay, and Stellwagen Basin
(USGS 1997a, 1998). 
Sediment transport in the region occurs primarily during storms.
Typically, waves during storms with winds from the northeast resuspend
sediments, which are transported by shallow currents from western
Massachusetts Bay toward Cape Cod Bay and by deeper currents to
Stellwagen Basin, where they are likely to remain. Cape Cod Bay is
partially sheltered from large waves by the arm of Cape Cod, and storm
waves are rarely large enough to resuspend sediments in Stellwagen
Basin, which is the deepest feature in the region. 
Environmental Concerns 
Within Boston Harbor, studies of the sediments are documenting recovery
following the cessation of sludge discharge, improvements to CSO
systems, and improved sewage effluent treatment. Conversely, relocating
the outfall has introduced concerns about potential effects on the offshore
sea floor. Concern is focused on three issues: eutrophication and related
low levels of dissolved oxygen, accumulation of toxic contaminants in
depositional areas, and smothering of animals by particulate matter. 
If transfer of the nutrient loads to offshore were to cause eutrophication,
depressed levels of dissolved oxygen could profoundly affect bottom
communities. Increasing the amount of particles and organic matter to the
bottom could disrupt normal benthic community structure in the vicinity

2000 OUTFALL MONITORING OVERVIEW 40 
of the discharge. Although source control and treatment plant
performance are designed to keep effluent contaminant concentrations too
low to affect the sediments, the location of the outfall in an area of
considerable sediment transport causes concern about accumulation of
toxic contaminants in the depositional areas and in Cape Cod Bay and
Stellwagen Basin. Similarly, concentrations of particulate matter are
expected to be low, but there remains some concern that bottom
communities near the outfall could be affected by deposition. 
Figure 4-1. Locations of nearfield soft-bottom stations (NF12 and NF17 are also
sampled by USGS)

2000 OUTFALL MONITORING OVERVIEW 41 
Monitoring Design 
Sea floor monitoring includes several components: measurements of
contaminant concentrations and other chemistry parameters in sediments,
sediment-profile imaging to provide a rapid assessment of potential
effects, studies of nearfield and farfield soft-bottom communities
(sampling sites in Figures 4-1, 4-2), and study of hard-bottom
communities (sampling sites in Figure 4-3). 
Figure 4-2. Locations of farfield soft-bottom stations

2000 OUTFALL MONITORING OVERVIEW 42 
In addition to MWRA’s outfall monitoring, long-term studies of sediment
transport and contaminant levels in Boston Harbor, Massachusetts Bay,
and Cape Cod Bay are conducted by USGS. Since 1977, USGS has
periodically sampled four stations within Boston Harbor, and since 1989
they have taken sediment cores three times a year from two stations, one
sandy and one muddy, near the Massachusetts Bay outfall (USGS 1997b;
Figure 4-1). 
Figure 4-3. Locations of hard-bottom transects

2000 OUTFALL MONITORING OVERVIEW 43 
Because concentrations were consistently low, the MWRA baseline
sediment-contaminant studies were considered adequate after 1995.
However, when outfall start-up was delayed, additional sampling was
conducted. In 1998, a “special contaminant study” was resumed at four
stations. The stations included in this study were selected because they
have a high percentage of fine-grained material, with those percentages
remaining stable during the monitoring period. They have high
concentrations of total organic carbon (TOC) and are located in the zone
of effluent particle deposition predicted by the Bays Eutrophication
Model. Should it occur, data from these stations would provide early
indications of any contaminant build-up. 
Prior to the startup of the outfall, the stations were sampled once per year,
in August. Starting in late 2000, because the outfall began operation, they
are being sampled three times per year, in April, August, and October.
(Results from the October 2000 survey are discussed in Section 6, Outfall
Monitoring.) Samples are analyzed for spores of the sewage indicator
bacterium Clostridium perfringens , sediment grain size, TOC, and
contaminants. 
Sediment-profile image surveys are conducted in August of each year at
20 nearfield and three farfield, western Massachusetts Bay, stations to give
an area-wide assessment of sediment quality and benthic community
status. They provide a more rapid assessment of benthic habitat
conditions than is possible from traditional faunal analyses. A system
called “Quick Look,” which uses digital video cameras along with film,
provides an even faster assessment. A real-time narration of the videotape
describes the substrate and estimates depth at to which oxygen penetrates,
known as the oxidation-reduction potential discontinuity (RPD). Later,
complete analyses of films provide information on prism penetration,
surface relief, apparent color RPD depth, sediment grain size, sediment
layering, fauna and structures, and successional stage of the soft-bottom
animal communities. 
Nearfield and farfield soft-bottom surveys are also conducted in August.
Sampling of 23 nearfield and western Massachusetts Bay stations is
designed to provide spatial coverage and local detail about the fauna in
depositional areas located within eight kilometers of the diffusers.
Farfield sampling of eight additional stations in Massachusetts and Cape
Cod bays contributes reference data on soft-bottom habitats. Samples are
analyzed for community parameters, Clostridium perfringens spores,
sediment grain size, TOC content, and contaminant concentrations.

2000 OUTFALL MONITORING OVERVIEW 44 
While most studies of benthic communities, including the MWRA
monitoring program, focus on the soft bottom areas with finer-grained
sediments, such depositional areas are few in the vicinity of the outfall.
Therefore, MWRA also conducts video and photographic surveys of the
hard-bottom habitats found on the tops and flanks of drumlins in western
Massachusetts Bay (Figure 4-3). Video and still photographs are taken at
waypoints along 6 transects, at Diffuser Head #44 of the outfall (which
will not be opened), and at Diffuser Head #2. These surveys are
conducted annually in June. Photographs are examined for substrate type,
amount of sediment drape, and biota. 
Results 
August 2000 marked the completion of sediment sampling for the baseline
period. Baseline monitoring of hard-bottom areas was completed in June
2000. 
Sediment Contaminants 
Spatial distribution of sediment grain-size patterns and TOC content from
sediments taken as part of the special contaminant study and the soft-
bottom community surveys remained stable in 2000, with no substantial
change from 1992 through 2000 (Kropp et al. 2001). Within the nearfield
(including farfield stations inshore from the outfall site), TOC was slightly
elevated but within the historic range. 
Figure 4-4. There is a gradient of decreasing C. perfringens spores with
distance from Deer Island and a decrease at Deer Island since the mid 1990s.
Data are normalized to percent fine-grained particles. 
Clostridium perfringens 
vs. Distance from Deer Island
0
150
300
450
600
750
1992 1993 1994 1995 1996 1997 1998 1999 2000
Year
cfu/g dw/% Fines
< 10 km (Harbor and others)
10 to 20 km
20 to 40 km
> 40 km
Mean value = 1,651
cfu/gdw/% Fines

2000 OUTFALL MONITORING OVERVIEW 45 
Concentrations of organic and inorganic contaminants in sediments
sampled during 2000 remained very low, well below established EPA or
NOAA guidelines. Concentrations of organic contaminants and some
metals (mercury, silver, copper, and cadmium) were, as in previous years,
lower in the farfield than in the nearfield. Concentrations of lead and
chromium were similar in both regions. 
During the early 1990s, USGS studies documented a decrease in
concentrations of Clostridium perfringens spores with increasing distance
from Boston Harbor (Parmenter and Bothner 1993). Analysis of MWRA
baseline data from 1992 through 2000 found a similar pattern, consistent
with the USGS findings (Figure 4-4). This pattern has been thought to
reflect inshore sewage effluent discharge—concentrations of the sewage
indicator decreased with increasing distance from Deer Island. 
Storms can also affect concentrations of contaminants in the sediments
(USGS 1997b). Concentrations of silver, Clostridium perfringens spores,
inventories of natural radioisotopes, and sediment texture in samples from
Massachusetts Bay stations changed abruptly between surveys conducted
during October of 1992 and February of 1993. USGS attributes these
changes to a December 1992 storm, which probably transported near-
shore sediments to the offshore. Sediment-trap studies currently underway
may provide better information on the effects of short-term events on
concentrations of contaminants within the sediments. 
Figure 4-5. Typical sediment profile image 
Sediment Profile Imaging 
Baseline sediment-profile imaging surveys were conducted in 1992, 1995,
and 1997-2000 (Kropp et al. 2001). The surveys have focused on areas
with fine-grained sediments, and for most of the monitoring period, most

2000 OUTFALL MONITORING OVERVIEW 46 
sampling stations have had fine sand to silty-fine sand as the dominant
sediment type (Figures 4-5, 4-6). In 2000, some coarser sediments were
found. The smallest sediment size at Station FF10, located just off
Nahant, was gravel, and the finest sediments at several nearfield stations
were sands. Bedforms, surface depositional patterns typically associated
with high energy, sandy conditions, were noted at six stations. These
findings indicate that in 2000, storms resuspended and transported
sediments from at least some stations. However, homogeneous, fine-
grained sediments were also found, particularly northwest and south of the
outfall. 
Assessment of the apparent RPD at many stations has often suffered from
shallow penetration of the prism, particularly at stations with coarser
sediments. In 2000, no image could be made at the gravel-and-pebble
bottom at Station FF10. At the sandy stations, no images penetrated
deeply enough to see the RPD layer. After accounting for these
difficulties, the grand average depth to the RPD layer was unchanged from
1999 (Figure 4-6). Over the course of the entire baseline period, the RPD
layer depth was shallower in 1997 and 1998, compared to the preceding
and succeeding years. 
Figure 4-6. Apparent color RPD layer depth for all data from nearfield stations,
including those for which the prism did not penetrate deeply enough. (Center
bar is median, dot is mean, box is interquartile range, and whiskers are total
range of the station data.) 
2000 
1999 
1998 
1997 
1995 
1992 
6 
5 
4 
3 
2 
1 
0 
All RPD values including > NF17 
Apparent Color RPD Layer Depth (cm)

2000 OUTFALL MONITORING OVERVIEW 47 
Biologically, in 1992, 1995, and 1997, pioneering or “Stage I”
communities prevailed in the nearfield. Stage II fauna became more
prevalent in 1998-2000. Data from 1997 were collected later than in other
years, and there is some evidence that the increasing trend in importance
of biological processes may have begun in 1995. In 2000, the sediment
surfaces continued to be dominated by biogenic structures and organism
activity. Stations with fine-grained sediments had high densities of
polychaete tubes, and the stations with coarser sediments were draped
with fine sediments and covered with tubes, sponges, and hydroid-like
organisms. 
Soft-bottom Communities 
Soft-bottom benthic communities have been distinguished throughout the
monitoring program by their patchiness. Among individual nearfield
samples collected in 2000, infaunal abundance varied four-fold (Kropp et
al. 2001). As in previous years, annelid worms were the most abundant
higher-level taxon at both nearfield and farfield stations, accounting for
more than 80% of the fauna at 15 nearfield stations. Crustaceans and
mollusks were the next most abundant fauna. 
In the nearfield, the polychaete Prionospio steenstrupi was the most
common organism at 16 stations. Other polychaetes that ranked as most
common included Dipolydora socialis, Exogone verugera , Mediomastus
californiensis , and Exogone hebes . Common amphipod crustaceans
included Crassicorophium crassicorne and Unciola inermis . The most
common mollusks were the northern dwarf-cockle Cerastoderma
pinnulatum and the nutclam Nucula delphinodonta . Common polychaetes
in the farfield included Prionospio steenstrupi , Cossura longocirrata , 
Euchone incolor , and Spio limicola . Multivariate analyses indicated that
the grouping by which stations can be sorted was very similar to previous
years. As in previous years, the grouping reflected sediment type and
biogenic activity as the major factors structuring the communities. 
Annual measurements of community parameters have shown somewhat
similar patterns in the nearfield and farfield (Figure 4-7). In the nearfield,
the baseline-monitoring years can be divided into two periods: the early
years from 1992-1996 when the infaunal community was in flux and the
later years when the community has remained relatively constant. The
changing communities in the early years are thought to result from the
severe winter storm in 1992. The effects of the storm were evident in the
two community parameters that are measured directly, total abundance of
organisms and total number of species, and in one of the calculated
indices, log-series alpha. Two other indices, Shannon diversity, and
Pielou’s evenness, did not detect any change from the storm, and these
measures may also prove less likely to detect any potential effect of the
outfall.

2000 OUTFALL MONITORING OVERVIEW 48 
Figure 4-7. Community parameters for soft-bottom communities. Nearfield
includes three western Massachusetts Bay farfield stations. 
40
45
50
55
60
65
70
75
80
85
1992 1993 1994 1995 1996 1997 1998 1999 2000
Year
Species per grab sample
Nearfield
Farfield
0
500
1000
1500
2000
2500
3000
3500
1992 1993 1994 1995 1996 1997 1998 1999 2000
Year
Abundance per grab sample
Nearfield
Farfield
8
10
12
14
16
18
1992 1993 1994 1995 1996 1997 1998 1999 2000
Year
Log-series Alpha
Nearfield
Farfield

2000 OUTFALL MONITORING OVERVIEW 49 
In the farfield, effects of the storm were not apparent. Total abundances
were lowest in 1992-1994, increased in 1995-1997, and increased further
in 1998-1999. Total number of species was low in 1992-1995, then rose
to a peak in 1998. Log-series alpha followed a similar pattern. 
Despite the apparent difference in nearfield and farfield response to the
1992 storm, overall patterns in the abundance of species appear to be bay-
wide (Figure 4-8). Over all the years of monitoring, the mean number of
species found throughout the bay has been quite stable, with a mean of
254 and a coefficient of variation of about eight percent. Despite large
changes in species richness per sample, overall variability has been small.
Such patterns of large-scale consistency in species richness despite
considerable small-scale and year-to-year patchiness have been
documented for many plant and animal communities (Brown et al. 2001). 
Any future substantial change in rate of disappearance or appearance of
species could indicate that a change in the Massachusetts Bay system has
occurred. Recognizing that a change in species richness could be
interpreted as an effect of the outfall, MWRA will continue to compare
trends observed in the nearfield with those observed in the farfield. 
Figure 4-8. Patterns of species abundance in Massachusetts Bay 
Dynam ics o f Infaunal Spe cie s Richne s s in M as s ach us e tts Bay fr om 1992 to 2000 
0
50
100
150
200
250
300
350
400
450
500
1992 1993 1994 1995 1996 1997 1998 1999 2000 
Ye ar
Nu m be r of Spe cie s 
Spec ies Pres ent
Mean
Es timated Number of Spec ies in Spec ies Pool
Number of Spec ies Pres ent A ll Y ears
433
141
254

2000 OUTFALL MONITORING OVERVIEW 50 
Hard-bottom Communities 
Baseline monitoring of the hard bottom in the vicinity of the outfall has
documented locally variable but temporally stable communities (Figure 4-
9, Kropp et al. 2001). Visibility was poor during the June 2000 survey,
due to a high amount of suspended matter in the water column. (June was
very rainy, and a northeaster, which dropped 4 inches of rain on Boston,
occurred 2-3 weeks before the survey.) Consequently, fewer taxa could be
seen clearly in the video and still photography. Nevertheless, the data
analysis continues to show the temporally stable pattern that has been
observed in past years. 
As in previous years, approximately half the organisms seen could be
identified to species. Other organisms were grouped into taxa that could
be described by general characteristics, such as “orange-tan encrusting.”
Sixty-five species and grouped taxa were identified in 2000. The most
abundant taxon was, as in previous years, coralline algae. Direct
collections made in September 2000 confirmed that this taxon is made up
of at least 5 species, including Leptophytum laevae , Leptophytum
foecundum , Phymatolithon laevigatum , Phymatolithon lamii , and 
Lithothamnion glaciale . Other common algae included dulse Rhodymenia
palmata and a red, filamentous alga Ptilota serrata . Shotgun kelp Agarum
cribosum was very abundant at one waypoint, where it was typically
overgrown by an organism that appeared to be a lacy bryozoan. 
The most abundant invertebrate was the northern seastar, Asterias
vulgaris , which was found at all waypoints. Other common invertebrates
included an unidentified orange or tan sponge, the horse mussel Modiolus
modiolus , three species of tunicates, and the blood sea star Henricia
sanguinolenta . Anemones are especially abundant on the smooth surface
of the outfall diffuser that is included in the monitoring. The most
common fish was the cunner Tautogolabrus adspersus , which was seen at
all waypoints. 
There was no indication that the amount of sediment drape was greater in
2000 than in prior years, despite the high amounts of particulate matter in
the water column that obscured the images. These findings suggest that
the particulate matter in the water column was not part of a long-term
event, but more likely resulted from runoff and resuspension during the
northeaster that occurred 2-3 weeks before the survey. 
As in previous years, algae usually dominated the tops of drumlins, while
encrusting or attached invertebrates were increasingly dominant on the
flanks. Abundance of encrusting coralline algae has been inversely
correlated with sediment drape throughout the baseline-monitoring
program, percent cover being greatest in areas with the least sediment.

2000 OUTFALL MONITORING OVERVIEW 51 
This relationship is not surprising, because an encrusting growth form
makes organisms susceptible to smothering. Consequently the coralline
algae may be good indicators of outfall effects. The overall similarities
among the 6 surveys conducted in 1996-2000 indicate that a substantial
departure from the baseline should be readily apparent. Should solid
material discharged from the outfall accumulate in the vicinity, a marked
decrease in the percent cover by coralline algae may be expected.
Changes in light penetration or water clarity would also reduce coverage
by coralline algae. 
Figure 4-9. Hard-bottom survey photograph from Transect 1, located about 1000 m north of the
outfall. Boulder and cobbles with very light sediment dusting and 80% coralline algae cover. 
Contingency Plan Thresholds 
Threshold parameters for sea floor monitoring include contaminant
concentrations, RPD depth, and benthic diversity and species composition
in soft-bottom communities (Table 4-1). Baseline monitoring for these
threshold was completed in August 2000. Those data were used to
calculate the thresholds as described in the contingency plan.

2000 OUTFALL MONITORING OVERVIEW 52 
Table 4-1. Contingency Plan baseline and threshold values for sea floor monitoring 
Location Parameter Baseline
Mean Caution Level Warning Level 
Acenaphthene 30 ppb dry None 500 ppb dry 
Acenaphylene 48 ppb dry None 640 ppb dry 
Anthracene 151 ppb dry None 1100 ppb dry 
Benz(a)pyrene 278 ppb dry None 1600 ppb dry 
Benzo(a)pyrene 258 ppb dry None 1600 ppb dry 
Cadmium 0.2 ppm dry None 9.6 ppm dry 
Chromium 76 ppm dry None 370 ppm dry 
Chrysene 255 ppb dry None 2800 ppb dry 
Copper 24 ppm dry None 270 ppm dry 
Dibenzo(a,h)anthracene 37 ppb dry None 260 ppb dry 
Fluoranthene 558 ppb dry None 5100 ppb dry 
Fluorene 50 ppb dry None 540 ppb dry 
Lead 44 ppm dry None 218 ppm dry 
Mercury 0.24 ppm dry None 0.71 ppm dry 
Naphthalene 70 ppb dry None 2100 ppb dry 
Nickel 17 ppm dry None 51.6 ppb dry 
p,p’-DDE 0.8 ppb dry None 27 ppm dry 
Phenanthrene 349 ppb dry None 1500 ppb dry 
Pyrene 516 ppb dry None 2600 ppb dry 
Silver 0.6 ppm dry None 3.7 ppm dry 
Total DDTs 3.5 ppb dry None 46.1 ppb dry 
Total HMWPAH 3559 ppb dry None 9600 ppb dry 
Total LMWPAH 1639 ppb dry None 3160 ppb dry 
Total PAH 5199 ppb dry None 44792 ppb dry 
Total PCBs 17 ppb dry None 180 ppb dry 
Sediment
toxic
contaminants,
nearfield 
Zinc 61 ppm dry None 410 ppm dry 
Sediments,
nearfield RPD depth 2.36 cm 1.18 cm None 
Species per sample 64.52 <47.95 or >81.09 None 
Fisher’s log-series
alpha 13.00 <10.13 or >15.58 None 
Shannon diversity 3.67 <3.32 or >4.02 None 
Benthic
diversity,
nearfield 
Pielou’s evenness 0.62 <0.56 or >0.67 None 
Species
composition,
nearfield 
Percent opportunists 0.75% 10% 25% 
With the completion of baseline sediment-profiling images, it is clear that
the number of sampling stations included in the program is adequate to
readily detect a caution level of decline in the RPD depth to half of its
baseline level. Levels measured have ranged from 1.73 cm in 1998 to
3.02 measured in 1995. None of these measurements approached the
caution level of a lessening of the RPD by half. 
The caution level for changes in species diversity has been set by the 2001
revision of the contingency plan as “appreciable change” from the
baseline. Also in 2001, OMSAP further defined that threshold as the 2.5 th
and 97.5 th percentiles of four baseline measurements: total species,

2000 OUTFALL MONITORING OVERVIEW 53 
Fisher’s log-series alpha, Shannon diversity, and Pielou’s evenness. None
of the thresholds would have been crossed during the baseline period. 
Caution and warning levels have also been set for the percentage of the
infaunal community that is made up of species known to be
“opportunists,” that is, species that are found in environments that have
been subjected to sudden change. MWRA recognizes seven species—
three amphipods in the genus Ampelisca and three polychaetes and one
bivalve—as opportunists of potential concern. Over the baseline period,
mean percent occurrence of these species has ranged from 0.31 to 1.11%
in the nearfield and from 0.10 to 1.00% in the farfield.

2000 OUTFALL MONITORING OVERVIEW 54 
5. Fish and Shellfish Baseline 
Background 
This section presents the results of fish and shellfish monitoring for the
year 2000. It marks the end of the baseline period, which ended when the
Massachusetts Bay outfall began operation in September 2000. 
Fisheries 
The fish and shellfish industry is an important part of the regional identity
and economy of Massachusetts. During 1999, commercial landings in
Massachusetts totaled almost 200 million pounds, valued at more than
$260 million (NMFS fisheries statistics for the most recent year for which
data are available). More than 25% of the total value was attributed to the
lobster fishery. Flounders, including winter flounder, made up almost
10% of the total value of the fishery. Although many shellfish beds are
closed due to coastal bacterial contamination, the fishery for oysters and
clams remains important to the region. The annual Massachusetts
aquaculture fishery is valued at $5-10 million. 
Recreational fishing is also important in coastal Massachusetts. There are
approximately 240,000 recreational anglers living within Massachusetts
coastal counties, and almost 3 million “angler trips” were taken in
Massachusetts during 2000. Striped bass, bluefish, mackerel, and cod are
the most popular sports fisheries within the Massachusetts territorial sea
(NMFS recreational fisheries data for 2000), and flounders are also
popular. 
Environmental Concerns 
One concern about relocating sewage effluent offshore, into relatively
clean waters, is that contaminants could adversely affect resource species,
either through direct damage to the fishery stocks or by contamination of
the fish, lobster, and other shellfish, rendering them unfit for human
consumption. Because many toxic contaminants adhere to particles,
animals that live on the bottom, in contact with sediments, and animals
that eat bottom-dwelling organisms are most likely to be affected.
Exposure to contaminated sediments could result in fin erosion, black gill
disease, or other, subtler, abnormalities in flounder, lobster, or other
bottom-dwelling animals. Shellfish that feed by filtering suspended matter
from large volumes of water are also potential bioaccumulators of toxic
contaminants. These shellfish are themselves resource species, and are
also prey to other fisheries species. Consumption of these animals by

2000 OUTFALL MONITORING OVERVIEW 55 
predators could result in transferring contaminants up the food chain and
ultimately to humans. 
. 
Figure 5-1. Sampling areas for fish and shellfish monitoring. Flounder are taken from Deer
Island Flats, Broad Sound, off Nantasket Beach, the outfall site, and eastern Cape Cod Bay.
Lobsters are taken from Deer Island Flats, the outfall site, and eastern Cape Cod Bay. In 2000,
mussel arrays were deployed at Boston Inner Harbor, Deer Island, and the outfall site.

2000 OUTFALL MONITORING OVERVIEW 56 
Monitoring Design 
The monitoring program focuses on three indicator species: winter
flounder, lobster, and blue mussel (Figure 5-1). Winter flounder and
lobster are important resource species in the region. The blue mussel is
also a fishery species and, when deployed in caged arrays, is a common
biomonitoring organism. 
Like all flatfish, winter flounder live on and eat food from the bottom,
often burying themselves in the sediments. Consequently, flounder can be
exposed to contaminants directly, through contact with the sediments, or
indirectly, by ingesting contaminated prey. Flounder are collected from
five locations to obtain specimens for age determination, gross
examination of health, and liver histology: Deer Island Flats, Broad
Sound, off Nantasket Beach, the outfall site, and eastern Cape Cod Bay.
Livers are examined to quantify three types of vacuolation (centrotubular,
tubular, and focal, representing increasing severity), microphage
aggregation, biliary duct proliferation, and neoplasia or tumors. These
histology parameters have been associated with chronic exposure to
contaminants. 
Chemical analyses of winter flounder tissues from Deer Island Flats, the
outfall site, and Cape Cod Bay are made to determine tissue burden and to
evaluate whether contaminant burdens approach human health
consumption limits. Chemical analyses of composite samples of fillets
and livers include PCBs, pesticides, mercury, and lipids. Liver samples
are also analyzed for PAHs, lead, silver, cadmium, copper, nickel, zinc,
and lipids. 
Lobsters live on a variety of surfaces within the region, including mud,
sand, gravel, and rock outcrops. Commercial lobstermen collect lobsters
for the monitoring program, with on-board scientists verifying the
sampling locations. Lobsters are taken from Deer Island Flats, the area
near the new outfall, and eastern Cape Cod Bay to determine specimen
health and tissue contaminant burden. Chemical analyses are performed
on composite samples. Meat (from the tail and claw) and hepatopancreas
are analyzed for lipids, PCBs, pesticides, and mercury. Hepatopancreas
samples are also analyzed for PAHs, lead, silver, cadmium, chromium,
copper, nickel, and zinc. 
Like other filter feeders, blue mussels process large volumes of water and
can concentrate toxic metals and organic compounds in their tissues.
Mussels can be readily maintained in fixed cages, so they are convenient
monitoring tools. Until 2000, mussels were collected from reference sites
in Gloucester and Sandwich. Gloucester mussels provided a reference for
organic contaminant analyses, and Sandwich mussels provided a reference
for inorganic contaminants. Beginning in 2000, a new reference area, with

2000 OUTFALL MONITORING OVERVIEW 57 
low levels of both organic and inorganic contaminants, was identified in
Rockport. 
Mussels have been deployed in replicate arrays at as many as five sites,
including the Boston Inner Harbor, Deer Island, Quincy Bay, the outfall
site, and Cape Cod Bay. In 2000, arrays were deployed at Boston Inner
Harbor, Deer Island, and the outfall site. After a minimum deployment of
40 days or a preferred deployment of 60 days, chemical analyses are
performed on composite samples of mussel tissue. Tissues are analyzed
for PCBs, pesticides, PAHs, mercury, and lead. 
Results 
Winter Flounder 
Fifty sexually mature (4-5 years old) winter flounder were taken from four
of the sampling sites in April 2000 (Lefkovitz et al. 2001). Only 26 fish
were taken from Deer Island Flats, and high winds precluded additional
sampling. Each of the fish was examined for physical characteristics.
Fifteen fish from Deer Island Flats, the outfall site, and eastern Cape Cod
Bay were designated for chemical analyses. All fish were used for
histological analyses. 
Figure 5-2. Prevalence of centrotubular hydropic vacuolation (CHV) 
Overall, the fish appeared healthy, without the severe fin erosion that was
prevalent in fish from Deer Island Flats in the mid- to late-1980s. Tumors
were absent. As in previous years, the milder centrotubular hydropic
vacuolation (CHV) was the most common form of vacuolation. 
0
20
40
60
80
100
1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000
Year
CHV (% Prevalence) 
ECCB
OS
BS
NB
DIF

2000 OUTFALL MONITORING OVERVIEW 58 
CHV prevalence at Deer Island Flats was higher than in 1999 (Figure 5-2),
possibly because the 1999 Deer Island fish were collected in May rather
than in April. As in previous years, there were no obvious relationships
between age or length and lesion presence, indicating that differences
among sampling areas are indicative of differences in environmental
conditions. 
Overall, body burdens of organic contaminants in edible tissues were
similar to burdens in previous years (Figure 5-3). Total PCB and DDT
(not shown) concentrations appear to have declined in fish from Deer
Island Flats since 1995. Mercury concentrations in flounder fillets have
been variable at all sites. 
Figure 5-3. Concentrations of representative contaminants in flounder fillets and livers (DIF =
Deer Island Flats, OS = Outfall Site, and ECCB = Eastern Cape Cod Bay) 
Total PCB in Flounder Fillets 1992-2000
0
100
200
300
400
500
600
700
800
900
1992 1993 1994 1995 1996 1997 1998 1999 2000
Year
ng/g dry weight 
DIF
OS
ECCB 
Mercury in Flounder Fillets 1992-2000
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
1992 1993 1994 1995 1996 1997 1998 1999 2000
Year
ug/g dry weight 
DIF
OS
ECCB 
Total PCB in Flounder Livers 1992-2000
0
2,000
4,000
6,000
8,000
10,000
1992 1993 1994 1995 1996 1997 1998 1999 2000
Year
ng/g dry weight 
DIF
OS
ECCB 
Mercury in Flounder Livers 1992-2000
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
1992 1993 1994 1995 1996 1997 1998 1999 2000
Year
ug/g dry weight 
DIF
OS
ECCB

2000 OUTFALL MONITORING OVERVIEW 59 
Concentrations of organic contaminants in flounder livers were
comparable to or lower than concentrations measured in prior years, and
generally similar to 1999 measurements. Over all the years of sampling,
concentrations of organic compounds have been highest in fish from Deer
Island Flats and lowest in those from eastern Cape Cod Bay. Metals
concentrations have been highest at the outfall site and eastern Cape Cod
Bay. At the outfall site, concentrations of lead, mercury, cadmium,
copper, and silver (only mercury shown) were at the upper end of the
historical range. The concentration of lead in flounder livers from Deer
Island Flats was the highest measured during the baseline period. 
Lobster 
Fifteen lobsters were taken from each sampling location during July and
August (Lefkovitz et al. 2001). The lobsters were approximately the same
weight and size at all sites. Mostly males were found at eastern Cape Cod
Bay. Females predominated at Deer Island Flats and the outfall site. No
gross abnormalities were noted in any of the lobsters collected during the
survey. As in previous years, contaminant concentrations in lobster meat
were low. The highest concentrations of most organic contaminants in tail
and claw meat were found in lobsters taken from Deer Island Flats, and
the lowest concentrations were found in lobsters taken from eastern Cape
Cod Bay (Figure 5-4). Following a different pattern, mercury
concentrations were highest in samples taken at the outfall site and lowest
in those from Cape Cod Bay. This pattern has also been consistent
throughout the baseline-monitoring period. Concentrations of mercury in
the claw and tail meat were within the historical range. 
The inter-regional pattern of organic contaminant burdens in lobster
hepatopancreas was the same in 2000 as in prior years, with the highest
concentrations in lobsters from Deer Island Flats. Overall, concentrations
of organic compounds, including total PCBs and DDTs (not shown), were
similar to or lower than those found in 1999, reversing a trend of increases
during the 1990s. Total PAHs appear to have declined throughout the
baseline period, although in 2000, levels were higher than those measured
in 1998 and 1999 in lobsters from Deer Island Flats and the outfall site.

2000 OUTFALL MONITORING OVERVIEW 60 
Figure 5-4. Concentrations of representative contaminants in lobster meat and hepatopancreas
(DIF = Deer Island Flats, OS = Outfall Site, and ECCB = Eastern Cape Cod Bay) 
MWRA investigated the causes of the apparent increases in organic
contaminant concentrations observed during the 1990s and determined
that they did not result from an analytical artifact caused by co-elution
encountered during the PCB and pesticide analyses. The study of the
industry-standard analytical methods showed that the methods may
provide overestimates of PCB concentrations. However, those errors are
not sufficient to explain the observed increases. The increases may reflect
later collection of lobsters than in earlier years. The lobsters taken in the
summer and fall may have spent a longer period inshore, while those taken
in the spring may have just arrived from deeper water. A 1999 drought
may also have contributed to the high concentrations during that year, if
lobsters followed the salt wedge upstream into more contaminated areas
and then moved back downstream before they were caught. A special
study evaluating these data will be completed during 2001. 
Historically, concentrations of metals in lobster hepatopancreas have been
more variable than concentrations of organic contaminants, with
concentrations often as high or higher in animals from the outfall site and
eastern Cape Cod Bay as in those from Deer Island Flats. In 2000,
concentrations of all inorganic contaminants except zinc were similar or 
Total PAH in Lobster Hepatopancreas 1994-2000
0
2,000
4,000
6,000
8,000
10,000
12,000
14,000
16,000
18,000
20,000
1994 1995 1996 1997 1998 1999 2000
Year
ng/g Dry Weight 
DIF
OS
ECCB 
Mercury in Lobster Meat 1992-2000
0
0.2
0.4
0.6
0.8
1
1.2
1.4
1.6
1.8
1992 1993 1994 1995 1996 1997 1998 1999 2000
Year
ug/g Dry Weight 
DIF
OS
ECCB 
Total PCB in Lobster Hepatopancreas 1992-2000
0
2,000
4,000
6,000
8,000
10,000
12,000
14,000
1992 1993 1994 1995 1996 1997 1998 1999 2000
ng/g Dry Weight 
DIF
OS
ECCB 
Year
Total PCB in Lobster Meat 1992-2000
0.00
50.00
100.00
150.00
200.00
250.00
300.00
350.00
400.00
450.00
500.00
1992 1993 1994 1995 1996 1997 1998 1999 2000
Year
ng/g Dry Weight 
DIF
OS
ECCB

2000 OUTFALL MONITORING OVERVIEW 61 
lower than those measured in 1999. Silver concentrations were notably
lower than those found in 1998 and 1999 (data not shown). 
Blue Mussel 
Full mussel arrays were recovered after 40 and 60 days (Lefkovitz et al. 
2001). Survival was high, ranging from 96 to 99% after 60 days, among
all mussel arrays recovered. 
As in previous years, contaminant burdens were highest in mussels
deployed in the Inner Harbor (Figure 5-5). Overall, contaminant
concentrations were low in mussels from Rockport and the outfall site,
moderate in mussels deployed at Deer Island, and high in mussels
deployed in the Inner Harbor. Mercury and lead concentrations were
within the historical range, but slightly higher than the very low 1998 and
1999 concentrations. PCB concentrations were also within the historical
range (the reference station mussels had the lowest levels of total PCBs
recorded during the program). Pesticide and PAH concentrations (not
shown) were also low. 
Figure 5-5. Concentrations of representative contaminants in mussels (BIH = Boston Inner
Harbor, DI = Deer Island, and OS = Outfall Site) 
Mercury in Mussels 1993-2000
0.00
0.05
0.10
0.15
0.20
0.25
0.30
0.35
0.40
0.45
0.50
1993 1994 1995 1996 1997 1998 1999 2000
Year
ug/g dry weight 
BIH
DI
OS
Gloucester
Sandwich
Rockport 
Lead in Mussels 1991 and 1993 - 2000
0
2
4
6
8
10
12
14
16
1991 1993 1994 1995 1996 1997 1998 1999 2000
Year
ug/g dry weight 
BIH
DI
OS
Gloucester
Sandwich
Rockport 
Total PCB in Mussels 1991-2000
0
100
200
300
400
500
600
700
800
900
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000
Year
ng/g dry weight 
BIH
DI
OS
Gloucester
Rockport 
Total DDT in Mussels 1991-2000
0
20
40
60
80
100
120
140
160
180
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000
Year
ng/g dry weight 
BIH
DI
OS
Gloucester
Rockport

2000 OUTFALL MONITORING OVERVIEW 62 
Contingency Plan Thresholds 
Threshold parameters for fish and shellfish monitoring include levels of
toxic contaminants in flounder, lobster, and mussels and liver disease in
flounder (Table 5-1). Some thresholds are based on U.S. Food and Drug
Administration (FDA) limits for maximum concentrations of specific
contaminants in edible portions of fish and fishery products. Others are
based on the baseline monitoring, which was completed in August 2000.
Those data were used to calculate thresholds, as described in the
contingency plan. 
Table 5-1. Contingency plan baseline and threshold values for fish and shellfish monitoring 
Parameter
Type/ 
Location 
Parameter Baseline Caution Level Warning Level 
PCB 0.033 ppm 1 ppm wet weight 1.6 ppm wet weight 
Mercury 0.074 ppm 0.5 ppm wet weight 0.8 ppm wet weight 
Chlordane 242 ppb lipid 484 ppb lipid None 
Dieldrin 63.7 ppb lipid 127 ppb lipid None 
Flounder tissue
nearfield 
DDT 775.9 ppb lipid 1552 ppb lipid None 
Flounder 
nearfield 
Liver disease
(CHV) 24.4% 44.9% None 
PCB 0.015 ppm 1 ppm wet weight 1.6 ppm wet weight 
Mercury 0.148 ppm 0.5 ppm wet weight 0.8 ppm wet weight 
Chlordane 75 ppb lipid 150 ppb lipid None 
Dieldrin 161 ppb lipid 322 ppb lipid None 
Lobster tissue
nearfield 
DDT 341.3 ppb lipid 683 ppb lipid None 
PCB 0.011 ppm 1 ppm wet weight 1.6 ppm wet weight 
Lead 0.415 ppm 2 ppm wet weight 3 ppm wet weight 
Mercury 0.019 ppm 0.5 ppm wet weight 0.8 ppm wet weight 
Chlordane 102.3 ppb lipid 205 ppb lipid None 
Dieldrin 25 ppb lipid 50 ppb lipid None 
DDT 241.7 ppb lipid 483 ppb lipid None 
Mussel tissue 
nearfield 
PAH 1080 ppb lipid 2160 ppb lipid None

2000 OUTFALL MONITORING OVERVIEW 63 
6. Outfall Monitoring 
The Massachusetts Bay outfall was commissioned on September 6, 2000,
marking the beginning of outfall monitoring (see Figure 6-1). This section
covers the period of September 6 through December 31, 2000. 
When the outfall began operation on September 6, the water column was
stratified and a fall phytoplankton bloom was underway. Plume-tracking
studies began immediately. Other studies that were conducted by the end
of 2000 included water-column surveys, a sediment-contaminant survey,
and a nutrient-cycling study. 
Figure 6-1. Outfall discharge photographed in June 2001. The discharging
plume is located in the lower right. 
Plume Observations 
A preliminary plume-tracking survey was conducted in late September
2000. The survey focused on the area immediately around the outfall. Its
objectives were to provide early information on initial plume dilution and
to examine the spatial variability in salinity structure. The information on
salinity structure was necessary for planning the more extensive plume-
tracking exercises scheduled for 2001. The survey used an in situ sensor
package that measures conductivity, temperature, depth, water clarity, and
altitude above the sea floor. The package can be operated at a constant

2000 OUTFALL MONITORING OVERVIEW 64 
depth, to collect vertical profiles, or as a “towyo,” that is, in a vertically
undulating pattern. 
The water column was strongly stratified during the plume-tracking
exercise. The sensors readily detected the plume beneath the pycnocline
and moving to the north. The survey found ammonia to be a particularly
good plume tracer (Figure 6-2). Lowered salinity also proved to be a good
plume indicator, and is likely to provide adequate sensitivity to see plume
dilutions of up to 100 or higher. 
Only minimal data were available to define the mixing zone. Those data
suggested that initial dilution was large, as had been expected, and that it
occurred in close proximity to the diffusers, less than 50 m horizontally
and vertically. Continued dilution beyond the hydraulic mixing zone was
probably gradual. 
The preliminary data provided initial assurances that plume behavior
matched model predictions. As predicted by the model, no effluent was
detected at the surface while the pycnocline remained strong. Later in the
year, after the pycnocline had broken down, photographic evidence and
information from water quality surveys indicated that effluent did reach
the surface, also as predicted by the model. 
Figure 6-2. Horizontal contour of NH4 at the pycnocline. The rectangle
represents the location of the diffuser. 
0.23
0.29
0.32
0.32
0.33
0.36
0.37
0.39
0.51
0.54
0.56
0.6
1.3
1.4
1.4
3.7
5.3
6.5
8.2 
1 2 3 4 5 6 9
70° 52' W 70° 50' W 70° 48' W 70° 46' W 70° 44' W 70° 42' W
42° 20' N
42° 22' N
42° 24' N
42° 26' N
0 1 2 3 4
kilometers
Parameter: Ammonium
Sampling Depth: Mid-Depth
Last Survey Day: 9/22/00
Sampling Event: WN00D
Minimum Value 0.23 μM at N05
Maximum Value 8.23 μM at N02
Contour Interval =1 μM

2000 OUTFALL MONITORING OVERVIEW 65 
Water-Column Observations 
Water quality surveys indicated that following initiation of discharge at
the new outfall, high and variable concentrations of ammonia occurred at
Station N21, which is located along the outfall diffuser. In the effluent,
ammonia concentrations remained relatively constant from September
through December. Although ammonia is used biologically and therefore
is not a conservative tracer, it is a useful tracer of the effluent plume in the
nearfield. The transfer of effluent from the harbor to the bay had a clear
signature on ammonia concentrations in the nearfield (Libby et al. 2001). 
On September 1, prior to outfall start-up, ammonia concentrations were
relatively low throughout the nearfield. By late September, concentrations
clearly indicated that effluent was present. In early October, data
indicated that the plume was trapped beneath the pycnocline, but by late
October and for the remainder of the year, it appeared that ammonia
concentrations were elevated over the entire water column in the nearfield.
(These elevated concentrations were much lower than the ammonia
concentrations seen in Boston Harbor when the discharge was located in
the harbor.) 
Using ammonia as a tracer, the monitoring data showed an areal pattern
that was similar to what had been predicted by the computer model of
outfall dilution (Figure 6-3). Monitoring data matched outfall dilution
predictions for before and after the discharge began. Data also matched
the model predictions for depth distribution (not shown). 
Chlorophyll levels were already elevated in the nearfield (Figure 6-4, top)
and throughout the region when the outfall began operation.
Concentrations were higher in October than in September, but there was
no indication that these increases could be attributed to the outfall, because
levels were high throughout the monitoring area (See Figure 3-8, p. 31).
Preliminary data (Figure 6-4, bottom) suggest that by the winter/spring of
2001, chlorophyll levels had declined to levels lower than 1998 and 1999. 
Dissolved oxygen concentrations and percent saturation reached their
minima in October, following the outfall start-up. This timing is normal,
as oxygen minima are reached just before stratification breaks down in the
fall. The survey mean concentration and saturation minima were within
the baseline range.

2000 OUTFALL MONITORING OVERVIEW 66 
Figure 6-3. Model predictions for effluent dilutions from Deer Island (top left) and
Massachusetts Bay (top right) outfalls; measured ammonia concentrations from pre-discharge
and post-discharge, October 1999 (bottom left) and October 2000 (bottom right). 
. 
There were no apparent shifts in phytoplankton abundance or community
composition following the outfall start-up. A fall bloom was underway,
and assemblages included abundant large, chain-forming diatoms, such as
were present during the baseline-sampling years. No blooms of harmful
or nuisance species occurred. 
0.16
0.53
0.85
1.34
0.23
0.31
14.61
0.02
0.66
0.39
0.49 0.49
0.85
0.50
0.23
1.35
16.02
0.57
0.09
0.17
0.51
4.34
0.62
0.07
10.45 10.45
0.56
0.29
13.23 0.74
0.62
0.35
19.92
0.76
0.52
0.41
0.10
0.06
0.18
0.38 0.38
1.67
0.19
0.30
0.32
0.35
0.45
0.22 
1 3 5 7 9 11 13 15 30
71° 00' W 70° 50' W 70° 40' W 70° 30' W 70° 20' W 70° 10' W
41° 50' N
42° 00' N
42° 10' N
42° 20' N
42° 30' N
42° 40' N
0 5 10 15 20
kilometers
Parameter: Ammonium
Sampling Depth: Surface
Last Survey Day: 10/8/99
Sampling Event: WF99E
Minimum Value 0.02 μM at N05
Maximum Value 19.92 μM at F30
Contour Interval =2 μM 
1.37 2.12
1.28
3.78
3.75
2.13
2.52
2.05
2.75
2.26
7.24
0.92
8.91
0.77
1.91
27.84
0.64
23.32
0.40
0.82
0.52
0.54
0.67
0.75
0.35
1.27
2.22
0.12
0.09
0.41
0.36
0.41
3.05
0.34
0.57
0.77
1.40
0.59
0.55
1.15
0.24
0.38
0.68
0.20
0.58
1.68 
1 3 5 7 9 11 13 15 30
71° 00' W 70° 50' W 70° 40' W 70° 30' W 70° 20' W 70° 10' W
41° 50' N
42° 00' N
42° 10' N
42° 20' N
42° 30' N
42° 40' N
0 5 10 15 20
kilometers
Parameter: Ammonium
Sampling Depth: Bottom
Last Survey Day: 10/12/00
Sampling Event: WF00E
Minimum Value 0.09 μM at N06
Maximum Value 27.84 μM at N14
Contour Interval =2 μM
Harbor outfall Ocean outfall

2000 OUTFALL MONITORING OVERVIEW 67 
Figure 6-4. Seasonal chlorophyll levels, 1992-winter/spring 2001 
Autumn Chl Seasonal Mean
0
50
100
150
200
250
1992 1993 1994 1995 1996 1997 1998 1999 2000
Areal chlorophyll (mg/m^2) 
autumn mean autumn caution level 
Year 
Post-Outfall
Start up 
Winter/Spring Chl Seasonal Mean
0
50
100
150
200
250
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001
Areal chlorophyll (mg/m^2) 
winter/spring mean winter/spring caution level 
Year 
Post-Outfall
Start up 
Summer Chl Seasonal Mean
0
50
100
150
200
250
1992 1993 1994 1995 1996 1997 1998 1999 2000
Areal chlorophyll (mg/m^2) 
summer mean summer caution level 
Year 
Post-Outfall
Start up

2000 OUTFALL MONITORING OVERVIEW 68 
Figure 6-5. Clostridium perfringens spore density at special contaminant study
stations 
Sediment Contaminants 
A sediment-contaminant survey was conducted in the fall of 2000 after the
outfall came on line. Three replicate samples from each of the four special
contaminant study stations were collected and analyzed for TOC, grain
size, Clostridium perfringens spores, and organic and inorganic
contaminants. Concentrations of TOC measured post discharge were
similar to those measured prior to start-up of the outfall. At the three
nearfield stations, concentrations of spores of the sewage tracer bacterium 
Clostridium perfringens were about twice as high in October as they had
been in August, although the values were not significantly different from
the baseline average. Concentrations were similar to those measured in
October 1998 (Figure 6-5). Concentrations of organic and inorganic
contaminants were similar to those measured prior to the outfall coming
on line. 
Special Contaminant Study 
Clostridium perfringens 
0
1,000
2,000
3,000
4,000
5,000
6,000
7,000
FF10 NF08 NF22 NF24
Station
cfu/g dry weight
Oct-98
Aug-99
Aug-00
Oct-00

2000 OUTFALL MONITORING OVERVIEW 69 
Benthic Flux 
MWRA has conducted studies to study benthic nutrient cycling and
oxygen dynamics in Massachusetts Bay (see Section 7, Special Studies).
One survey was conducted in late August, just before the outfall began
operation, and the final survey of 2000 took place after the outfall began
discharging to Massachusetts Bay (Tucker et al. 2001). 
As would be expected from such a short interval, none of the
measurements made at that time indicated a change in benthic processes.
Typically, sediments are thought to integrate effects of multiple stresses,
so any effects would be detected after a longer time. 
Contingency Plan Threshold Results 
Because the outfall did not begin operation until September, most ambient
contingency plan thresholds were not applicable in 2000 (Table 6-1). 
MWRA reported three exceedances of ambient caution thresholds for the
period that the outfall was in operation. All three exceedances occurred in
the water column. They included dissolved oxygen percent saturation in
the nearfield and in Stellwagen Basin, and autumn nearfield chlorophyll. 
Dissolved Oxygen Percent Saturation 
In October 2000, dissolved oxygen percent saturation fell below the
caution level of 80% in the nearfield and in Stellwagen Basin. Therefore,
the regulatory agencies, OMSAP, and the public were notified. Dissolved
oxygen concentrations remained well above the standards. 
Subsequently, the thresholds related to dissolved oxygen were modified.
In April 2001, EPA and MADEP suggested adding the phrase “unless
background conditions are lower” to the thresholds. This addition makes
the thresholds more consistent with the state water quality standard, which
was the intended basis for the thresholds. MWRA calculated background
using methodology suggested by EPA and those thresholds have been
implemented on an interim basis. Now, the threshold will be exceeded if
an observed value crosses both the original threshold and the background
values. Neither percent saturation nor dissolved oxygen concentration
have fallen below the background levels since the outfall start-up in
September 2000. Figure 6-6 shows the fluctuations of bottom dissolved
oxygen percent saturation, along with the threshold and background
levels, since the start of monitoring in 1992.

2000 OUTFALL MONITORING OVERVIEW 70 
Figure 6-6. Patterns of percent saturation in bottom water dissolved oxygen for the nearfield
(left) and Stellwagen Basin (right). Values often fell below the state standards for percent
saturation but rarely fell below the background levels. 
Nearfield Chlorophyll Autumn 2000 
The fall 2000 average chlorophyll level was 212 mg/m 2 , which exceeded
the seasonal caution level of 161 mg/m 2 , triggering notification of EPA,
MADEP, OMSAP, and the public (see Figure 6-4). In reviewing the data,
MWRA determined that the high values for chlorophyll in the fall were
independent of the effluent outfall and instead reflected a large-scale
region-wide occurrence, which began prior to the outfall beginning
operation. 
Increased algal levels were first noted in early September, before the
outfall went on line. Satellite imagery confirmed that there was a region-
wide algal bloom that ranged from New Jersey to the Bay of Fundy (see
Figure 3-8 in Section 3, Water Column Baseline). The monitoring team
closely followed the progress of this bloom throughout the fall, winter,
and following spring. 
Throughout this period, there were no unusual elevations of nuisance algal
species; the diatoms making up the fall 2000 bloom were members of the
normal coastal plankton community. There were no effects on dissolved
oxygen concentrations. In fact, concentrations of dissolved oxygen in the
water column were somewhat higher than usual. Benthic chlorophyll
levels, which would indicate whether large amounts of algae were settling
to the bottom, were normal. Benthic respiration, which would indicate if
an unusual amount of oxygen were being used if excess algae were being
broken down in the sediments, was also normal. Particulate organic
carbon and phytoplankton cell counts peaked in early September (before
the outfall went on line), remaining at moderate levels through late
October, then declining to low, winter levels. The fall 2000 particulate 
60
70
80
90
100
110
120
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 
60
70
80
90
100
110
120
1992 199 3 1994 1995 1996 1997 1998 1999 2000 2001 
caution level warning level
background level outfall start-up
nearfield survey mean Stellwagen Basin survey mean

2000 OUTFALL MONITORING OVERVIEW 71 
organic carbon levels and phytoplankton abundances were well within the
range observed throughout baseline sampling. 
The spring 2001 nearfield average chlorophyll concentration was 78
mg/m 2 , well within the contingency plan threshold of 182 mg/m 2 . In
summary, all evidence suggests that the fall 2000 threshold exceedance
was part of a region-wide pattern of elevated chlorophyll levels,
independent of the MWRA outfall and that there were no immediate
adverse effects from the fall bloom. 
Table 6-1. Contingency plan thresholds and threshold testing results for 2000 ambient
discharge monitoring (Results for 2000 effluent discharge monitoring are in Table 2-2.) 
Parameter Background
or Baseline 
Caution
Level 
Warning
Level 
September 6 –
December 31,
2000 Results 
Water Column Thresholds 
Nearfield bottom water,
dissolved oxygen
concentration 
5.75 mg/l 6.5 mg/l 6.0 mg/l Not exceeded 
7.1 mg/l 
Stellwagen Basin bottom
water, dissolved oxygen
concentration 
6.2 mg/l 6.5 mg/l 6.0 mg/l Not exceeded 
7.3 mg/l 
Nearfield bottom water,
dissolved oxygen saturation 64.3% 80% 75% 
Caution Level
exceeded 
78% 
Stellwagen Basin, dissolved
oxygen saturation 66.3% 80% 75% 
Caution Level
exceeded 
78% 
Nearfield bottom water,
dissolved oxygen depletion
rate 
0.0244 mg/l/d 0.037 mg/l/d 0.049 mg/l/d Not applicable 
Nearfield chlorophyll, annual 71 mg/m 2 107 mg/m 2 143 mg/m 2 Not applicable 
Nearfield chlorophyll,
winter/spring 81 mg/m 2 182 mg/m 2 None Not applicable 
Nearfield chlorophyll, summer 51 mg/m 2 80 mg/m 2 None Not applicable 
Nearfield chlorophyll, autumn 90 mg/m 2 161 mg/m 2 None 
Caution Level
exceeded 
212 mg/m 2 
Nearfield Phaeocystis ,
winter/spring 470,000 cells/l 2,020,000
cells/l None Not applicable 
Nearfield Phaeocystis , summer 7.2 cells/l 334 cells/l None Not applicable 
Nearfield Phaeocystis , autumn 300 cells/l 2,370 cells/l None Not exceeded 
0 cells/l

2000 OUTFALL MONITORING OVERVIEW 72 
Parameter Background
or Baseline 
Caution
Level 
Warning
Level 
September 6 –
December 31,
2000 Results 
Nearfield Pseudonitzschia ,
winter/spring 6,200 cells/l 21,000 cells/l None Not applicable 
Nearfield Pseudonitzschia ,
summer 13,000 cells/l 38,000 cells/l None Not applicable 
Nearfield Pseudonitzschia ,
autumn 9,700 cells/l 24,600 cells/l None Not exceeded 
12,600 cells/l 
Nearfield Alexandrium Maximum =
163 cells/l 100 cells/l None 
Not exceeded 
No Alexandrium 
present 
Farfield PSP toxin extent 
Never
observed at
certain
southern Mass
Bay stations 
New
incidence None 
Not exceeded 
No PSP in Mass.
Bay 
Plume initial dilution None None Less than
predicted Not applicable 
Sediment Thresholds 
Nearfield, sediment depth of
redox discontinuity 2.36 cm 1.18 cm None Not applicable 
acenaphthene 30 ppb dry none 500 ppb dry Not applicable 
acenaphthylene 48 ppb dry none 640 ppb dry Not applicable 
anthracene 151 ppb dry none 1100 ppb dry Not applicable 
benz(a)anthracene 278 ppb dry none 1600 ppb dry Not applicable 
benzo(a)pyrene 258 ppb dry none 1600 ppb dry Not applicable 
cadmium 0.2 ppm dry none 9.6 ppm dry Not applicable 
chromium 76 ppm dry none 370 ppb dry Not applicable 
chrysene 255 ppb dry none 2800 ppb dry Not applicable 
copper 24 ppm dry none 270 ppm dry Not applicable 
dibenzo(a,h)anthracene 37 ppb dry none 260 ppb dry Not applicable 
fluoranthene 558 ppb dry none 5100 ppb dry Not applicable 
fluorene 50 ppb dry none 540 ppb dry Not applicable 
lead 44 ppm dry none 218 ppm dry Not applicable 
mercury 0.24 ppm dry none 0.71 ppm dry Not applicable 
naphthalene 70 ppb dry none 2100 ppb dry Not applicable 
nickel 17 ppm dry none 51.6 ppm dry Not applicable 
p,p'-DDE 0.8 ppb dry none 27 ppb dry Not applicable

2000 OUTFALL MONITORING OVERVIEW 73 
Parameter Background
or Baseline 
Caution
Level 
Warning
Level 
September 6 –
December 31,
2000 Results 
phenanthrene 349 ppb dry none 1500 ppb dry Not applicable 
pyrene 516 ppb dry none 2600 ppb dry Not applicable 
silver 0.6 ppm dry none 3.7 ppm dry Not applicable 
total DDTs 3.5 ppb dry none 46.1 ppb dry Not applicable 
total HMWPAH 3559 ppb dry none 9600 ppb dry Not applicable 
total LMWPAH 1639 ppb dry none 3160 ppb dry Not applicable 
total PAH 5199 ppb dry none 44,792 ppb
dry Not applicable 
total PCBs 17 ppb dry none 180 ppb dry Not applicable 
zinc 61 ppm dry none 410 ppm dry Not applicable 
Nearfield benthos, species per
sample 64.52 <47.95 or
>81.09 None Not applicable 
Nearfield benthos, 
Fisher’s log-series alpha 13.00 <10.13 or
>15.88 None Not applicable 
Nearfield benthos, 
Shannon diversity 3.67 <3.32 or
>4.02 None Not applicable 
Nearfield benthos, 
Pielou’s evenness 0.62 <0.56 or
>0.67 None Not applicable 
Nearfield benthos, opportunists 0.75% 10% 25% Not applicable 
Fish and Shellfish 
Nearfield flounder, PCB 0.033 ppm wet 1 ppm wet 1.6 ppm wet Not applicable 
Nearfield flounder, mercury 0.074 ppm wet 0.5 ppm wet 0.8 ppm wet Not applicable 
Nearfield flounder, chlordane 242 ppb lipid 484 ppb lipid None Not applicable 
Nearfield flounder, dieldrin 63.7 ppb lipid 127 ppb/g
lipid None Not applicable 
Nearfield flounder, DDT 775.9 ppb lipid 1552 ppb
lipid None Not applicable 
Nearfield flounder, liver
disease 24.4% 44.9% None Not applicable 
Nearfield lobster, PCB 0.015 ppm wet 1 ppm wet 1.6 ppm wet Not applicable 
Nearfield lobster, mercury 0.148 ppm wet 0.5 ppm wet 0.8 ppm wet Not applicable 
Nearfield lobster, chlordane 75 ppb lipid 150 ppb lipid None Not applicable 
Nearfield lobster, dieldrin 161 ppb lipid 322 ppb lipid None Not applicable 
Nearfield lobster, DDT 341.3 ppb lipid 683 ppb lipid None Not applicable 
Nearfield mussel, PCB 0.011 ppm wet 1 ppm wet None Not applicable 
Nearfield mussel, lead 0.415 ppm wet 2 ppm wet 3 ppm wet Not applicable

2000 OUTFALL MONITORING OVERVIEW 74 
Parameter Background
or Baseline 
Caution
Level 
Warning
Level 
September 6 –
December 31,
2000 Results 
Nearfield mussel, mercury 0.019 ppm wet 0.5 ppm wet 0.8 ppm wet Not applicable 
Nearfield mussel, chlordane 102.3 ppb lipid 205 ppb lipid None Not applicable 
Nearfield mussel, dieldrin 25 ppb lipid 50 ppb lipid None Not applicable 
Nearfield mussel, DDT 241.7 ppb lipid 483 ppb lipid None Not applicable 
Nearfield mussel, PAH 1080 ppb lipid 2160 ppb
lipid None Not applicable

2000 OUTFALL MONITORING OVERVIEW 75 
7. Special Studies 
Background 
Besides monitoring the effluent and the water column, sea floor, and fish
and shellfish in Massachusetts Bay and the surrounding area, MWRA
conducts special studies in response to specific permit requirements,
scientific questions, and public concerns. For example, MWRA has an
ongoing study of Boston Harbor, which in 2000, documented the first
changes in water quality following diversion of the effluent from the
harbor to Massachusetts Bay. MWRA is also monitoring bacterial water
quality in Massachusetts Bay, has ongoing studies of nutrient cycling in
the harbor and the bay, and makes observations of marine mammals
during water column and other surveys. 
Water Quality in Boston Harbor 
Over the past decade, MWRA has been documenting the effects on Boston
Harbor due to source reduction and facilities upgrades, including ending
of sludge discharges, transfer of all effluent to Deer Island for secondary
treatment, implementation of plans to control CSOs, and finally, in 2000,
ending effluent discharges to the harbor. MWRA efforts have included
monitoring water quality at the former outfalls and at other locations in the
harbor. Monitoring within the harbor has focused on three issues:
eutrophication, water clarity, and effluent indicator bacteria. The focus on
eutrophication has included measurements of nutrient concentrations, algal
quantity, and dissolved oxygen concentration. 
From 1998 through August 2000, monitoring within the harbor focused on
the effects of the upgrade to secondary treatment at Deer Island and then
the transfer of Nut Island flows through this upgraded facility. During this
period, there was a large reduction in ammonia concentrations (Figure 7-
1) and a large increase in water clarity, as measured by Secchi disk depth
(Figure 7-2) at the former Nut Island outfalls and elsewhere in the
southern portion of the harbor. Some increase in ammonia levels were
observed off Deer Island, due to the increased loads, but the same area
showed an improvement in water clarity, because of the improved solids
removal at Deer Island.

2000 OUTFALL MONITORING OVERVIEW 76 
Figure 7-1. Ammonia levels in waters in the vicinity of the Deer Island and Nut
Island outfalls 
During the last four months of 2000, monitoring focused on the changes
resulting from the end of discharge from Deer Island. Within days of
closing the harbor outfall, improvements in water quality were apparent.
Ammonia concentrations decreased and water clarity increased in the
vicinity of the former outfall. 
By the end of 2000, improvements in water quality were detectable at
stations further away from the former harbor outfalls. These
improvements included reductions in nitrogen concentrations, including
ammonia, reductions in phosphorus concentrations, and improved water
clarity. Drops in ammonia concentrations were detected even at the
former Nut Island site (Figure 7-1). MWRA expects that further
improvements will be detected in 2001. 
Site o f fo rm er D eer Is. Ou tfall #001 
0
20
40
60
80
100
120
J F M A M J J A S O N D J F MA M J J AS O N D J F M AM J J A S O N D J F M A M J J A S O ND J F M 
micromo les/liter
1998 1997 1999 2000 2001 
Start of Mas s .
Ba y dis ch arge
Trans fer of N I fl ow s to D I 
Site of form er N ut Islan d Outfall #101 
0
20
40
60
80
100
120
J F M A M J J A S O ND J F M A M J J A S O N D J F M A M J J A S O N D J F M AM J J A S ON D J F M 
microm oles/liter
1998 1997 1999 2000 2001 
Start of Mas s .
Ba y dis ch arge
Trans fer of N I flow s to D I

2000 OUTFALL MONITORING OVERVIEW 77 
Figure 7-2. Secchi disk depths in waters in the vicinity of the Deer Island and Nut
Island outfalls 
Massachusetts Bay Bacteria Monitoring 
MWRA monitors bacterial water quality near the new outfall and at other
locations in Massachusetts Bay (Figure 7-3) under a “Monitoring and
Notification Agreement” included in a memorandum of understanding
(MOU) between MWRA and the Massachusetts Division of Marine
Fisheries (DMF). The purpose of the monitoring is to assure that the
operation of the outfall does not adversely affect shellfish-growing waters.
Results of the studies will also be used by DMF to identify areas in
Massachusetts Bay suitable for shellfish harvesting. The monitoring
involves collection of water from the surface and beneath the pycnocline
at twelve locations in the bay. Samples are collected during periods of
stratification, and are analyzed for fecal coliform bacteria and another
sewage indicator, Enterococcus . Fecal coliform bacteria are used by the
FDA as an indicator for classifying shellfish-growing areas. Enterococcus 
is the EPA-preferred indicator of public health risk in marine waters used
for recreation. Surveys are conducted monthly: three baseline surveys
were performed between 1999 and September 2000, and the first post-
discharge survey was conducted in October 2000. 
Site of form er D eer Is. Ou tfall #001 
0
1
2
3
4
5
6
J F M A M J J AS ON D J F M A MJ J A S O N D J FM A M J J A S ON D J F M A M J J A S ON D J F M 
mete rs 
S tart of M ass.
B ay d isc harge
Transfer of NI flo ws to DI 
2001 1998 1997 1999 2000
Site o f fo rm er Nu t Islan d Ou tfall #101 
0
1
2
3
4
5
6
J F M A M J J A S O N D J F M AM J J AS O N D J F M A M J J A S O N D J F M A MJ J AS ON D J F M 
meters 
Start of M ass .
Ba y dis cha rg e 
2001 1998 1997 1999 2000 
Trans fe r of NI flow s to D I

2000 OUTFALL MONITORING OVERVIEW 78 
Figure 7-3. Locations of bacteria monitoring stations 
Fecal coliform counts in Massachusetts Bay have remained low following
the opening of the new outfall (Table 7-1). Many samples had counts that
were below detection limits; those samples were assigned the value of the
detection limit, 2 colonies/100 ml. Mean number of colonies increased
slightly at stations near the outfall diffusers and shoreward; no changes
were found offshore. 
As with fecal coliform counts, Enterococcus counts have been very low in
Massachusetts Bay (Table 7-2). As with fecal coliform bacteria, counts
for many samples were below detection limits and were assigned a value
of 1 colony/100 ml, the detection limit. Geometric means have increased
slightly following the commissioning of the outfall; only stations near the
outfall diffuser have shown any change. 
BOSTON
QUINCY
HINGHAM
REVERE 













   
NAHANT
SALEM
LYNN
HULL 
Massachusetts
Bay
Boston
Harbor 

 Offshore sampling location
Outfall diffuser 

 
Sampling location near outfall diffuser
Shoreward sampling location 



 Former DI outfall sampling location

2000 OUTFALL MONITORING OVERVIEW 79 
Table 7-1. Fecal coliform bacteria counts from the Boston Harbor outfall
location and Massachusetts Bay. Water quality standard in Massachusetts Bay
is ≤ 200 colonies per 100 ml. Unrestricted shellfishing standard is ≤ 14 colonies
per 100 ml. 
Geometric mean fecal coliform counts 
(colonies/ 100 ml) 
Massachusetts Bay Former
(Harbor)
Outfall 
Near Outfall
Diffuser Shoreward Offshore 
Before outfall
opening 8.6 2.0 2.1 2.0 
After outfall
opening 5.9 2.2 2.3 2.0 
Table 7-2. Entercoccus bacteria counts from the Boston Harbor outfall location 
and from Massachusetts Bay. Swimming standard for Massachusetts beaches is 
≤ 35 colonies/ 100 ml. 
Geometric mean Enterococcus counts 
(colonies/ 100 ml) 
Massachusetts Bay Former
(Harbor)
Outfall 
Near Outfall
Diffuser Shoreward Offshore 
Before outfall
opening 6.8 1.0 1.2 1.0 
After outfall
opening 5.3 1.1 1.2 1.0 
Nutrient Flux 
Sediments in coastal areas such as Boston Harbor can play an important
role in nutrient cycling and oxygen dynamics. Breakdown of organic
matter in the sediments consumes oxygen and releases nutrients.
Denitrification, a process that converts nitrate to gaseous forms of
nitrogen, causes nitrogen to be lost to the atmosphere. Consequently,
when an offshore outfall was planned, scientists were concerned about a
possible increase in nitrogen loads. If denitrification rates were high
within the harbor, then moving the outfall into deeper waters with lower
denitrification rates might increase the nitrogen load to the region. 
MWRA has conducted studies of benthic nutrient cycling within Boston
Harbor since 1992. In 2000, studies were conducted at four sites: the
central outer harbor, off Long Island in the former sludge disposal area,
Hingham Bay in the southern harbor, and Quincy Bay, also in the southern
harbor (Tucker et al. 2001). Results of the studies have shown that
denitrification rates within the harbor are high, as had been predicted.
However, the studies have also shown that little of the nutrient inputs to
the harbor are cycled through the sediments and lost to the system.

2000 OUTFALL MONITORING OVERVIEW 80 
Consequently, moving the outfall offshore is unlikely to affect the total
nitrogen load to the bay. 
The studies have also documented recovery of the harbor since the
cessation of sludge disposal in 1991. For the first years after sludge inputs
ceased, rates of respiration and nutrient flux were extremely high at the
former disposal site. Rates have decreased since 1998. 
MWRA also conducts studies of nutrient cycling and oxygen dynamics in
Massachusetts Bay. Studies conducted in 2000 marked the completion of
baseline studies and the first measurements to be made after the outfall
began operation. Studies were conducted at three stations near the new
outfall and at one station in Stellwagen Basin. As was expected after such
a brief period, no changes were detected following start-up of the outfall.
Further, if the outfall plume continues to act as predicted by model
calculations, no detectable changes are expected in the future (see Section
6, Outfall Monitoring). 
Marine Mammal Observations 
Several endangered or threatened species of whales and turtles regularly
visit Massachusetts and Cape Cod bays, including the right, humpback,
finback, sei, and blue whales. Species that are not endangered or
threatened include the minke whale, harbor porpoise, gray seal, harbor
seal, and several kinds of dolphins. 
Since 1995, MWRA has included endangered species observers on
monitoring surveys. In 2000, observers were included on 23 surveys
(McLeod et al. 2001). Besides providing monitoring data, presence of
trained marine mammal observers addresses a request by NMFS that
MWRA provide observational data and minimize the chances of collision
of its survey vessels with a right whale. 
During these surveys, 55 individual whales, 11 Atlantic white-sided
dolphins, 21 pilot whales, and more than 50 unidentified dolphins were
sighted by the observers or other members of the survey team (Figure 7-
4). Included in the sightings were 29 humpback whales, 4 finback whales,
and 3 minke whales. Other whales could not be identified to species. No
right whales were observed in 2000. Forty-seven of the sightings were
within the boundaries of the Stellwagen Bank National Marine Sanctuary,
and two minke whales were seen in the nearfield.

2000 OUTFALL MONITORING OVERVIEW 81 
Figure 7-4. Whale sightings during 2000 
The data from these surveys are difficult to interpret, because whale
populations are known to fluctuate between years, and the observations
are opportunistic, tied to surveys with other missions, rather than
systematic and specifically designed to inventory mammal populations. In
general, however, observations in 2000 were similar to those in 1998 and

2000 OUTFALL MONITORING OVERVIEW 82 
1999. For example, 28 large baleen whales were sighted in 1998, 27 in
1999, and 31 in 2000. 
General observations of large baleen whales in the Stellwagen Bank area
indicated that only a few humpback and fin whales used the area in May
(noted by the Whale Center of New England and reported in McLeod et
al. 2001). Whales were abundant over the southern flank of Stellwagen
Bank from June through September, and over the entire area in October.
An unusual observation was that two juvenile humpback whales spent a
week within a mile of the coast, between Nahant and Boston, even
entering Boston Harbor. One of these whales remained near the coast
through December, entering and feeding in Salem, Beverly, and
Gloucester harbors.

2000 OUTFALL MONITORING OVERVIEW 83 
8. Stellwagen Bank 
National Marine Sanctuary 
The Gerry E. Studds Stellwagen Bank National Marine Sanctuary
comprises 842 square miles of area located at the boundary of
Massachusetts Bay and the Gulf of Maine. It is approximately 25 miles
east of Boston, 3 miles north of Provincetown, and 3 miles south of
Gloucester. The most prominent feature within the sanctuary is
Stellwagen Bank, a sand-and-gravel plateau, with water depths of about 65
feet. The bank rises about 165 feet above Stellwagen Basin to its west.
Currents from the Gulf of Maine and Stellwagen Basin create a rich
habitat for marine life. Stellwagen Bank is popular as a fishing ground
and for whale-watching excursions. 
The sanctuary is currently revising its 1993 management plan. Scoping
comments made public in January 2000 listed eleven issues of concern
(Table 8-1). 
Table 8-1. Issues of concern for the Stellwagen Bank National Marine Sanctuary 
Management Plan Issues 
Ship strikes of whales and other whale-ship interactions 
Whale watching 
Research 
Education and outreach 
Marine conservation zones 
Fishing activity 
Mariculture 
Effects of MWRA discharge 
Extension of the sanctuary boundaries 
Enforcement of sanctuary regulations 
Installation of submerged cables or pipelines within sanctuary
boundaries 
A preliminary draft plan addressing all the concerns is planned for 2001.
Meanwhile, the MWRA permit recognizes the concerns about possible
effects of the outfall on the sanctuary and requires an annual report of
those possible effects. 
The plume-tracking exercises that began after the outfall began operation
in 2000 provided an early indication that the plume was rapidly diluted
and behaved as predicted by the transport and dilution models. During
those first studies, the plume moved towards the north rather than towards
the sanctuary, and dilution of approximately 1:100 occurred in close
proximity to the diffusers, <5 m horizontally and vertically. These

2000 OUTFALL MONITORING OVERVIEW 84 
preliminary measurements provided an initial assurance that the outfall
will not affect the waters of the sanctuary. More extensive measurements
will be reported in the coming years. 
MWRA’s regular water-column and sea-floor monitoring programs
include stations in and near the sanctuary. Five water-column stations,
including four within the sanctuary and one just outside the northern
border are considered “boundary” stations, that is, they mark the boundary
between Massachusetts Bay and the Gulf of Maine. These stations are
important to MWRA, not just because of their location within a marine
sanctuary, but also because water column processes within Massachusetts
Bay are largely driven by the processes in wider region of the Gulf of
Maine. Eight water-column stations located just inshore from the
sanctuary are considered “offshore” stations by the MWRA program.
Two sea-floor stations are within the sanctuary, and two additional
stations are inshore from the sanctuary but in waters of similar depths and
with similar sediments as those found within the sanctuary bounds. 
Baseline water-column sampling has indicated that the stations within the
sanctuary are healthy and similar to other farfield stations. Nutrient levels
at boundary stations are consistently with the same range as the nearfield
Figure 8-1). Annual mean chlorophyll concentrations were elevated at the
boundary stations in 2000, as they were in other regions, but as in other
years, they did not differ significantly from the nearfield or other offshore
stations (Figure 8-2). 
Figure 8-1. Survey mean dissolved inorganic nitrogen in the nearfield and at the
boundary in the Stellwagen Bank National Marine Sanctuary 
Survey Mean DIN 
0
2
4
6
8
10
12 
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001
YEAR
DIN (mM)
Nearfield
Boundary
Outfall Start-up

2000 OUTFALL MONITORING OVERVIEW 85 
Figure 8-2. Survey mean areal chlorophyll levels in the nearfield and at the
boundary in the Stellwagen Bank National Marine Sanctuary 
The annual survey mean concentration of dissolved oxygen was 7.3 mg/l,
slightly higher than the nearfield value, as is typical. Levels were within
the range for dissolved oxygen concentrations in the baseline-sampling
period (Figure 8-3). Percent oxygen saturation fell below 80% but was
well above the background value. 
In 2000, assemblages found in whole-water phytoplankton samples taken
from the boundary area were very similar to those of other farfield stations
and to nearfield stations, with the April Phaeocystis bloom being the most
noticeable event in all geographic regions. Zooplankton assemblages were
also similar for boundary, other farfield, and nearfield stations. The
limited data collected after the outfall began operation in 2000 have
provided no indication that effluent is transported to the sanctuary in
concentrations that would adversely affect productivity or plankton
communities. 
Sea-floor studies for 2000 were completed prior to the outfall coming on
line. In future years, MWRA will be able to evaluate possible effects of
the outfall on the sanctuary by analyzing data from the two stations that
are included within its borders and from another two stations in similar
locations. During the baseline period, these four stations (FF04, FF05,
FF11, and FF14) have had similar benthic communities, dominated by
annelids. Multivariate analysis of infauna data from all farfield stations
indicated that these four stations were similar enough to be considered one
of four farfield “groups.” The other three groups could be defined by their
location, depth, and sediment type and included (1) northern, shallow
stations, (2) Cape Cod bay, shallow stations, and (3) stations with coarse
sediments. 
Survey Average Areal Chlorophyll
0
100
200
300
400
500
600
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001
Year
Chlorophyll (mg/m2) Nearfield
Boundary
Outfall Start-up

2000 OUTFALL MONITORING OVERVIEW 86 
Figure 8-3. Survey mean dissolved oxygen concentrations and percent
saturation in Stellwagen Basin, 1992-2000 
The Stellwagen Basin and other deep stations have shown less similarity
with respect to contaminant levels. The two offshore stations outside the
sanctuary tend to be defined by slightly elevated levels of total PAHs,
while slightly elevated levels of metals defined one of the stations within
the sanctuary, and the other station did not align more closely with either
group. 
The bacteria monitoring that MWRA carries out in Massachusetts Bay
includes two offshore stations located just shoreward from the sanctuary.
Data from these stations showed no increase of fecal coliform or 
Enterococcus bacteria after the outfall opened (see Tables 7-1 and 7-2 in
Section 7, Special Studies). Ongoing monitoring of these stations will
provide an additional means of determining whether the outfall has any
effect on the sanctuary. 
Stellwagen Bottom Water DO %SAT
40
50
60
70
80
90
100
110
120
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001
DO %SAT
Mean Caution Warning Background
Year Outfall Start-up 
Stellwagen Bottom Water DO
4
5
6
7
8
9
10
11
12
13
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001
DO (mg L -1 )
Mean Caution Warning Background
Year Outfall Start-up

2000 OUTFALL MONITORING OVERVIEW 87 
One major concern of the sanctuary is for the whales that migrate through
it and that feed within its boundaries. The sanctuary draws as many as one
million whale watchers each year. As expected, most of the whales
observed during MWRA surveys (discussed in Section 7, Special Studies)
were seen in the sanctuary. Only a few humpback and fin whales used the
Stellwagen Bank area in May (noted by the Whale Center of New England
and reported in MacLeod et al. 2001). Whales were abundant over the
southern flank of Stellwagen Bank from June through September, and
over the entire area in October.

2000 OUTFALL MONITORING OVERVIEW 88 
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2000 OUTFALL MONITORING OVERVIEW 92 
List of Acronyms 
BEM Bays Eutrophication Model 
BIH Boston Inner Harbor 
BOD Biochemical oxygen demand 
cBOD Carbonaceous biochemical oxygen demand 
CCB Cape Cod Bay 
CD-ROM Compact disk 
CHV Centrotubular hydropic vacuolation 
C-NOEC No observable effect concentration 
CSO Combined sewer overflow 
DI Deer Island 
DIF Deer Island Flats 
DMF Massachusetts Division of Marine Fisheries 
ECCB Eastern Cape Cod Bay 
EPA U.S. Environmental Protection Agency 
FDA U.S. Food and Drug Administration 
IAAC Inter-agency Advisory Committee 
LC50 50% mortality concentration 
MADEP Massachusetts Department of Environmental Protection 
MEG Model Evaluation Group 
MGD Million gallons per day 
MOU Memorandum of understanding 
MWRA Massachusetts Water Resources Authority 
NASA National Air and Space Administration 
NMFS National Marine Fisheries Service 
NPDES National Pollutant Discharge Elimination System 
OMSAP Outfall Monitoring Science Advisory Panel 
OMTF Outfall Monitoring Task Force 
OS Outfall site 
PAH Polycyclic aromatic hydrocarbon 
PCB Polychlorinated biphenyl 
PIAC Public Interest Advisory Committee 
RPD Redox potential discontinuity 
PSP Paralytic shellfish poisoning 
SeaWiFS Sea-viewing Wide Field-of-view Sensor 
SEIS Supplemental Environmental Impact Statement 
USGS U.S. Geological Survey 
TCR Total chlorine residual 
TOC Total organic carbon 
TSS Total suspended solids 
WHOI Woods Hole Oceanographic Institution

Massachusetts Water Resources Authority 
Charlestown Navy Yard 
100 First Avenue 
Boston, MA 02129 
(617) 242-6000