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1998 overview

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1998
Outfall monitoring overview
Massachusetts Water Resources Authority
Environmental Quality Department
Report ENQUAD 00-04

1998
Outfall Monitoring Overview 
submitted to
Massachusetts Water Resources Authority Environmental Quality Department lOO First
A venue
Charlestown N avy Yard Boston, MA 02129
prepared by
Christine Werme
Norwell, MA 02061
and
Carlton D. Hunt Battelle
397 Washington Street Duxbury, MA 02332
March 20,2000

Citation:
Werme C, Hunt CD. 2000. 1998 Outfall monitoring overview. Boston:
Massachusetts Water Resources Authority. Report ENQUAD 00-04. 66 p.

1998 OUTFALL MONITORING OVERVIEW 
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, improved treatment, and
effective dilution. One aspect of the project, moving the treated wastewater outfall from
the harbor to Massachusetts Bay, has caused some environmental concerns. To address
these concerns, MWRA implemented an extensive monitoring program to measure the
health of Boston Harbor and the bays. Furthermore, the joint U.S. Environmental
Protection Agency (EPA) and Massachusetts Department of Environmental Protection
(MADEP) permit for the new outfall, which was issued in 1999, requires extensive
monitoring of the effluent, water column, sea floor, and fish and shellfish. It links the
monitoring program to a contingency plan. The contingency plan identifies corrective
actions for unexpected impacts resulting from operation of the outfall.
This Outfall Monitoring Overview presents a scientific summary of monitoring data
collected through 1998 and includes information relevant to the contingency plan.
Because the outfall is not yet operational, these data represent the baseline conditions in
the vicinity of the outfall site and further afield in Massachusetts and Cape Cod bays.
Most MWRA monitoring began in 1992, resulting in a relatively long period in which to
conduct baseline studies. This long period has allowed MWRA to document greater
natural variability than would have been observed in briefer baseline monitoring.
During 1998, effluent monitoring reflected continued improvements in effluent quality,
due to source reduction and secondary treatment. In the water column, there was no
spring bloom of phytoplankton, and it appears that such blooms may not be as
characteristic of the area as was previously thought. The year was also marked by
unusually prolonged stratification of the water column, with the lowest levels of
dissolved oxygen in bottom waters occurring in December. Although low, these levels
did not fail the state standard of 6 mg/L. The average number of individuals and species
in soft-bottom communities near the outfall site, which decreased from 1992 to 1993 and
subsequently rose, leveled off in 1997 and 1998. Concentrations of contaminants in
sediment samples from the vicinity of the site were similar to those found by previous
studies. Contaminant levels in muscle tissues of fish and shellfish remained well below
levels of concern. During 1998, MWRA also conducted several special studies,
including runs of the Bays Eutrophication Model (BEM), which indicated that relocating
the outfall will not affect water quality in Massachusetts Bay, assessment of the value of
a food-web model, and a study of cobble-boulder habitats, which indicated that the area
around the outfall a site is not significant for settling of or habitation by recently-settled
juvenile lobsters.

II

1998 OUTFALL MONITORING OVERVIEW

1998 OUTFALL MONITORING OVERVIEW 
Table of Contents 
1. Introduction..................................................................................................................... 1
Background ..................................................................................................................... 1
Outfall Permit.................................................................................................................. 3
Monitoring Program........................................................................................................ 4
Contingency Plan ............................................................................................................ 7
Data Management and Reporting ................................................................................... 8
Outfall Monitoring Overview ......................................................................................... 9
2. Effluent ......................................................................................................................... 10
Background ................................................................................................................... 10
Effluent Treatment .................................................................................................... 10
Environmental Concerns........................................................................................... 10
Monitoring Design ........................................................................................................ 12
Results........................................................................................................................... 13
Contingency Plan Thresholds ....................................................................................... 16
3. Water Column............................................................................................................... 17
Background ................................................................................................................... 17
Circulation and Water Properties.............................................................................. 17
Environmental Concerns........................................................................................... 19
Monitoring Design ........................................................................................................ 20
Results........................................................................................................................... 22
Physical Conditions .................................................................................................. 22
Water Quality............................................................................................................ 22
Phytoplankton Communities..................................................................................... 27
Zooplankton Communities........................................................................................ 28
Marine Mammal Observations ................................................................................. 29
Contingency Plan Thresholds ....................................................................................... 30
4. Sea Floor ....................................................................................................................... 33
Background ................................................................................................................... 33
Bottom Characteristics and Sediment Transport ...................................................... 33
Environmental Concerns........................................................................................... 33
Monitoring Design ........................................................................................................ 34
Results........................................................................................................................... 37
Sediment Contaminants ............................................................................................ 37
Sediment Profile Imaging ......................................................................................... 37
Soft-bottom Communities......................................................................................... 38
Hard-bottom Communities ....................................................................................... 41
Contingency Plan Thresholds ....................................................................................... 42
5. Fish and Shellfish.......................................................................................................... 43
Background ................................................................................................................... 43
Fisheries .................................................................................................................... 43
Environmental Concerns........................................................................................... 43

1998 OUTFALL MONITORING OVERVIEW IV 
Monitoring Design ........................................................................................................ 43
Results........................................................................................................................... 45
Winter Flounder ........................................................................................................ 45
Lobster ...................................................................................................................... 47
Blue Mussel .............................................................................................................. 49
Contingency Plan Thresholds ....................................................................................... 51
6. Special Studies .............................................................................................................. 53
Background ................................................................................................................... 53
Bays Eutrophication Model .......................................................................................... 53
Food Web Model .......................................................................................................... 54
Nutrient Flux................................................................................................................. 55
Lobster Settling............................................................................................................. 56
7. Summary....................................................................................................................... 57
Background ................................................................................................................... 57
Effluent ......................................................................................................................... 58
Water Column............................................................................................................... 58
Sea Floor ....................................................................................................................... 59
Fish and Shellfish.......................................................................................................... 60
Special Studies .............................................................................................................. 61
References......................................................................................................................... 63
List of Acronyms .............................................................................................................. 66

1998 OUTFALL MONITORING OVERVIEW V
List of Figures 
Figure 1-1. Map of Massachusetts and Cape Cod bays. ..................................................... 2
Figure 2-1. Daily effluent flow in 1998 ............................................................................ 13
Figure 2-2. Solids loads, 1988-1998 ................................................................................. 14
Figure 2-3. Annual loads of PAHs.................................................................................... 14
Figure 2-4. Total nitrogen load, monthly mean fecal coliform concentration, monthly
average TSS concentrations, and monthly BOD ...................................................... 15
Figure 3-1. Water circulation in the Gulf of Maine .......................................................... 17
Figure 3-2. Water column sampling stations .................................................................... 21
Figure 3-3. Charles River discharge, 1990-1998 .............................................................. 22
Figure 3-4. Temperature and dissolved inorganic nitrogen profiles................................. 23
Figure 3-5. Chlorophyll profiles ....................................................................................... 24
Figure 3-6. Survey mean chlorophyll distribution, 1992-1999......................................... 25
Figure 3-7. Survey mean dissolved oxygen in nearfield bottom waters........................... 25
Figure 3-8. Rate of decline of dissolved oxygen concentrations in bottom waters in the
nearfield .................................................................................................................... 26
Figure 3-9. Phytoplankton variability in the nearfield...................................................... 27
Figure 3-10. Survey mean total phytoplankton abundance—inter-annual and regional
comparison................................................................................................................ 28
Figure 3-11. Zooplankton variability in the nearfield....................................................... 28
Figure 3-12. Survey mean total zooplankton abundance—inter-annual and regional
comparison................................................................................................................ 29
Figure 3-13. Whale sightings during 1998 ....................................................................... 30
Figure 3-14. Abundance of the nearshore zooplankton species, Acartia.......................... 31
Figure 4-1. Location of hard-bottom transects ................................................................. 35
Figure 4-2. Location of soft-bottom stations .................................................................... 36
Figure 4-3. Typical sediment profile image...................................................................... 38
Figure 4-4. Mean (± 95 % confidence intervals) numbers of individuals per sample for
those collected 1992 to 1998..................................................................................... 38
Figure 4-5. Mean (± 95 % confidence intervals) number of species per sample collected
from 1992 to 1998..................................................................................................... 39
Figure 4-6. Mean (± 95 % confidence intervals) diversity measured as log-series alpha for
samples collected from 1992 to 1998. ...................................................................... 39
Figure 4-7. Typical hard-bottom survey photograph........................................................ 41
Figure 5-1. Flounder sampling stations and mussel deployment sites. Lobsters are taken
from Deer Island Flats, eastern Cape Cod Bay, and the future outfall site............... 45
Figure 5-2. Concentrations of contaminants in flounder fillets and liver ......................... 46
Figure 5-3. Prevalence of centrotubular hydropic vacuolation (CHV)............................. 47
Figure 5-4. DDT in lobster from Deer Island Flats (DIF), the future outfall site, and
eastern Cape Cod Bay (ECCB)................................................................................. 48
Figure 5-5. Annual average concentrations of PCBs and mercury in lobster meat at the
future outfall site ....................................................................................................... 49
Figure 5-6. Average annual concentrations of PCBs and mercury in mussels at the future
outfall site.................................................................................................................. 50

1998 OUTFALL MONITORING OVERVIEW

VI

1998 OUTFALL MONITORING OVERVIEW VII
List of Tables 
Table 1-1. Roster of panel and committee members. ......................................................... 4
Table 1-2. Roster of task force members ............................................................................ 5
Table 1-3. Summary of the monitoring program ................................................................ 6
Table 1-4. Summary of contingency plan trigger parameters............................................. 7
Table 1-5. List of monitoring reports.................................................................................. 9
Table 2-1. Parameters meausured in effluent ................................................................... 11
Table 2-2. Threshold values for effluent monitoring........................................................ 17
Table 3-1. Shellfish monitoring stations........................................................................... 32
Table 3-2. Threshold values for water column monitoring .............................................. 32
Table 4-1. Threshold values for sea floor monitoring ...................................................... 42
Table 5-1. Threshold values for fish and shellfish monitoring......................................... 52

1998 OUTFALL MONITORING OVERVIEW 1
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 to the
harbor ended in 1991, and MWRA is working to minimize effects of
wastewater discharge. Those efforts include source reduction to
prevent pollutants from entering the waste stream, improved treatment
before discharge, and effective dilution once the effluent enters the
marine environment.
MWRA has undertaken projects to control flows of contaminants from
combined sewer overflows (CSO). An ongoing industrial
pretreatment/pollution prevention program has been implemented to
remove toxic contaminants before they reach the treatment facilities.
New operator training programs and process control and maintenance
tracking systems are in place.
During 1995, a new primary treatment plant at Deer Island was
brought on line, and disinfection facilities were completed. The first
battery of secondary treatment began in 1997. During 1998, the
second battery of secondary treatment was completed, and discharge
from the Nut Island Treatment Plant ended. Until then, approximately
100 million gallons per day of sewage from MWRA’s South System
received only primary treatment before being discharged into Quincy
Bay. Now, that sewage is diverted to Deer Island for secondary
treatment before being discharged into the harbor.
Future improvements include bringing a final battery of secondary
treatment on line and 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
from seven potential sites because it had a water depth and current
patterns that would promote effective dilution, it was least likely to
affect sensitive resources, and it was feasible to construct an outfall to
the location.
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 will be at the sea floor, at water

1998 OUTFALL MONITORING OVERVIEW 2 
depths of about 100 feet (MWRA 1997a). Initial dilution at the outfall
will be about 5 times that of the existing outfall, which is also
shallower, in 50 feet of water. The offshore location of the new outfall
ensures that within a tidal cycle, even shoreward currents will not
transport effluent to beaches or shellfish beds near Boston 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 of MWRA’s work, there is 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 caused some concerns. Those concerns
have been recognized by the joint permit for the outfall issued by the
U.S. Environmental Protection Agency (EPA) and the Massachusetts
Department of Environmental Protection (MADEP). 
Figure 1-1. Map of Massachusetts and Cape Cod Bays 
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

1998 OUTFALL MONITORING OVERVIEW 3
Outfall Permit 
The new outfall will be regulated by a permit issued by EPA and
MADEP under the National Pollutant Discharge Elimination System
(NPDES). The permit, issued in May of 1999, covers the treatment
plant operation and maintenance, sludge, and CSO system as well as
the outfall. It requires MWRA to expand and implement an ongoing
pollution prevention program that encompasses all users of the
system—industrial, commercial, and residential.
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 developed in response to the EPA
Supplemental Environmental Impact Statement (SEIS, EPA 1988).
The permit also requires MWRA to update, maintain, and run the
three-dimensional Bays Eutrophication Model, to track effluent
plumes for evaluation of the dilution at the discharge, and to
implement a contingency plan, which includes environmental quality
parameters and thresholds for corrective action.
The permit establishes an independent panel of scientists to review
monitoring data and provide advice on key scientific issues related to
the permit. This panel, called the Outfall Monitoring Science
Advisory Panel (OMSAP), is to conduct peer reviews of monitoring
reports, evaluate the data, and advise EPA and MADEP on
implications. OMSAP is also to provide advice concerning any
proposed modifications to the monitoring or contingency plans (Table
1-1).
OMSAP may form specialized focus groups when specific technical
issues require expanded depth or breadth of expertise. Two standing
sub-committees also advise OMSAP. The Public Interest Advisory
Committee (PIAC) represents local, non-governmental organizations,
academia, and environmental groups and advises OMSAP on values
and uses of the local natural systems as they relate to public concerns.
The Inter-agency Advisory Committee (IAAC) represents state and
federal agencies and provides OMSAP with advice concerning
environmental regulations.

1998 OUTFALL MONITORING OVERVIEW 4 
Table 1-1. Roster of panel and committee members 
OMSAP as of December 1998 
Robert Beardsley, Woods Hole Oceanographic Institution
Robert Chen, University of Massachusetts, Boston
Norbert Jaworski, retired
Robert Kenney, University of Rhode Island
Scott Nixon, University of Rhode Island
Judith Pederson, MIT Sea Grant
William Robinson, University of Massachusetts, Boston
James Shine, Harvard School of Public Health
Andrew Solow, Woods Hole Oceanographic Institution (chair)
Catherine Coniaris, New England Water Pollution Control Commission
(OMSAP assistant) 
IAAC as of December 1998 
MA Coastal Zone Management
Margaret Brady
Christian Krahforst (alternate)
MA Department of Environmental Protection
Russell Isaac
Steven Lipman (alternate)
MA Division of Marine Fisheries
Leigh Bridges
Jack Schwartz (alternate)
National Marine Fisheries Service
Salvatore Testaverde (chair)
David Dow (alternate)
Stellwagen Bank National Marine Sanctuary
Brad Barr
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 1998 
Association for the Preservation of Cape Cod
Scott Mitchell
Bays Legal Fund
Wayne Bergeron
The Boston Harbor Association
Vivian Li
Joan LeBlanc (alternate)
Cape Cod Commission
Patty Daley
Center for Coastal Studies
Peter Borrelli
Conservation Law Foundation
Anthony Chatwin
New England Aquarium
Marianne Farrington
Massachusetts Audubon Society
Robert Buchsbaum
MWRA Advisory Board
Joe Favaloro
Safer Waters in Massachusetts
Salvatore Genovese
Polly Bradley (alternate)
Save the Harbor/Save the Bay
Cate Doherty (chair)
Stop the Outfall Pipe
Mary Loebig
Wastewater Advisory Committee
Susan Redlich 
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. In anticipation of these requirements, MWRA
began baseline monitoring in 1991. During the intervening years, both
baseline and discharge monitoring plans have been developed and
refined. The existing plan was developed by MWRA with direction
from an Outfall Monitoring Task Force (OMTF) made up of scientists,
regulators, and environmental advocacy groups (Table 1-2; MWRA
1997a). The OMTF was disbanded upon creation of OMSAP.

1998 OUTFALL MONITORING OVERVIEW 5 
Table 1-2. Roster of task force members 
Outfall Monitoring Task Force as of August 1998 
Members of the scientific community
Robert Buchsbaum
Donald Cheney
John Farrington
Jonathan Garber
Diane Gould
Norbert Jaworski
Joseph Montoya
Judith Pederson
Jerry Schubel (chair)
MA Department of Environmental Protection
Russell Isaac
MA Division of Marine Fisheries
Leigh Bridges
Jack Schwarz (alternate)
MA Coastal Zone Management
Margaret Brady
Christian Krahforst (alternate)
National Marine Fisheries Service
Salvatore Testaverde
US Army Corps of Engineers
Thomas Fredette
US Environmental Protection Agency
Matthew Liebman
Janet Labonte (alternate)
David Tomey (alternate)
US Geological Survey
Richard Signell
Wastewater Advisory Committee
Susan Redlich
Save the Harbor/Save the Bay
Cate Doherty
Safer Waters in Massachusetts
Polly Bradley
Center for Coastal Studies
Russell DeConti
Cape Cod Commission
Patty Daley
Susan Nickerson (alternate) 
The outfall monitoring program focuses on critical constituents in
treatment plant effluent, such as nutrients, toxic contaminants, organic
material, pathogens, and solids. 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 (Table 1-3). Special studies 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 ecosystem (including
Boston Harbor) before (baseline) and after (discharge) the outfall
location is moved from the harbor to the bay.
Baseline monitoring, which began in 1991 for flounder studies and
1992 for other parameters, was initially planned to last for a minimum
of 3 years. Delays in outfall construction (originally planned for
completion in 1995) have allowed a relatively long period for baseline
studies. Thus, MWRA has been able to document greater natural
variability within the system than would have been observed in briefer
baseline monitoring. The extended time period 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
1995, Pawlowski 1996, Rex 1997).

1998 OUTFALL MONITORING OVERVIEW 6 
Table 1-3. Summary of the monitoring program. 
Task Objective Sampling Locations
And Schedule
Analyses
Effluent
Weekly Nutrients
Daily Organic material (cBOD)
Several times monthly Toxic contaminants
3x/day Bacterial indicators
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
To be implemented after the
outfall begins operation
Salinity
Temperature
Currents
Rhodamine dye
Bacterial Indicators
Nutrients
Metals
Solids
Mooring (USGS) Provides continuous
oceanographic data near
outfall location
Continuous monitoring
Single station
3 depths
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
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
5 locations
Tissue contaminant
concentrations
Physical abnormalities
Blue mussel Evaluate biological condition
and potential contaminant
bioaccumulation
1 survey/year
5 locations
Tissue contaminant
concentrations

1998 OUTFALL MONITORING OVERVIEW 7
Contingency Plan 
MWRA has developed a contingency plan (MWRA 1997b), which
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 what corrective actions should
be taken if the problem appears to be related to the discharge. The
contingency plan identifies threshold parameters (Table 1-4), which
are environmentally significant components of effluent or the
ecosystem that, if certain levels are exceeded, indicate a potential for
environmental risk. These levels are called thresholds. The plan
provides a process for evaluating parameters that exceed thresholds
and identifying appropriate responses. 
Table 1-4. Summary of contingency plan threshold parameters 
Monitoring
Area
Parameter
Fecal coliform bacteria
Residual chlorine
Total suspended solids
Biological oxygen demand
Toxicity
PCBs
Floatables
Permit violations
Effluent
Total nitrogen load
Dissolved oxygen concentration
Dissolved oxygen depletion rate
Chlorophyll
Nuisance and noxious algae
Zooplankton
Water Column
Effluent dilution
Benthic community structure
Sediment oxygen
Sea Floor
Sediment toxic metal and organic chemicals
PAHs, pesticides, mercury and PCBs in mussels
and flounder and lobster meat
Lead in mussels
PAHs in caged mussels
Fish and Shellfish
Liver disease in flounder 
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, parameters have
“caution” and “warning” thresholds. Exceeding caution levels would
indicate a need for increased attention or study. If MWRA discharges
cause a caution level to be exceeded, MWRA will expand its
monitoring to closely track any change in effluent quality and
environmental conditions, while working closely with OMSAP and the

1998 OUTFALL MONITORING OVERVIEW 8 
regulators to determine whether the data indicate an unacceptable
effect resulting from the outfall.
Exceeding warning levels would indicate a need for a response to
avoid potential adverse environmental effects. If a threshold is
exceeded at a warning level, the proposed response will include both
early notification to EPA and MADEP and, if the outfall has
contributed to the adverse environmental effects, the quick
development of a response plan. Response plans include a schedule
for implementing actions, such as additional monitoring, making
further adjustments in plant operations, or undertaking an engineering
feasibility study regarding specific potential corrective activities. 
Data Management and Reporting 
The outfall monitoring program has generated extensive data sets
documenting baseline environmental conditions. As of November
1999 the database included over three million measurements. Data
quality is maintained through program-wide quality assurance/quality
control procedures. After thorough 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 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 analyses, although they are retained in the database
and included in raw data reports. Any corrections are thoroughly
documented. Each data report notes any special data quality
considerations associated with the data set.
As discharge monitoring results become available, they will be
compared with contingency plan thresholds using computer programs
that calculate each threshold parameter value from the data, compare it
to the threshold, and notify the project staff of any caution or warning
threshold exceedances. Similar computer programs will compare
effluent results with contingency plan effluent thresholds.
MWRA’s NPDES permit requires extensive reporting on the
monitoring program, including synthesis reports for each technical
area of the project, regular reports on effluent quality, changes to the
monitoring program or contingency plan, and any exceedances of
contingency plan thresholds and actions taken to address them (Table
1-5). Data that exceed thresholds must be reported within 5 days after
the result becomes available, and MWRA must make all reasonable
efforts to report all data within 90 days of each sampling event.

1998 OUTFALL MONITORING OVERVIEW 9 
Selected reports are posted on MWRA’s web site
(www.mwra.state.ma.us), with hard copies placed in repository
libraries in Boston and on Cape Cod. The permit also requires an
annual report to Stellwagen Bank National Marine Sanctuary that
includes all monitoring data that relate to the sanctuary and documents
the effects of the discharge on sanctuary resources and qualities. 
Table 1-5. List of monitoring reports 
Report Description/Objectives
Outfall Monitoring Plan
Phase I—Baseline Studies (MWRA
1991)
Phase II—Discharge Monitoring
(MWRA 1997a)
Discusses goals, strategy, and design of
baseline and discharge monitoring programs.
Quarterly Wastewater Performance
Report
Summarize effluent quality, threshold
exceedences, and corrective actions
Contingency Plan (MWRA 1997b) Describes development of threshold
parameters and values and MWRA’s planned
contingency measures.
Program Area Synthesis Reports
(Annual)
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.
The State of Boston Harbor Reports Discuss a range of topics related to Boston
Harbor and recent harbor monitoring results.
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. The report provides a scientific summary of each
year of monitoring and includes information relevant to the
contingency plan, such as threshold exceedances, responses, and
corrective activities. If monitoring data have suggested that
monitoring activities, parameters, or thresholds should be added or
modified, the report is to summarize those recommendations.
This year’s report presents monitoring program results for baseline
field data collected through 1998. Because the outfall is not yet
operational, the report only compares data to the thresholds that are
based upon fixed values, such as water quality criteria and other
specific permit requirements. Baseline data, which are still being
collected, will be used to calculate some thresholds, e.g. , chlorophyll,
for which water quality standards or permit limits do not exist. This
report also discusses parameters for which thresholds will be
determined and finalized from a complete set of baseline data.

1998 OUTFALL MONITORING OVERVIEW 10
2. Effluent
Background
Effluent Treatment 
The MWRA strategy for improving the environmental quality of
Boston Harbor without degrading the Massachusetts and Cape Cod
bays region relies upon pollutant source reduction and effective
treatment. MWRA’s Toxic Reduction and Control Program sets and
enforces limits on what industries can discharge into the sewage
system. Secondary treatment at the Deer Island Treatment Plant is
designed to remove at least 85% of the total suspended solids and the
biological oxygen demand, 50-90% of the toxic contaminants, 10-15%
of the nutrients, and 80 to more than 99% of the pathogens (before
disinfection). Making sure that the source reduction and treatment are
working as designed is the most important step MWRA can take to
ensure that the new outfall does not cause any harm to the
environment. 
Environmental Concerns 
Effluent constituents of concern include nutrients, organic material,
toxic contaminants, human pathogens, solids, and “floatables” (Table
2-1). Floatables include oil and grease slicks, as well as plastic and
other debris, and are aesthetically unpleasant.
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 significantly reduced by secondary treatment.
Organic material 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.
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

1998 OUTFALL MONITORING OVERVIEW 11 
wastewater have dramatically declined since 1989, due to source
reduction and secondary treatment. Continued source control and
monitoring of contaminants in the effluent should ensure that
concentrations remain at low levels.
Pathogens, including bacteria, viruses, and protozoa from human and
animal waste, can cause disease. Human exposure to water-borne
pathogens can occur through consumption of contaminated shellfish or
through physical contact while swimming. MWRA is required to meet
water quality standards for bacteria.
Suspended solids, small particles of debris in the water column,
decrease water clarity, sometimes adversely affecting marine plants
and algae. Excess suspended solids detract from people’s aesthetic
perception of the environment, as do oil and grease slicks and floating
debris. 
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
Chlorine, Total Residual Grab 3/Day
PCB, Aroclors 24-hr Composite 1/Month
LC50 24-hr Composite 1/Month
C-NOEC 24-hr Composite 1/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 Recoverable Grab 1/Month
Copper, Total Recoverable 24-hr Composite 1/Month
Arsenic (Total) 24-hr Composite 1/Month
Hexachlorobenzene 24-hr Composite 1/Month
Aldrin 24-hr Composite 1/Month
Heptachlor Epoxide 24-hr Composite 1/Month
PCBs, Total 24-hr Composite 1/Month
Volatile Organic Compounds Grab 1/Month

1998 OUTFALL MONITORING OVERVIEW 12
Monitoring Design 
The main purpose of effluent monitoring is to measure the
concentrations and variability of chemical and biological constituents
of the effluent. Effluent monitoring assesses compliance with NPDES
permit limits, which are based upon state and federal water quality
standards and criteria, ambient conditions, and the outfall dilution.
The permit includes numeric limits for suspended solids, fecal
coliform bacteria, pH, chlorine, polychlorinated biphenyls (PCBs), and
biological oxygen demand (BOD). In addition, state water quality
standards establish limits for 158 pollutants, and the permit prohibits
any discharge that would cause or contribute to an exceedance of any
of those limits. Allowable concentrations of those contaminants are
based on the predicted dilution at the new outfall. Actual dilution will
be measured when outfall operation begins, and the allowable
concentrations will be altered if dilution is less than has been
predicted. 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 marine organisms
and establishes strict limits based on those tests. Effluent monitoring
also provides accurate mass loads of effluent constituents so that fate,
transport, and risk of contaminants can be assessed.
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 carbonaceous biological oxygen demand
(cBOD). Monitoring for toxic contaminants includes analyses for
heavy metals of concern, chlorinated pesticides, PCBs, volatile organic
compounds, acid-base neutral compounds, total residual chlorine, and
cyanide. Toxicity is tested using whole effluent samples. Tests for
acute toxicity of the effluent 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 larval growth and survival and sea urchin
( Arbacia punctulata ) 1-hour fertilization tests. Pathogen monitoring
consists of enumeration of fecal coliform. Total suspended solids
(TSS) and settleable solids are also measured. Methods for measuring
floatables are still under discussion.

1998 OUTFALL MONITORING OVERVIEW 13
Results 
A major milestone was achieved during 1998, when primary sewage
treatment at Nut Island ceased, and all sewage was directed to Deer
Island for secondary treatment. When the second of three batteries of
secondary treatment began operation in 1998, the treatment plant
operated at a level that complies with the 1999 NPDES permit for the
new outfall.
Daily effluent flow from the treatment plants during 1998 reflected the
weather patterns for the region, with a relatively stormy winter and
spring (Figure 2-1). Record rainfalls occurred throughout the spring,
and there was a major storm in June. 
Figure 2-1. Daily effluent flow in 1998 
The total solids load discharged into Boston Harbor was less than in
any previous year, reflecting the cessation of sludge discharge in 1991,
and the implementation of secondary treatment in 1997 and 1998, and
the transfer of Nut Island flow to Deer Island (Figure 2-2). Loads for
many contaminants, including PAHs (Figure 2-3), metals, pesticides,
and PCBs were lower in 1998 than in prior years. 
Daily flow in 1998
0
100
200
300
400
500
600
700
800
900
1000
Jan-98
Feb-98
Mar-98
Apr-98
May-98
Jun-98
Jul-98
Aug-98
Sep-98
Oct-98
Nov-98
Dec-98
Date
Flow (MGD)
Daily Flow

1998 OUTFALL MONITORING OVERVIEW 14 
Figure 2-2. Solids loads in 1988-1998
Figure 2-3. Annual loads of PAHs 
Although it effectively removes most contaminants, secondary
treatment yields little benefit for nutrient removal, and accordingly,
annual nitrogen loads have remained relatively constant throughout the
baseline-monitoring period. During 1994-1996, when primary treated
effluent was discharged, loading ranged from 10,800 metric tons/year
in 1992 to the 1996 high of 12,700 metric tons/year. After 1996,
improvements to the system resulted in declines in total nitrogen to
10,800 metric tons/year in 1998, a level about 12% lower than had
been predicted in the EPA SEIS (Figure 2-4). 
DITP Annual Loading - PAH 
0
2000
4000
6000
8000 
93 94 95 96 97 98 99
Total PAH (Kg/yr)

1998 OUTFALL MONITORING OVERVIEW 15 
Concentrations of solids, bacteria, total metals, PAHs, pesticides, and
PCBs all were lower in 1998 than they were for any prior year. There
were only 7 days in which the treatment plant did not meet daily
standards for bacterial counts, compared to 139 days in 1988, and all
weekly and monthly standards were met. These results reflect the
initiation and continued implementation of secondary treatment. (Note
that during 1997, the method of assessing organic material changed
from measuring both carbonaceous and nitrogenous biological oxygen
demand (BOD) to the more directed measuring of carbonaceous
biological oxygen demand (cBOD). The 1999 permit level is for
cBOD.) 
Figure 2-4. Total nitrogen load, total days per year exceeding bacteria indicator levels,
monthly average TSS concentrations, and monthly BOD 
. 
Monthly Average TSS, Deer Island, 1994-1998
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
Year
TSS (mg/L)
TSS
TSS Limit 1999 Permit
1994 1995 1996 1997 1998
Monthly BOD, Deer Island 1994-1998
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
Year
BOD (Monthly Average in mg/L) BOD
cBOD
cBOD Limit 1999 Permit
1994 1995 1996 1997 1998
Total Nitrogen Discharged by MWRA
0
2000
4000
6000
8000
10000
12000
14000
16000
1990 1991 1992 1993 1994 1995 1996 1997 1998
Year 
Nitrogen ( mtons/yr) 
Total Nitrogen
Warning
Caution
Total Days per Year Bacterial Indicator Levels
Above Treatment Limits
0
10
20
30
40
50
60
70
80
90
100
1 2 3 4 5 6 7 8 9 10 11
YEAR
Days per year above limit Days >10,000
Days >201 and <10,000
1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998

1998 OUTFALL MONITORING OVERVIEW 16
Contingency Plan Thresholds 
Although the 1999 permit was not in effect in 1998, the treatment
plant essentially operated in compliance with the limits that the permit
set. Few results in 1998 were higher than the limits of contingency
plan thresholds that will be in effect when the outfall begins operation.
These measurements may have resulted from operational upsets
during start-up of secondary treatment or the transfer of effluent from
Nut Island to Deer Island. Contingency plan trigger parameters are
shown in Table 2-2. During 1998, fecal coliform monthly average
concentrations ranged from 5-11 colonies/100 ml, well below the
future threshold. Biological oxygen demand, measured as BOD5,
ranged from 23.1-94.5 mg/L. (Because the permit did not exist, the
few measurements that exceeded thresholds were not flagged.)
MWRA anticipates continued improvements as the final battery of
secondary treatment becomes available and secondary treatment
continues to be optimized. 
Table 2-2. Threshold values for effluent monitoring 
Parameter Caution Level Warning Level 1998 Results
Fecal coliform bacteria* 14,000 fecal coliforms/100
ml (monthly 90 th percentile,
weekly mean, and daily
minimum—minimum of 3
consecutive samples)
Never exceeded
Chlorine, residual 631 ug/L daily,
456 ug/L monthly
Not applicable
Total suspended solids 45 mg/L weekly
30 mg/L monthly
Not applicable**
cBOD 40 mg/L weekly,
25 mg/L monthly
Not applicable
Toxicity Acute: effluent LC50<50%
for shrimp and fish
Chronic: effluent NOEC for
fish survival and growth and
sea urchin fertilization <1.5%
effluent
Not applicable
PCBs Aroclor=0.045 ng/L Never exceeded
Floatables 5 gal/day Not measured
Permit violations 5 violations/year >5% of the time Not applicable
Total nitrogen load 12,500 mtons/year 14,000 mtons/year Not exceeded
* Existing standard is 200 col/100 ml; threshold is based on a 70-fold dilution at the new outfall.
**During 1998, the treatment plant essentially operated in compliance with the not-yet-issued 1999
permit.

1998 OUTFALL MONITORING OVERVIEW 17
3. Water Column
Background
Circulation and Water Characteristics 
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, from Beardsley 
et al. 1997). A general southeast coastal current flows southwestward
into the bays by Cape Ann and 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 the bays. 
Figure 3-1. Water circulation in the Gulf of Maine

1998 OUTFALL MONITORING OVERVIEW 18 
Waters in Massachusetts and Cape Cod bays have been thought to
follow a typical annual cycle, although wind and other factors greatly
influence the pattern. During November through April, waters are
well mixed and nutrient levels are high. As light levels increase in the
early spring, phytoplankton usually begin a period of rapid growth
known as a bloom. If it occurs, the spring bloom begins in the
shallowest waters of Cape Cod Bay. Blooms in deeper waters follow
in 2-3 weeks. While phytoplankton provide year-round food for
zooplankton, spring blooms are typically followed by an increase in
zooplankton abundance. Zooplankton are prey for many marine
animals, including right whales.
Later in the spring, the surface waters warm and stratify (see Figures
3-4 and 3-5). Stratification effectively separates the surface and
bottom waters, preventing replenishment of nutrients to the surface
waters and replenishment of oxygen to the bottom waters. The
surface-water phytoplankton deplete the available nutrients and
undergo senescence, sinking to the bottom. Bacteria use up oxygen as
they decompose the phytoplankton, and oxygen levels are typically
lowest from August through October in the bottom waters. In surface
waters, dissolved oxygen concentrations remain high throughout the
year.
In the fall, cooling surface waters and strong winds allow mixing of
the water column. Nutrients brought to the surface can stimulate a fall
phytoplankton bloom. Fall blooms usually end in early winter with
declining light levels. 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. Year-to-year variability
in bottom temperature and dissolved oxygen concentrations are largely
related to wind patterns. If winds are persistent southerly during the
summer, this condition promotes upwelling, which leads to colder
bottom temperatures and higher dissolved oxygen concentrations.
Weaker southerly winds result in less upwelling, with consequently
warmer bottom temperatures and lower dissolved oxygen
concentrations.

1998 OUTFALL MONITORING OVERVIEW 19
Environmental Concerns 
Water column monitoring focuses upon concerns that relocation of the
outfall will introduce effects from the 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, changes in the nutrient balance in Massachusetts and
Cape Cod bays are thought to have the most potential for affecting the
health of marine life in the water column of the bays.
Excess nutrients, particularly nitrogen, could promote algal blooms
followed by low dissolved oxygen levels when the phytoplankton die,
sink, and decompose. Changes in the relative levels of nutrients could
stimulate undesirable algae to become present or dominant among the
useful algae in the system. Two types of undesirable algae are of
concern: nuisance species, such as brown tides, which affect the
appearance of the water, and noxious species, such as some red tides,
which, if sufficiently concentrated, can be toxic to marine mammals,
fish, and humans. Undesirable algae can also affect the species
composition of the plankton community.
Excess organic material from the wastewater effluent is another
concern. Decomposition of organic material consumes the oxygen
necessary for survival of marine life. Because of the concern that low
dissolved oxygen levels 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 periods of low oxygen
in bottom waters near the outfall are inversely correlated with
temperature. Understanding physical conditions in the region will be
important in interpreting monitoring data when the outfall begins to
operate. (A discussion of the monitoring of the health of the benthic
community, also potentially affected by excess organic material, is
included in Section 4.)
The toxic contaminants discharged in the MWRA effluent are
projected to be at extremely low concentrations. Effluent dilution will
be studied when the outfall begins operation, but monitoring for
effects of toxic contaminants will be focused upon the sediments and
fish and shellfish rather than on the water column.

1998 OUTFALL MONITORING OVERVIEW 20
Monitoring Design 
Water column monitoring includes assessments of water quality and
plankton in Massachusetts and Cape Cod bays. It includes five major
components: nearfield surveys, farfield surveys, plume-tracking
surveys after the outfall is operational, continuous recording, and
remote sensing.
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 effluent may be detected. Farfield
surveys assess differences across the bays and seasonal changes over a
large area. In 1998, 17 nearfield and 6 farfield surveys were
conducted. Samples were taken from 48 stations in Boston Harbor,
Massachusetts Bay, and Cape Cod Bay (Figure 3-2). Five stations at
the boundary of the monitoring area were in or near the Stellwagen
Bank National Marine Sanctuary.
Parameters measured in water column monitoring include dissolved
inorganic and organic nutrients, particulate forms of nutrients,
chlorophyll, total suspended solids, dissolved oxygen, phytoplankton
abundance and species composition, zooplankton abundance and
species composition, respiration, and productivity. Nutrient
measurements include the major forms of nitrogen, phosphorus, and
silica.
Once the outfall becomes operational, plume-tracking surveys will
determine the location, migration, and biological and chemical
characteristics of the effluent plume leaving the outfall and mixing
with the ambient waters. The continuous recording component of the
program captures temporal variations in water quality between
nearfield water surveys. Remote sensing captures spatial variations in
water quality on a regional scale.
Certified whale watchers monitor marine mammals on all nearfield
surveys and farfield water column surveys conducted between
February and April. Besides providing monitoring data, presence of
trained marine mammal observers addresses a request by the National
Marine Fisheries Service.

1998 OUTFALL MONITORING OVERVIEW 21 
Figure 3-2. Water column sampling stations

1998 OUTFALL MONITORING OVERVIEW 22
Results
Physical Conditions 
During 1998, the Massachusetts and Cape Cod bays region was
influenced, as was much of the country, by weather patterns associated
with the El Niño event in the equatorial Pacific. The winter of 1997-
1998 was relatively warm. Winter and spring were disrupted by many
storms and record rainfalls. This unusual rainfall pattern was reflected
in flow measurements in the Charles River, which were unusually high
in the spring of 1998 (Figure 3-3). There was also a major storm in
June.
These conditions resulted in warm water temperatures in the early
spring and a slight delay in the onset of stratification. Due to the high
river flow during late winter through mid-spring, surface salinity was
lower in western Massachusetts Bay than in any year since the
beginning of the monitoring program. The unusually low salinity in
surface waters gave rise to strong stratification during the summer.
The fall overturn and return to winter conditions were also delayed.
The water column remained stratified until November in much of the
nearfield, and a deep halocline was still present in December at the
deeper eastern nearfield stations. 
Figure 3-3. Charles River discharge 1990-1998 
Over the year, average winds were favorable to upwelling. Through
June of 1998, however, winds favored downwelling and strong
throughflow from the Gulf of Maine to Massachusetts Bay. Relatively
strong southerly winds, causing upwelling, occurred during the
summer. Weak downwelling conditions were present during the final
months of the year. 
Water Quality 
No spring phytoplankton bloom was observed in Massachusetts Bay
for 1998, and elevated nutrient concentrations persisted in the surface

1998 OUTFALL MONITORING OVERVIEW 23 
waters until May (Libby et al. 1999). An early decrease in nutrient
concentrations during February indicated that a bloom may have
begun, but it never developed fully. In Cape Cod Bay, a bloom may
have occurred prior to the first survey, which took place in February. 
Figure 3-4. Temperature and dissolved inorganic nitrogen profiles. The
entrance to Boston Harbor is to the left, and the eastern boundary of
Massachusetts Bay is to the right. 
0 10 20 30 40 50
Distance (km)
-100
-80
-60
-40
-20
0
Depth (m)
F23 F24 N20N21N16 F19 F27
3 5 7 9 11 13 15 21
Parameter: Temperature
Last Survey Day: 8/25/98
Sampling Event: WF98B
Boston-Nearfield Transect
Contour Interval =2 C
0 10 20 30 40 50
Distance (km)
-100
-80
-60
-40
-20
0
Depth (m)
F23 F24 N20N21N16 F19 F27
3 5 7 9 11 13 15 19
Parameter: Temperature
Last Survey Day: 2/27/98
Sampling Event: WF982
Boston-Nearfield Transect
Contour Interval =2 C
0 10 20 30 40 50
Distance (km)
-100
-80
-60
-40
-20
0
Depth (m)
F23 F24 N20N21N16 F19 F27
1 3 5 7 9 11 13 19
Parameter: No3+no2+nh4
Last Survey Day: 2/27/98
Sampling Event: WF982
Boston-Nearfield Transect
Contour Interval =2 μM
0 10 20 30 40 50
Distance (km)
-100
-80
-60
-40
-20
0
Depth (m)
F23 F24 N20N21N16 F19 F27
1 3 5 7 9 11 13 26
Parameter: No3+no2+nh4
Last Survey Day: 8/18/98
Sampling Event: WF98B
Boston-Nearfield Transect
Contour Interval =2 μM
Temperature ( ° C)
Temperature ( ° C)
DIN ( μ m)
DIN ( μ m)

1998 OUTFALL MONITORING OVERVIEW 24 
Figure 3-5. Chlorophyll profiles 
Generally, conditions were appropriate for development of a bloom
(Figures 3-4, 3-5). Elevated nutrient levels, increasing light
availability, increasing temperatures, and the onset of seasonal
stratification were appropriate. Other factors that may have influenced
phytoplankton populations include zooplankton grazing, the makeup
of the resident phytoplankton assemblage, and physical, chemical, or
biological forces. Possibly, the mild weather allowed relatively large
zooplankton populations to persist through the winter, and these
populations may have grazed phytoplankton at a rate that precluded
expression of the bloom.
The years of baseline monitoring suggest that spring blooms, generally
thought to be characteristic for coastal waters, may not be typical for
Massachusetts Bay. Large blooms that occurred in 1992 and 1997
were dominated by the nuisance species Phaeocystis pouchetii (Figure
3-6). Phaeocystis pouchetii can occur at any time during the year, but
was not present in 1998.
A fall bloom was observed in 1998, as in most previous years. The
1998 bloom developed from a general increase in the numbers of a
variety of chain-forming diatoms. The bloom was more clearly
observed in increased concentrations of chlorophyll and peak
production rates than in phytoplankton abundance. Unusually, this
bloom persisted through the winter of 1998-1999. 
0 10 20 30 40 50
Distance (km)
-100
-80
-60
-40
-20
0
Depth (m)
F23 F24 N20N21N16 F19 F27
1 3 5 7 9 11 13 17
Parameter: Fluorescence
Last Survey Day: 2/27/98
Sampling Event: WF982
Boston-Nearfield Transect
Contour Interval =2 μg/L
0 10 20 30 40 50
Distance (km)
-100
-80
-60
-40
-20
0
Depth (m)
F23 F24 N20N21N16 F19 F27
1 3 5 7 9 11 13 20
Parameter: Fluorescence
Last Survey Day: 8/18/98
Sampling Event: WF98B
Boston-Nearfield Transect
Contour Interval =2 μg/L

1998 OUTFALL MONITORING OVERVIEW 25 
Figure 3-6. Survey mean chlorophyll distribution, 1992-1999 
Major storm events and the lack of input of organic matter from a
spring bloom resulted in relatively high concentrations of dissolved
oxygen in June. Later, the persistent stratified conditions in 1998 led
to decreases in bottom dissolved oxygen concentrations from June
through December in the nearfield. The pulse of organic matter from
the fall bloom further depressed dissolved oxygen levels to minimum
concentrations in December (Figure 3-7). Rates of DO decline in 1998
were comparable to previous years (Figure 3-8). Because the early
summer levels had been high, minimum dissolved oxygen
concentrations were not low in comparison to prior years despite the
extended period of stratification. 
Figure 3-7. Survey mean dissolved oxygen in nearfield bottom waters 
5
6
7
8
9
10
11
12
13
1992 1993 1994 1995 1996 1997 1998 1999 2000
DO (mg/L) 
0 .0
1 .0
2 .0
3 .0
4 .0
5 .0
6 .0
7 .0
8 .0
9 .0
1 0 .0
1 9 9 2 1 9 9 3 1 9 9 4 1 9 9 5 1 9 9 6 1 9 9 7 1 9 9 8 1 9 9 9 2 0 0 0
C h lo ro p h y ll ( g /L ) 
Phaeocystis 
bloom Phaeocystis 
bloom

1998 OUTFALL MONITORING OVERVIEW 26 
Figure 3-8. Rate of decline of dissolved oxygen concentrations in bottom waters in the
nearfield 
Year Slope
(mg/L/day)
Intercept*
(mg/L)
R 2
1992 -0.024 11.0 0.808
1993 -0.025 11.1 0.885
1994 -0.031 10.1 0.929
1995 -0.027 9.9 0.932
1996 -0.025 10.3 0.978
1997 -0.020 9.8 0.632
1998 -0.032 11.5 0.938
*Predicted DO on June 1 based on:
DO = Slope * Date + Intercept 
5
6
7
8
9
10
11
12
Jun Jul Aug Sep Oct Nov
Dissolved Oxygen (mg/L)
1992
1993
1994
1995
1996
1997
1998 
1992 1993
1995
1994
1996
1997 
1998

1998 OUTFALL MONITORING OVERVIEW 27
Phytoplankton Communities 
Species composition was generally similar to previous years (Libby et
al. 1999). The size and seasonal pattern of phytoplankton abundance
fell within the range of previous years. This pattern applied for the
nearfield (Figure 3-9) and also for the boundary, Boston Harbor, Cape
Cod Bay, and coastal regions (Figure 3-10). However, because the
seasonal patterns are so variable, no one year of baseline monitoring
has exactly replicated another. Overall, diatoms and microflagellates
are numerically most abundant. Diatoms dominate the communities in
biomass. As in previous years, winter was dominated by diatoms
throughout the region. During March through May, diatoms continued
to be abundant, along with the dinoflagellate Heterocapsa rotundatum .
Cryptomonads were also present, particularly at nearshore stations.
Microflagellates reached their peak abundance during the summer. A
subdominant increase in pennate diatoms occurred in Boston Harbor
and nearby coastal areas during late August. Localized blooms of
diatoms occurred throughout the fall in the nearfield, while
microflagellates continued to dominate in Cape Cod Bay. 
Figure 3-9. Phytoplankton variability in the nearfield (survey mean,
minimum, and maximum) 
Total Phytoplankton Abundance - Nearfield
0
2
4
6
8
10
12
14
J M S J M S J M S J M S J M S J M S J M S J M S J
10 6 Cells/L
1992 1993 1994 1995 1996 1997 1998 1999

1998 OUTFALL MONITORING OVERVIEW 28 
Figure 3-10. Survey mean total phytoplankton abundance—inter-annual and
regional comparison 
(“Boundary” represents one station at the north of Massachusetts Bay.) 
Zooplankton Communities 
Total zooplankton abundance at nearfield stations generally increased
from February through April, reached a peak in May, and remained
moderately high through December (Figures 3-11, 3-12). Farfield
stations followed a similar pattern, but data were quite variable. 
Figure 3-11. Zooplankton variability in the nearfield 
Total Phytoplankton Abundance - Area Mean
0
2
4
6
8
10
12
J M S J M S J M S J M S J M S J M S J M S J M S J
10 6 Cells/L
Boundary Nearfield Harbor Cape Cod Bay Coastal
1992 1993 1994 1995 1996 1997 1998 1999
Total Zooplankton Abundance - Nearfield
0
100,000
200,000
300,000
400,000
500,000
600,000
J M S J M S J M S J M S J M S J M S J M S J M S J
Individuals/m 3
1992 1993 1994 1995 1996 1997 1998 1999

1998 OUTFALL MONITORING OVERVIEW 29 
Figure 3-12.Survey mean total zooplankton abundance—inter-annual and
regional comparison 
(“Boundary” represents one station at the north of Massachusetts Bay.) 
The zooplankton community was dominated by copepod nauplii,
copepodites, and adults of the small species Oithona similis and 
Pseudocalanus spp., with seasonal occurrences of gastropod and
bivalve veligers and other species. Overall, meroplankton are a
relatively minor component of the community. As in other years, the
zooplankton community in the nearfield was similar to that observed
in Cape Cod Bay. The Massachusetts Bay communities are typical
North Atlantic coastal assemblages, similar to those found in the
broader region, including the Gulf of Maine and Buzzards Bay (Libby 
et al. 1999). 
Marine Mammal Observations 
Marine mammal observers were present on 21 of 37 MWRA surveys
conducted during 1998, including all nearfield surveys, 3 farfield
surveys, and 2 fecal coliform surveys (Figure 3-13; McLeod 1999).
(As part of an agreement with the Massachusetts Division of Marine
Fisheries, MWRA conducts monthly monitoring for fecal coliform
bacteria in the outfall area.) Sightings included 23 individual whales,
five groups of whales, and more than 32 Atlantic white-sided dolphins.
Species observed included right, humpback, and minke whales. Whale
sightings were distributed throughout the bays. Eight of the sightings
occurred within the boundaries of the Stellwagen Bank National
Marine Sanctuary, and six whales were seen in the nearfield. 
Total Zooplankton Abundance - Area Mean
0
50,000
100,000
150,000
200,000
250,000
300,000
J M S J M S J M S J M S J M S J M S J M S J M S J
Individuals/m 3
Boundary Nearfield Harbor Cape Cod Bay Coastal
1992 1993 1994 1995 1996 1997 1998 1999

1998 OUTFALL MONITORING OVERVIEW 30 
Figure 3-13. Whale sightings during 1998 
Contingency Plan Thresholds 
Threshold parameters for water column monitoring include minimum
dissolved oxygen concentration in nearfield and Stellwagen Basin
bottom waters, dissolved oxygen depletion rate in nearfield bottom
waters, chlorophyll level, nuisance algae, zooplankton species in the
nearfield, paralytic shellfish toxin extent, and dilution (Table 3-2).
During 1998, dissolved oxygen concentrations never dropped below
caution or warning levels. During 1992-1998, mean dissolved oxygen
concentrations ranged from 6.15 to 11.2 mg O2/L. Concentrations
were lower than the caution level twice during October 1994.
Chlorophyll thresholds will be calculated from a complete set of
baseline data. Through 1998, the annual mean chlorophyll level has
ranged from 1.06 ug/L in 1997 to 2.28 ug/L in 1993. Phytoplankton

1998 OUTFALL MONITORING OVERVIEW 31 
community thresholds will focus on nuisance species and upon a
spread of paralytic shellfish toxin into areas where it has not been
detected (Table 3-1). Alexandrium tamarense , Phaeocystis pouchetii ,
and Pseudo-nitzchia multiseries have been extremely rare during the
baseline-monitoring period. Currently, a caution level for zooplankton
has been established as a shift towards the type of community,
dominated by the copepod Acartia, currently seen nearshore, near
Boston Harbor (Figure 3-14). This threshold remains under
discussion. Initial dilution will be measured through a dye study when
discharge begins, and a warning level would be exceeded if dilution is
less than was predicted by EPA as a basis for the permit. 
Figure 3-14. Survey mean abundance of the nearshore zooplankton species,
Acartia 
Acartia Abundance - Area Mean
0
5,000
10,000
15,000
20,000
25,000
30,000
35,000
40,000
45,000
J M S J M S J M S J M S J M S J M S J M S J M S J
Individuals/m 3
Boundary Nearfield Harbor Cape Cod Bay Coastal
1992 1993 1994 1995 1996 1997 1998 1999

1998 OUTFALL MONITORING OVERVIEW 32 
Table 3-1. Massachusetts DMF shellfish PSP monitoring stations 
Primary Stations Secondary Stations
Gloucester—Annisquam Yacht Club Rockport—Granite Street
Hull—Point Allerton Cohasset—Border Street
Cohasset—Little Harbor Scituate/Marshfield—South River, Humarock
Scituate—Scituate Harbor Marshfield—Green Harbor
Marshfield—Damon’s Point Duxbury—Eaglenest Creek
Plymouth—Manomet Point Plymouth—Plymouth Harbor
Sandwich—Cape Cod Canal Plymouth—Elisville Harbor
Dennis—Sesuit Harbor Sandwich—Sandwich Harbor
Barnstable—Marispan Creek
Provincetown—The Dike 
Table 3-2. Threshold values for water column monitoring 
Location Parameter Caution Level Warning Level 1998
Results
Bottom water
(nearfield and
Stellwagen Basin)
Dissolved oxygen
concentration
Monthly mean <6.5
mg/L (June-October)
Monthly mean <6.0
mg/L
(June-October)
Never below
threshold
Bottom water
(nearfield)
DO depletion rate 1.5x baseline
(June-October)
2x baseline (June-
October)
Not applicable,
baseline
monitoring
Nearfield Chlorophyll level Annual mean >1.5x
baseline
Annual mean >2x
baseline
Not applicable,
baseline
monitoring
Nearfield Chlorophyll level 95 th percentile of the
baseline seasonal
mean
Not applicable,
baseline
monitoring
Nearfield Nuisance algae
abundance
Appreciable change
in seasonal mean
concentration of 
Alexandrium
tamarense or 
Phaeocystis
pouchetii . Also 
Pseudo-nitzchia
multiseries >
500,000 cells/L
Not applicable,
baseline
monitoring
Nearfield Zooplankton
abundance
Shift toward inshore
community
Threshold
under
discussion
Farfield PSP toxin extent New incidence None
measured
Plume Initial dilution Effluent dilution less
than predicted by EPA
as basis for NPDES
permit
Not applicable

1998 OUTFALL MONITORING OVERVIEW 33
4. Sea Floor
Background
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 basins, 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 m high, with crests covered by gravel and
boulders. Cape Cod Bay, Stellwagen Basin, and Boston Harbor
represent long-term sinks for fine-grained sediments (USGS 1997,
1998).
Sediment transport in the system occurs primarily during storms.
Typically, strong storms with winds from the northeast resuspend
sediments, which are transported by counter-clockwise currents from
western Massachusetts Bay to the offshore and toward Cape Cod Bay,
where they are likely to remain. Cape Cod Bay is 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 
While studies of Boston Harbor sediments are documenting its
recovery following the cessation of sludge discharge, improvements in
CSOs, and improved sewage effluent treatment, there are concerns
about potential effects of the relocated outfall on the sea floor. There
are three specific concerns: eutrophication and related low dissolved
oxygen levels, accumulation of toxic contaminants in depositional
areas, and smothering of animals by particulate matter. If transfer of
the nutrient loads to the offshore site were to cause eutrophication,
depressed levels of dissolved oxygen could profoundly affect bottom
communities. 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 of Cape Cod Bay and

1998 OUTFALL MONITORING OVERVIEW 34 
Stellwagen Basin. Similarly, concentrations of particulate matter are
expected to be low, but there remains some concern that bottom
communities could be smothered. The most likely adverse effect of the
outfall would be a disruption of normal benthic community structure
by increasing the amount of food available to the bottom. 
Monitoring Design 
Sea floor monitoring includes several components: measurements of
contaminants in sediments, sediment-profile imaging to provide a
rapid assessment of potential effects, studies of nearfield and farfield
soft-bottom communities, and study of hard-bottom communities. For
farfield stations located within Stellwagen Bank National Marine
Sanctuary, MWRA has obtained a permit from the sanctuary to collect
sediments. USGS has also conducted long-term studies of sediment
transport and contaminant levels in Boston Harbor and Massachusetts
and Cape Cod bays. These projects continue to be active.
Sediment contaminant studies were included in 1998 after a two-year
hiatus. During 1996, the OMTF determined that the baseline for
routine annual sediment contaminant measurements was adequate, so
no sampling occurred in 1996 or 1997. During 1997, an OMTF focus
group asked MWRA to institute a targeted study to examine possible
short-term effects of the new outfall. This study includes four stations
selected for specific parameters: 
• They include a high percentage of fine-grained material, with those
high percentages remaining stable over the monitoring period. 
• They have high concentrations of total organic carbon (TOC). 
• They are located in the zone of effluent particle deposition
predicted by the Bays Eutrophication Model. 
• They expand the areas sampled three times per year by USGS.
After the outfall begins operation, these stations will be sampled three
times per year. A pilot study of the stations was conducted during
October 1998. Samples were 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 3 farfield 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 of the oxidation-reduction potential

1998 OUTFALL MONITORING OVERVIEW 35 
discontinuity (RPD), the depth at which sediments change from being
oxic to anoxic. Quick Look was used for the first time in 1998 and
yielded results that were comparable to more detailed, computer-based
methods. Later, complete analyses of the films provide information on
sediment grain size, sediment layering, fauna and structures, general
benthic successional stage, prism penetration, surface relief, and
apparent color RPD depth.
Nearfield and farfield soft-bottom surveys are also conducted in
August. Sampling of 20 nearfield stations is designed to provide
spatial coverage and local detail about the fauna in depositional
environments within 8 km of the diffusers (see Figure 4-2). Farfield
sampling of 11 stations in Massachusetts and Cape Cod bays will
contribute reference data on soft-bottom habitats. Samples are
analyzed for community parameters, Clostridium perfringens spores,
sediment grain size, and TOC content.
While most studies of benthic communities, including the MWRA
program, focus upon the soft bottom, areas with finer-grained
sediments, such depositional habitats are relatively rare 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 4-1).
Video and still photographs are taken at waypoints along 6 transects
and at Diffuser #44 of the new outfall. These surveys are conducted in
June. Photographs are examined for substrate type, amount of
sediment drape, and biota. 
Figure 4-1. Location of hard-bottom transects 
!
! !
! !
!
!
! !
!
!
!
!
!
!
!
!
!
!
!
!
!
! 
T1-1
T1-2 T1-3
T1-4
T2-1
T2-2
T2-3 T2-4
T2-5
T4-1
T4-3
T6-1
T6-2
T7-1
T7-2
T8-1
T8-2
T9-1
T10-1
T4/T6-4
Diffuser # 44-C
T1-5
T4-2 
25
35
20
25
30
25
30
30
30
30
35
30
25
35
25
25
30
35
30
25
25
25
30 35
25
30
25
25
25
30
30 25
30
30
30
25
25
30
30 30
30
5
25
25
40
25
25
35
20
5 42°21'30"
42°21'30"
42°22'00"
42°22'00"
42°22'30"
42°22'30"
42°23'00"
42°23'00"
42°23'30"
42°23'30"
42°24'00"
42°24'00"
42°24'30"
42°24'30"
70°49'00"
70°49'00"
70°48'30"
70°48'30"
70°48'00"
70°48'00"
70°47'30"
70°47'30"
70°47'00"
70°47'00"
70°46'30"
70°46'30" 70°46'00"
Depth (meters):
Outfall Diffuser 
! T6-1 Hardbottom Station Locations
LEGEND
N 0 500 1000 1500 Meters
15
20
25
30
35
40 
Massachusetts Bay 
STUDY AREA

1998 OUTFALL MONITORING OVERVIEW 36 
Figure 4-2. Location of soft-bottom stations 
"
"
"
"
"
"
"
"
"
"
" 
FF01
FF04
FF05
FF06
FF07
FF09
FF10
FF11
FF12
FF13
FF14 
4 2 ° 0 0 ' 4 2 ° 0 0 '
4 2 ° 1 5 ' 4 2 ° 1 5 '
4 2 ° 3 0 ' 4 2 ° 3 0 '
7 1°00 '
7 1°00 '
7 0°45 '
7 0°45 '
7 0°3 0 '
7 0°3 0 '
7 0°1 5 '
7 0°1 5 ' 
N
LEGEND
Stellwagen Bank
National Marine Sanctuary
Outfall Diffuser
F01 SamplingLocation Name
0 5 10 15 Kilom eters 
#
#
#
#
# #
#
# #
#
#
#
#
#
#
#
#
#
#
# 
π
π
π 
FF10
FF12
FF13
NF02
NF04
NF05
NF07
NF08 NF09
NF10
NF12 NF13
NF14
NF15
NF16
NF17
NF18
NF19
NF20
NF21
NF22
NF23
NF24
0 1 2 3 Kilometers
NF02 Sampling Location Name
Depth (meters):
LEGEND
N π Farfield 
# Nearfield
15
20
25
30
35
40
Outfall Diffuser
42°18'
42°18'
42°19'
42°19'
42°20'
42°20'
42°21'
42°21'
42°22'
42°22'
42°23'
42°23'
42°24'
42°24'
42°25'
42°25'
42°26'
42°26'
42°27'
42°27'
70°57'
70°57'
70°56'
70°56'
70°55'
70°55'
70°54'
70°54'
70°53'
70°53'
70°52'
70°52'
70°51'
70°51'
70°50'
70°50'
70°49'
70°49'
70°48'
70°48'
70°47'
70°47'

1998 OUTFALL MONITORING OVERVIEW 37
Results
Sediment Contaminants 
As found in USGS studies and previous baseline monitoring,
concentrations of organic and inorganic contaminants in sediments
near the new outfall were low (Kropp et al. 1999). Levels of
contaminants were well below established EPA and NOAA guidelines.
Concentrations of chlorinated pesticides and PCBs were extremely
low, averaging less than 10 ng/g. Although consistently low,
variability in the concentrations of organic contaminants was found
within and among the four stations. Higher concentrations were found
in samples with fine sediments and high concentrations of TOC.
Concentrations of metals were also extremely low, less than 10 times
the method detection limits, and generally less variable than the
organic compounds. 
Sediment Profile Imaging 
Sediment profile imaging surveys were conducted in 1992, 1995,
1997, and 1998 (Figure 4-3). Throughout that time, the sediments
were consistent, with very fine sand to silty-fine sand as the dominant
sediment type (Kropp et al. 1999). Assessment of the apparent color
RPD through time has been complicated by shallow penetration of the
prism. At many stations, one or more replicate image has not
penetrated deeply enough to see the RPD layer. Allowing for that
difficulty, it appears that the RPD layer depth became shallower
between 1992-1995 and 1997-1998. Pioneering or “Stage I”
communities prevailed in the nearfield during 1992 to 1997, whereas
Stage II fauna were more common in 1998. The occurrence of Stage
III fauna, those animals representing the highest successional stage,
also increased in 1998, although these advanced successional
communities did not lead to a deepening of the RPD. The monitoring
data reflect the physically dynamic processes that dominate the
nearfield. Data from 1998 may indicate a recent increase in the
importance of biological processes in structuring the sediment
environment.

1998 OUTFALL MONITORING OVERVIEW 38 
Figure 4-3. Typical sediment profile image 
Soft-bottom Communities 
During the course of baseline monitoring, samples from the bays have
routinely had twice as many species as those from Boston Harbor.
Total infaunal abundance and numbers of species have varied (Figures
4-4 to 4-5; Kropp et al. 1999). Two distinct patterns have been noted
in comparing data from nearfield and farfield stations. At farfield
stations, mean total species and log-series alpha, a measure of species
diversity, remained roughly stable from 1992 through 1995, then
increased substantially in 1996 and 1997. In contrast, the average
number of species at nearfield stations decreased about 33% from
1992 to 1993. Numbers of species subsequently rose until they leveled
off in 1997 and 1998. In 1998, total species and log-series alpha were
similar to 1997 values for both nearfield and farfield stations. 
Figure 4-4. Mean (± 95 % confidence intervals) numbers of individuals per
sample for those collected from 1992 to 1998 
0
500
1000
1500
2000
2500
3000
3500
1992 1993 1994 1995 1996 1997 1998
Year
Abundance per Grab Sample
Nearfield
Farfield
NF Average

1998 OUTFALL MONITORING OVERVIEW 39 
Figure 4-5. Mean (± 95 % confidence intervals) number of species per
sample collected from 1992 to 1998
Figure 4-6. Mean (± 95 % confidence intervals) diversity measured as log-
series alpha for nearfield samples collected from 1992 to 1998 
Multivariate analyses of the 1998 nearfield data indicated that the
stations could be separated into two major groups. One group was
associated with medium to fine sandy sediments and was distinguished
by high abundances of the annelid worms, Polygordius sp. A and 
Spiophanes bombyx . The other group was dominated by the annelid
species, Prionospio steenstrupi , Mediomastus californiensis , and 
Aricidea catherinae . These taxa are often associated with somewhat
“muddy” sediments, although they can found in a wide range of
sediment types.
Multivariate analyses of the farfield data divided the stations into three
dissimilar groups. One cluster included stations characterized by the 
0
10
20
30
40
50
60
70
80
90
1992 1993 1994 1995 1996 1997 1998
Year
Species per Grab Sample
Nearfield
Farfield
NF Average
0
2
4
6
8
10
12
14
16
18
1992 1993 1994 1995 1996 1997 1998
Year
Log-Series Alpha
Nearfield
Farfield
NF Average

1998 OUTFALL MONITORING OVERVIEW 40 
annelid, Prionospio steenstrupi , and the nut clam, Nucula
delphinodonta . The second group included stations located along the
eastern portions of the bay, from Cape Ann to Cape Cod, and included
a diverse fauna. The third cluster comprised only samples from one
station in Cape Cod Bay, dominated by the annelid, Tharyx acutus ,
and the amphipod, Leptocheirus pinguis .
In the nearfield, the temporal patterns of total individual and species
richness indices reflect destruction and recovery from storm surges
that occurred during December 1992. The storm surges associated
with a December 12, 1992 storm were quite high, among the highest
measured since the early 1980s. Extreme changes in bottom
characteristics of some stations occurred during that winter, including
one station changing from more than 80% mud to 99% sand and
gravel.
The patterns of increasing species richness during 1994 and 1995 have
not been explained. MWRA has evaluated possible explanations: 
• Are Massachusetts Bay benthic populations exhibiting a cyclic
pattern, driven by long-term weather patterns? 
• Is the bay undergoing eutrophication? 
• Have methodological differences in treatment of samples occurred
as technicians have learned more about the bay?
Only one of these possible explanations, a cyclic pattern, is likely.
Cycles of 7-8 years have been observed in other benthic systems. It
would be important to understand such a cycle, as ignoring it could
lead to misinterpreting monitoring results. If a natural cycle in
Massachusetts Bay resulted in a decrease in species richness at the
same time that the outfall began operation, the response could be
interpreted as an outfall effect. Thus, it will be important to compare
changes in the nearfield with those in the farfield.
The other possible explanations are not likely. The baseline data to
date do not indicate that the bay is undergoing eutrophication. Water-
column monitoring documented lower average concentrations of
chlorophyll in both nearfield and farfield waters during 1995-1997,
compared to 1992-1994 or 1998. Nor is there evidence for changes in
methodology or taxonomic expertise. The total number of species
identified during each year has changed very little since 1992, and
periodic changes in analysts have not corresponded with substantial
changes in species richness.

1998 OUTFALL MONITORING OVERVIEW 41
Hard-bottom Communities 
Analyses of the past four years of video and still photographs have
shown a temporally stable pattern in the structure of hard-bottom
communities (Kropp et al. 1999, Figure 4-7). The amount of sediment
drape varied within sites, with totally clean rocks adjacent to rocks
heavily covered with sediment. Consequently, there was considerable
small-scale, within-site heterogeneity in distributions of many taxa.
However, the consistency over time indicates that a major change
between years should be readily detectable.
Algae usually dominated the tops of drumlins, while encrusting or
attached invertebrates were increasingly dominant on the flanks. The
encrusting coralline algae Lithothamnion spp. were the most common
algae. Abundance of Lithothamnion spp. was inversely correlated
with sediment drape, percent cover being greatest in areas with the
least sediment. This relationship is not surprising, because the
encrusting growth form of Lithothamnion spp. makes them susceptible
to smothering. Consequently, Lithothamnion spp. may be good future
indicators of outfall effects. 
Figure 4-7. Typical hard-bottom survey photograph

1998 OUTFALL MONITORING OVERVIEW 42
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). For
contaminants, a caution level has been set at 90% of EPA or NOAA
sediment guidelines, and to date, all contaminant concentrations have
been well below those levels. A caution level of decline in RPD depth
to half its baseline level would be readily observed. Levels measured
during monitoring ranged from 1.73 cm in 1998 to 3.02 in 1995. If
only data collected through 1998 were used, the caution level would be
set at 1.26. The caution level for benthic diversity will also be based
upon a full set of baseline data and has not yet been determined.
Caution and warning levels for species composition are based on the
premise that increases in opportunistic species would indicate
environmental stress. Pollution-tolerant species, such as Capitella 
spp., Streblospio benedicti , Polydora cornuta , and Mulinia lateralis ,
and moderately pollution-tolerant species, such as Ampelisca
abdita/vadorum , make up about 50% of the species in Boston Harbor.
Opportunistic species have been rare in the nearfield and farfield
throughout the baseline period. 
Table 4-1. Threshold values for sea floor monitoring 
Parameter Caution Level Warning Level 1998 Results
Depth of redox potential
discontinuity
Redox potential
discontinuity declines to
less than half the baseline
depth
To be based on
baseline data
Contaminants 90% of EPA or NOAA
sediment guidelines
EPA sediment criteria Never exceeded
Benthic diversity Appreciable change after
allowing for storm effects
To be based on
baseline data
Species composition 25% of abundance is
opportunistic species
50% of abundance is
opportunistic species
Not exceeded

1998 OUTFALL MONITORING OVERVIEW 43
5. Fish and Shellfish
Background
Fisheries 
The fish and shellfish industry is an important part of the regional
identity and economy of Massachusetts. During 1998, the total
Massachusetts fishery was valued at more than $200 million. Almost
25% of that value was attributed to the lobster fishery. Sea scallops,
cod, winter flounder, and goosefish, also known as monkfish, made up
another 40% (NMFS fisheries statistics). Although many shellfish
beds in the region are closed due to coastal bacterial contamination,
the fishery for oysters and clams remains substantial.
Recreational fishing is also important to the region. In 1998, striped
bass, bluefish, flounders, and cod were the most popular sports
fisheries within the Massachusetts territorial sea (NMFS recreational
fisheries data). 
Environmental Concerns 
One concern about relocating the sewage effluent offshore, into
relatively clean waters, is that contaminants will adversely affect
resource species, either through direct damage to the fishery stocks or
by contamination of the fish, lobster, and other shellfish. Because
many toxic contaminants adhere to particles, animals that live on the
bottom, in contact with sediments, and those 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, more subtle, abnormalities in flounder, lobster, or other
bottom-dwelling animals. Shellfish that feed by filtering suspended
matter from large quantities of water are also potential
bioaccumulators of toxic contaminants. Consumption of these animals
by predators could result in transferring contaminants up the food
chain and ultimately to humans. 
Monitoring Design 
The monitoring program focuses on three indicator species: winter
flounder, lobster, and blue mussel. Winter flounder and lobster are

1998 OUTFALL MONITORING OVERVIEW 44 
important resource species, and the blue mussel, deployed in caged
arrays, is a common biomonitoring species.
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 stations within Boston Harbor and the bays to obtain
specimens for age determination, gross examination of health,
chemical analyses, and liver histology (Figure 5-1). Chemical
analyses of tissues are made to determine tissue burden and whether
contaminant burdens approach human health consumption limits.
Chemical analyses of composite samples of fillets and livers include
PCBs/pesticides and mercury. Liver samples are also analyzed for
PAHs, lead, silver, cadmium, copper, nickel, and zinc. Livers are
examined to quantify three types of vacuolation (centrotubular,
tubular, and focal), macrophage aggregation, biliary duct proliferation,
and neoplasia. These histology parameters have been associated with
chronic exposure to contaminants.
Lobsters live on a variety of surfaces within the region, including mud,
sand, gravel, and rock outcrops. Lobsters are collected from Deer
Island Flats, the area near the new outfall in Massachusetts Bay, and
eastern Cape Cod Bay to determine specimen health and tissue burden
of contaminants. Chemical analyses are performed on composite
samples. Edible meat and hepatopancreas are analyzed for
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. Mussels are collected from reference
sites in Gloucester and Sandwich and deployed in replicate arrays at
five sites. (Two of the sites, Quincy Bay and Cape Cod Bay, were
new to the program in 1998.) Gloucester mussels provide a reference
for organic contaminant analyses, and Sandwich mussels provide a
reference for inorganic contaminants. Separate groups are used as
references, because mussels harvested in Gloucester have very low
levels of organic contaminants, and mussels from Sandwich have very
low levels of metals. After a minimum deployment of 40 days or a
preferred deployment of 60 days, chemical analyses are performed on
composite samples of mussel tissue. Gloucester mussel tissue is
analyzed for PCBs/pesticides and PAHs. Sandwich mussel tissue is
analyzed for mercury and lead.

1998 OUTFALL MONITORING OVERVIEW 45 
Figure 5-1. Flounder sampling stations (left) and mussel deployment sites (right). Lobsters
are taken from Deer Island Flats, eastern Cape Cod Bay, and the outfall site. 
Results
Winter Flounder 
Winter flounder, each a minimum of 30 cm in length, were caught
during April 1998 at each of the five stations (Lefkovitz et al. 1999).
Catch per unit effort, defined as number of fish obtained per minute of
bottom trawling, was highest at the outfall site and Broad Sound and
lowest in eastern Cape Cod Bay. Total length and weight were
comparable to recent years at all stations.
As in other years, concentrations of organic compounds in edible
tissues were highest in fish from Deer Island Flats (Figure 5-2). Body
burdens were consistently similar to or lower than those measured in
previous years. Chlorinated pesticide concentrations have been
relatively constant since 1992. Total PCB concentrations have been
somewhat variable, with maximum concentrations measured in 1995.
Concentrations of mercury, the only metal measured in edible tissues,
have also been variable, with the lowest concentrations consistently
measured in fish from Cape Cod Bay. 
!
!
! !
! 
Broad Sound
Outfall Site
East Cape
Cod Bay
Deer Island Flats
Off Nantasket Beach 
! Flounder Stations
41°45'
41°45'
42°00'
42°00'
42°15'
42°15'
42°30'
42°30'
71°00'
71°00'
70°45'
70°45'
70°30'
70°30'
70°15'
70°15'
0 5 10 15 Kilometers
Outfall Diffuser
Stellwagen Bank
National Marine Sanctuary
LEGEND
N 
!
!
!
!
$
$
$ 
Cape Cod Bay
Outfall Site
Deer Island Light
Sandwich
Gloucester
Boston Inner
Harbor
Quincy 
42°00'
42°00'
42°15'
42°15'
42°30'
42°30'
71°00'
71°00'
70°45'
70°45'
70°30'
70°30'
70°15'
70°15' 
$ Mus sel Collection Locations
0 5 10 15 Kilometers
Outfall Diffuser
Stellwagen Bank
National Marine Sanctuary
LEGEND
N
Mus sel Array Deployment Locations ! 
Mussel Bioaccumulation

1998 OUTFALL MONITORING OVERVIEW 46 
Figure 5-2. Concentrations of contaminants in flounder fillets and liver 
Concentrations of organic compounds in liver tissues mirrored the
trends observed in edible tissues and were generally lower than in
prior years. Highest concentrations were generally found in fish from
Deer Island Flats and lowest in those from Cape Cod Bay.
Fin erosion was significantly more common in fish from Deer Island
Flats than at other stations, but those levels were lower than those
observed a decade ago, before the baseline monitoring program began.
Neoplasia and hydropic vacuolation were absent except for one
neoplasm occurrence in a fish from Broad Sound. The prevalence of
tubular and centrotubular hydropic vacuolation was highest at Deer
Island Flats and Broad Sound, intermediate at the outfall site and off
Nantasket Beach, and lowest at the eastern Cape Cod Bay site.
Overall, levels of tubular and centrotubular vacuolation have not
changed significantly between 1991 and 1998 (Figure 5-3). 
Total Mercury (Hg) in Flounder Livers
0.0
0.2
0.4
0.6
0.8
1.0
1992 1993 1994 1995 1996 1997 1998 1999
Year
ug/g dry wt.
Deer Island
Outfall Site
East Cape Cod Bay
Total Mercury (Hg) in Flounder Fillets
0.0
0.2
0.4
0.6
0.8
1.0
1992 1993 1994 1995 1996 1997 1998 1999
Year
ug/g dry wt.
Deer Island
Outfall Site
East Cape Cod Bay
Total PCB in Flounder Fillets
0
100
200
300
400
500
600
700
800
1992 1993 1994 1995 1996 1997 1998 1999
Year
ng/g dry wt.
Deer Island
Outfall Site
East Cape Cod Bay
Total PCB in Flounder Liver
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
10000
1992 1993 1994 1995 1996 1997 1998 1999
Year
ng/g dry wt.
Deer Island
Outfall Site
East Cape Cod Bay

1998 OUTFALL MONITORING OVERVIEW 47 
Figure 5-3. Prevalence of centrotubular hydropic vacuolation (CHV) 
Lobster 
For analysis of contaminant concentrations, fifteen lobsters were
collected from each location by commercial lobstermen (Lefkovitz et
al. 1999). Sampling was completed in September. Lobsters were
approximately the same length and weight at all sites, but sex ratio
varied. Roughly equal numbers of both sexes were taken from Deer
Island Flats, mostly males were taken at the outfall site, and only
males were taken from eastern Cape Cod Bay. With minor exceptions,
no deleterious conditions, such as black gill disease, were noted.
Mean concentrations of organic compounds in lobster meat were
highest in samples taken from Deer Island Flats and lowest in those
from Cape Cod Bay (Figure 5-4). This general pattern has been
constant throughout the baseline period, indicating that either lobsters
do not migrate between the sites, or that contaminants are quickly
equilibrated within an organism. Concentrations of all organic
compounds measured in 1998 were among the lowest measured
throughout the duration of the program (Figure 5-5). Following a
different pattern, mercury concentrations were highest in samples from
the outfall site and lowest in those from Cape Cod Bay. Mercury
concentrations were lower than in 1997 but have not varied much
throughout the baseline period.
Across the study area, mean concentrations of organic compounds in
lobster hepatopancreas showed the same trend as edible tissue, with
the highest concentrations in lobsters from Deer Island Flats. Metals
concentrations showed a different pattern. Concentrations of metals 
Prevalence of Centro-Tubular Hydropic Vacuolation
(CHV) in FLounder Liver
0
25
50
75
100
1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999
Year
Percent Prevalence
Deer Island
Nantasket Beach
Broad Sound
Outfall Site
Eastern Cape Cod Bay

1998 OUTFALL MONITORING OVERVIEW 48 
tended to be highest at the outfall site and lowest in eastern Cape Cod
Bay. Unlike meat, concentrations of organic compounds in
hepatopancreas tended to have remained the same or increased in
1998. Concentrations of most metals in hepatopancreas samples have
remained relatively constant since 1992. Concentrations of silver
appear to have increased since 1995. 
Figure 5-4. DDT in lobster from Deer Island Flats (DIF), the outfall site,
and eastern Cape Cod Bay (ECCB) 
Total DDT in Lobster Edible Meat
0
5
10
15
20
25
30
35
40
45
50 
DIF OUTFALL ECCB 
Station
Concentration ng/g dry wt. 
1992
1993
1994
1995
1996
1997
1998
B asel i ne M ean ( 92- 98)
+/ -95% C I

1998 OUTFALL MONITORING OVERVIEW 49 
Figure 5-5. Annual average concentrations of PCBs and mercury in lobster
meat at the outfall site 
Blue Mussel 
Recovery of caged mussels in 1998 was unfortunately not perfect
(Lefkovitz et al. 1999). After 40 days, arrays were recovered from all
sites except Quincy Bay, where only the Sandwich mussels used as the
reference for inorganic contaminants were recovered. After 60 days,
full arrays were recovered from the Inner Harbor and Cape Cod Bay.
No cages were recovered from the outfall or Deer Island sites. In
Quincy Bay, only Sandwich mussels were recovered. Consequently
40-day samples were used in analyses for the outfall and Deer Island
site. The Sandwich mussels had to serve as a reference for organic as
well as inorganic contaminants for Quincy Bay. 
0
5
10
15
20
25
30
35
40
1992 1993 1994 1995 1996 1997 1998 
PCB Tissue Concentration (ppb wet wt) Caution Threshold = 34.1 ppb
n = 2
No CI Calculated
n = 3
n = 3
n = 3
n = 3
n = 3
n = 2
No CI Calculated
Warning Threshold = 1600 ppb*
* The warning threshold is 80% of the FDA level
-0.1
-0.05
0
0.05
0.1
0.15
0.2
0.25
0.3
0.35
0.4
1992 1993 1994 1995 1996 1997 1998 
Mercury Tissue Concentration (ppm wet wt) n = 3
n = 3
n = 3
n = 3
n = 3
n = 2
No CI Calculated
n = 2
No CI Calculated
Caution Threshold = 0.31 ppm
Warning Threshold = 0.8 ppm*
* The warning threshold is 80% of the FDA level

1998 OUTFALL MONITORING OVERVIEW 50 
Among the stations previously studied, concentrations of contaminants
have been highest at the Boston Inner Harbor site and lowest at the
outfall site. That relation continued in 1998, with concentrations in
mussels deployed in Cape Cod Bay being lower than other stations.
Overall, contaminant levels measured in 1998 were among the lowest
measured since 1991, particularly at Deer Island and the outfall site
(Figure 5-6). Lead and mercury concentrations have varied more than
concentrations of organic compounds, but overall concentrations were
lower than those measured in 1997. 
Figure 5-6. Average annual concentrations of PCBs and mercury in mussels
at the outfall site 
0
5
10
15
20
25
30
35
40
1992 1993 1994 1995 1996 1997 1998 
PCB Tissue Concentration (ppb wet wt) Caution Threshold = 34.1 ppb
n = 2
No CI Calculated
n = 3
n = 3
n = 3
n = 3
n = 3
n = 2
No CI Calculated
Warning Threshold = 1600 ppb*
* The warning threshold is 80% of the FDA level 
-0.005
0
0.005
0.01
0.015
0.02
0.025
0.03
0.035
0.04
0.045
1992 1993 1994 1995 1996 1997 1998
Mercury Tissue Concentration (ppm wet wt)
Caution Threshold = 0.043 ppm
Warning Threshold = 0.8 ppm* 
* The warning threshold is 80% of the FDA level
n = 8
n = 8
n = 5
n = 5
n = 8

1998 OUTFALL MONITORING OVERVIEW 51
Contingency Plan Thresholds 
For fish and shellfish monitoring, contingency plan thresholds are
based upon U.S. Food and Drug Administration (FDA) limits for
maximum concentrations of specific contaminants in edible portions of
fish and fishery products or will be developed from a complete set of
baseline data. Trigger parameters include mercury, chlordane,
dieldrin, DDT, and PCBs in winter flounder, lobster, and mussel, lead
and PAHs in mussels, and liver disease in flounder (Table 5-1).
In 1998, as in previous baseline monitoring years, concentrations of
contaminants in muscle tissues of flounder and lobster and in total
edible tissue from mussels were well below thresholds based upon
FDA limits. Concentrations of PCBs in hepatopancreas in lobsters
taken from Deer Island Flats have slightly exceeded FDA limits since
1996. In lobsters taken from the outfall site, concentrations of PCBs in
hepatopancreas have come close to the FDA limits since 1995. These
results are consistent with a Massachusetts advisory regarding
consumption of lobster hepatopancreas, known as tomalley, from
lobsters caught in Massachusetts waters.
Originally thresholds for contaminants in edible tissues were set at
caution levels of 50% of the FDA advisory and warning levels of 80%
of the FDA advisory concentrations. During 1997, the OMTF
recommended a more protective caution level for PCBs, and MWRA
decided to take a similar approach for all tissue thresholds. MWRA
has also proposed using non-normalized tissue concentrations rather
than lipid-normalized concentrations for lower and more easily
calculated thresholds. This proposal was presented in the 1997 fish
and shellfish report (Mitchell et al. 1998), but it has not yet been
evaluated by OMSAP. In the 1998 fish and shellfish report (Lefkovitz 
et al. 1999), MWRA is further proposing to simplify the thresholds by
basing all of them on wet weights, rather than using dry weights for
those contaminants that do not have FDA limits.
Several thresholds for fish and shellfish monitoring will be calculated
from baseline monitoring results. For contaminant analyses, caution
levels are now set as twice baseline levels. The caution level for
flounder liver pathology is based upon the baseline prevalence of
centrotubular hydropic vacuolation (CHV) in fish from Boston Harbor.
As in previous years, no results from the 1998 baseline were near the
projected range for those thresholds.

1998 OUTFALL MONITORING OVERVIEW 52 
Table 5-1. Threshold values for fish and shellfish monitoring 
Organism Parameter Caution Level Warning Level 1998
Results
Mussels, flounder,
lobster meat
Toxic compounds,
PAH, pesticides,
mercury, total
PCBs
2x baseline 80% of FDA advisory
level for all listed
contaminants
Never
exceeded
Mussels Lead 2x baseline 3 ug/g wet weight Never
exceeded
Flounder Liver disease
incidence
Flounder liver
disease (CHV)
greater than harbor
baseline prevalence
None Not applicable,
part of
baseline

1998 OUTFALL MONITORING OVERVIEW 53
6. Special Studies
Background 
Besides monitoring the effluent, water column, bottom, and fish and
shellfish, MWRA conducts special studies in response to specific
permit requirements, scientific questions, and public concerns. In
1998, MWRA conducted several studies: 
• Model runs to evaluate the effects of nutrient load and point of
discharge on water quality. 
• Consideration of whether a model should be developed to
characterize the seasonal abundance of important prey species for
endangered species. 
• Ongoing assessment of the role of the sediments in nutrient
cycling. 
• Assessment of potential lobster habitat in the vicinity of the new
outfall site. 
Bays Eutrophication Model 
The outfall permit requires that MWRA update, maintain, and run the
Bays Eutrophication Model (BEM) developed by Hydroqual, Inc. and
USGS. The model predicts conditions caused by nutrient loading and
will be used to support decisions about the need for nutrient limits and
the appropriate level for any such limit for the discharge.
The BEM was initially calibrated using data from the 1992 baseline
harbor and outfall monitoring program (Hydroqual and Normandeau
1995) and prior studies of Massachusetts Bay (Geyer et al. 1992,
Townsend et al. 1991). Recently, a new run of the 1992 data with
updated hydrodynamic functions was generated, along with runs for
1993 and 1994 (HydroQual 2000). The results of the comparison
indicate that the BEM captures the principal processes that relate
primary production and dissolved oxygen to bay-wide circulation,
water column temperature and stratification, nutrients, and light. The
model does not reproduce the single-species blooms that occur
occasionally, but it does reproduce a number of the spatial and
temporal features of phytoplankton biomass and primary production
observed in Boston Harbor and Massachusetts and Cape Cod bays.
The BEM was then used to evaluate the effects of the magnitude of
nitrogen loading and the point of discharge on the system. Five new

1998 OUTFALL MONITORING OVERVIEW 54 
runs were conducted to complement the results using the current
outfall location and 1992 organic carbon and nutrient levels. The new
runs compared the current outfall location with the new location.
Organic carbon and nutrient levels were set at zero, the 1992 level, and
twice the 1992 level.
The results of the model runs indicated that relocation of effluent from
Boston Harbor to the new outfall site would have little effect upon the
water quality of Massachusetts and Cape Cod bays, while significantly
improving conditions in the harbor. The model results indicated that
the region is more sensitive to the magnitude of nutrient inputs than to
the location of the discharge. The results also suggested that a large
change, such as doubling nutrient inputs, would be necessary for
perceivable changes in plankton biomass in Cape Cod Bay to occur.
The results from the model runs were not surprising in the context of
total nutrient loading to the system. Using the 1992 base conditions,
the BEM computes that over an annual cycle, only 3% of the total
nitrogen entering Massachusetts Bay derives from the effluent outfall.
Approximately 93% of the nitrogen enters with inflowing waters from
the Gulf of Maine. These observations are consistent with
observations that the majority of waters within the system are more
representative of oligotrophic than eutrophic conditions. 
Food Web Model 
Besides updating, maintaining, and running the BEM, the outfall
permit notes that during 1998, MWRA developed a scope of work for
a food web model to characterize the seasonal abundance of important
prey species for endangered species in Massachusetts and Cape Cod
bays. The permit required EPA and MADEP to comment on the scope
of work, MWRA to submit a revised plan, and the regulators to
determine whether developing a food web model was warranted.
MWRA planned an incremental approach to assessing the value of
developing a food web model and presented it to OMSAP at the end of
1998. The scope of work included four parts: 
• Evaluate recent monitoring data to determine whether conditions
assumed in the SEIS for the proposed outfall and NOAA
Biological Opinion concerning endangered species remained true. 
• Compare dilution fields and expectations based on more recent
three-dimensional modeling. 
• Perform the BEM sensitivity and mass balance analysis. 
• Review approaches to food web modeling.

1998 OUTFALL MONITORING OVERVIEW 55 
Review of monitoring data and refined model projections, completed
during 1998 (Hunt et al. 1999), indicated that changes in
Massachusetts and Cape Cod bays will not be worse than predicted by
the SEIS and NOAA’s 1993 Biological Opinion on the outfall.
Rather, nitrogen loading from MWRA sewage effluent is less than had
been predicted in 1988. Thus, changes to the system will probably be
less than had been predicted—plankton biomass and species
distributions are not expected to change.
Preliminary review of modeling approaches has led MWRA to agree
with right whale biologists that development of a food-web model will
not be the best means for protecting right whales in the region. Such
models are most effective when measuring major perturbations, which
are not expected. Further, information on species-by-species plankton
biomass and the degree of importance of the bays to the whales is
incomplete. Rather than developing a Massachusetts-specific model,
taking a broader approach to whale research over the entire species
range would be more protective of the populations. 
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. Through denitrification, coastal sediments can also act as a
nitrogen sink, converting nitrate to gaseous forms of nitrogen, which is
lost to the atmosphere. If denitrification rates are high within the
harbor, then moving the outfall into deeper waters with lower
denitrification rates may change the nitrogen load to the region.
Since 1992, MWRA has conducted studies of benthic nutrient cycling
in Boston Harbor. In 1998, 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 in the
southern harbor (Tucker et al. 1999). Results of those studies have
shown that denitrification rates within the harbor sediments are
typically high, with more than half the nitrogen mineralized in the
sediments subsequently being lost through denitrification. However,
only a relatively minor percentage of the nitrogen inputs to Boston
Harbor is cycled through the sediments, so only a small percentage of
the nitrogen introduced to the system is lost to denitrification. Moving
the outfall is not likely to affect the total nitrogen load to the bay.
MWRA also conducts studies of nutrient cycling and oxygen
dynamics in Massachusetts Bay. These studies may be important in
evaluating the causes of low dissolved oxygen levels after discharge

1998 OUTFALL MONITORING OVERVIEW 56 
from the outfall begins. Baseline studies were conducted from 1992-
1997. No measurements were made in 1998, but the studies were
resumed in 1999. 
Lobster Settling 
One concern not addressed in routine monitoring was whether or not
the area near the new outfall could be an important habitat for young
lobsters. If it were, the outfall could affect young lobsters as they
settle from the plankton to a benthic life stage. The outfall could also
affect yearling and older juvenile lobsters, which are thought to be
relatively nonmobile, obligate shelter-dwellers. It was not known if
the area around the outfall is a significant site for lobster settling,
although some experts suggested that the cobble habitats in the
nearfield were too deep and too cold to be preferred.
Therefore, in 1998, a study of cobble-boulder habitats in the vicinity of
the new outfall was conducted to determine the density of the early
benthic-phase lobsters, particularly new recruits and yearlings (Lavalli
and Kropp 1998). Potential lobster habitats were selected for
evaluation by examining videotape and reports, identifying the habitats
most likely to shelter juvenile lobsters. Three sites near the outfall
were then compared to two inshore, reference sites, known to be
juvenile lobster habitat. The study was conducted during the period of
peak settling. Lobsters were sampled by suction, enumerated, and
measured for carapace length.
The assessment of lobster habitat was completed in early September.
Data from the reference stations were similar to observations of those
sites in previous years, indicating that 1998 was a typical year for
lobster settlement. Significantly fewer young-of-the-year, yearling,
and early benthic-phase lobsters were taken from stations near the
outfall site, indicating that those sites are not significant sites for
lobster settlement. The distinct pycnocline that develops at the outfall
site and the depth of the water probably keep lobsters from settling in
great numbers. The relatively few lobsters that may settle near the
new outfall may be at a further disadvantage compared to those
lobsters at inshore sites, because the lower water temperatures would
slow growth and prevent the juveniles from outgrowing predators.

1998 OUTFALL MONITORING OVERVIEW 57
7. Summary
Background 
Since its creation in 1985, MWRA has worked to end long-standing
violations of the Clean Water Act that resulted from discharge of
sewage sludge and poorly treated effluent into Boston Harbor. Sludge
discharges have ended, and MWRA is working to minimize the effects
of effluent discharge. The MWRA program includes source reduction,
improved treatment, and effective dilution once the effluent reaches
the marine environment. Dilution will be accomplished by diverting
the effluent to a new outfall and diffuser system, located 9.5 miles
offshore in Massachusetts Bay.
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 of MWRA’s work, there is general agreement 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 caused some concerns.
EPA and MADEP recognized these concerns when they issued the
NPDES permit for the new outfall. The permit includes high standards
for plant performance, a monitoring program to ensure compliance
with permit conditions and assess potential effects, and a contingency
plan, which describes how MWRA and the regulatory agencies will
respond to determine causes for problems detected by monitoring and
implement corrective actions. The contingency plan identifies
environmentally significant components of effluent or the ecosystem
and threshold levels, which, if exceeded, indicate a potential for
environmental risk.
This Outfall Monitoring Overview is one of a series of annual reports
required by MWRA. It provides a scientific summary of each year of
monitoring and includes information relative to the contingency plan,
such as threshold exceedances, responses, and corrective actions. This
year’s report presents monitoring results for baseline field data
collected from 1991 through 1998.

1998 OUTFALL MONITORING OVERVIEW 58
Effluent 
The MWRA strategy for improving the environmental quality of
Boston Harbor without degrading the offshore environment relies upon
source reduction and improved treatment. Ensuring that the effluent
meets permit limits is the most important action MWRA can take to
ensure that the outfall does not cause any harm to the environment.
Effluent constituents of concern include nutrients, organic material,
toxic constituents, human pathogens, solids, and floatables. Effluent
monitoring assesses compliance with permit limits for contaminant
concentrations, which are based upon national water quality criteria,
ambient conditions, and projected outfall dilution. (Actual dilution
will be measured when the outfall begins operation.) Monitoring also
provides calculations of total loads of contaminants to the system.
When the second of three batteries of secondary treatment began
operation in 1998, the treatment plant essentially began to operate in
compliance with the 1999 permit. Loading for many contaminants
was lower than had been predicted by early 1997 data, and few
exceedances of thresholds established in the 1999 permit occurred. 
Water Column 
Circulation, water properties, and biology of Massachusetts and Cape
Cod bays are mainly driven by the larger pattern of water flow from
the Gulf of Maine. During much of the year, a weak,
counterclockwise current persists. The water column has been thought
to follow a typical annual cycle of spring and fall phytoplankton
blooms, but wind and other factors greatly influence the pattern.
Water column monitoring focuses upon concerns that relocation of the
outfall will introduce effects from the organic material, nutrients, and
toxic contaminants in the effluent. Of the possible outcomes, changes
in the nutrient balance are thought to have the most potential for
affecting the health of the bays. Water column monitoring includes
five major components: nearfield surveys, farfield surveys, future
plume-tracking surveys, continuous recording, and remote sensing.
During 1998, Massachusetts and Cape Cod bays, like much of the
country, were influenced by weather patterns associated with the El
Niño event in the equatorial Pacific. The winter of 1997-1998 was
relatively warm, and winter and spring were disrupted by many storms
and record rainfalls. Over the year, average winds were favorable to
upwelling.

1998 OUTFALL MONITORING OVERVIEW 59 
No spring phytoplankton bloom was observed in Massachusetts Bay
for 1998, although elevated nutrient concentrations, increasing light
availability, and increasing temperatures were appropriate for
development of a bloom. Reasons for lack of a bloom were not clear.
Heavy zooplankton grazing following a warm winter, the lack of
dominance by a single species, and other physical, chemical, or
biological factors may have contributed to the outcome.
Major storm events and lack of a declining spring bloom resulted in
relatively high concentrations of dissolved oxygen during June. Later,
persistent stratified conditions led to decreasing bottom dissolved
oxygen concentrations from June through December. The pulse of
organic matter from the fall bloom further depressed dissolved oxygen
concentrations.
Threshold parameters for water column monitoring include dissolved
oxygen concentration in nearfield and Stellwagen Bank bottom waters,
dissolved oxygen depletion rate in nearfield bottom waters,
chlorophyll level, nuisance algae, zooplankton species in the nearfield,
paralytic shellfish toxin extent, and dilution. Despite the protracted
period of oxygen depletion, dissolved oxygen concentrations did not
drop below contingency plan thresholds. Most other thresholds will be
based upon a complete set of baseline monitoring data. Initial dilution
will be measured when discharge begins, and a warning level would be
exceeded if dilution is less than was predicted by EPA as a basis for
the permit. 
Sea Floor 
Sediment transport within the system occurs primarily during storms.
Typically, strong storms with winds from the northeast resuspend and
transport fine sediments, which are transported by currents to western
Massachusetts Bay to the offshore and toward Cape Cod Bay, where
they are likely to remain. Cape Cod Bay is sheltered from large waves
by the arm of Cape Cod, and waves are rarely large enough to
resuspend sediments in Stellwagen Basin, which is the deepest feature
in the region.
There are several environmental concerns about the possible effects of
the new outfall on the sea floor: eutrophication and related low
dissolved oxygen levels, accumulation of toxic contaminants in
depositional areas, smothering of animals by particulate matter, and
disruption of normal community structure by excess food input. Sea
floor monitoring includes measurements of contaminants in sediments,
sediment profile imaging, studies of near- and farfield of soft-bottom
communities, and study of hard-bottom communities. Sediment

1998 OUTFALL MONITORING OVERVIEW 60 
contaminant studies were included in 1998 after a two-year hiatus.
They focused on stations that will be used to examine possible short-
term effects of the new outfall.
As in previous studies, concentrations of all organic and inorganic
contaminants near the new outfall were low, well below EPA or
NOAA guidelines. Sediment profile images indicated that the RPD
layer depth became shallower between 1992-1995 and 1997-1998.
This change appears to be linked to the interaction of physical and
biological processes that structure bottom communities. Total infaunal
abundance and species abundance have varied throughout baseline
monitoring. Overall the average number of species decreased about
25% from 1992 to 1993. Number of species subsequently rose until
they leveled off in 1997 and 1998. This pattern is not fully understood
but may reflect destruction and recovery from December 1992 storms.
Hard bottom communities have been stable during baseline
monitoring.
Threshold parameters for sea floor monitoring include contaminant
concentrations, RPD depth, benthic diversity in soft-bottom
communities, and species composition. All contaminant
concentrations were well below the established thresholds, and
baseline data indicate that any exceedances of thresholds based on
baseline monitoring will be easily detected. 
Fish and Shellfish 
The fish and shellfish industry is an important part of the regional
identity and economy of Massachusetts. One concern about relocating
the sewage effluent off shore is that contaminants will adversely affect
resource species, either through direct damage to the fishery stocks or
by contamination of the fish, lobster, and other shellfish.
The monitoring program focuses on three indicator species. Winter
flounder and lobsters are important resources to the region. The blue
mussel, deployed in caged arrays, is a common biomonitoring species.
Monitoring includes examination of health and measurement of
organic and inorganic contaminants.
As in previous monitoring years, most contaminant levels and
prevalence of liver disease were highest in flounder taken from Deer
Island Flats. Similarly, levels of most contaminants were highest in
lobsters from Deer Island Flats. Among stations previously studied,
concentrations of contaminants in mussels were highest in Boston
Inner Harbor and lowest at the outfall site. Contaminant

1998 OUTFALL MONITORING OVERVIEW 61 
concentrations in mussels from a new site in Cape Cod Bay were even
lower than at the outfall site.
Contingency plan thresholds for fish and shellfish monitoring are
based upon FDA limits for maximum concentrations of specific
contaminants in edible portions of fish and fisheries products or will
be developed from a complete set of baseline data. In 1998, as in
previous baseline monitoring years, concentrations of contaminants in
muscle tissues of flounder and lobster and in total edible tissue from
mussels were well below thresholds based upon FDA limits.
Concentrations of PCBs in hepatopancreas in some lobsters have come
close to or exceeded FDA levels. Accordingly, Massachusetts has an
advisory regarding consumption of lobster hepatopancreas, known as
tomalley. 
Special Studies 
Besides monitoring the effluent, water column, bottom, and fish and
shellfish, MWRA conducts special studies in response to specific
permit requirements, scientific questions, and public concerns. In
1998, MWRA conducted several studies.
The outfall permit requires that MWRA update, maintain, and run the
Bays Eutrophication Model (BEM) developed by Hydroqual, Inc. and
USGS. During 1998, five new model runs were made to evaluate the
effects of the magnitude of nitrogen loading and the point of discharge
on the system. These runs indicated that relocation of the outfall
would have little or no effect on the water quality of Massachusetts or
Cape Cod bays. The model indicates that only 3% of the total nitrogen
entering Massachusetts Bay derives from the outfall. Approximately
93% of the nitrogen enters with inflowing waters from the Gulf of
Maine.
The outfall permit also requires MWRA to assist its regulators in
determining whether developing a food web model to characterize
abundance of prey of endangered species is warranted. MWRA
reviewed monitoring data and modeling approaches to reach a
conclusion that a food web model would not be the most appropriate
means for protecting the right whale and other endangered species in
Massachusetts and Cape Cod bays. Nitrogen loading from MWRA
effluent is less than had been predicted and is not likely to cause any
changes in plankton biomass or species composition. Food web
models are most effective when they measure larger perturbations.
Further, exact information on species-by-species plankton biomass,
which would be necessary for an appropriate model, is incomplete.

1998 OUTFALL MONITORING OVERVIEW 62 
MWRA has conducted ongoing assessments of nutrient cycling and
oxygen dynamics of the sediments to determine whether moving the
outfall offshore could cause a change in the nutrient budget. Those
studies have indicated that denitrification rates are high in Boston
Harbor sediments, but that only a small portion of the total nitrogen in
the system is cycled through the sediments. Moving the outfall
offshore is not expected to change the nitrogen budget of the region.
Another concern not addressed by routine monitoring has been that
juvenile lobsters would be affected if the area around the outfall were a
significant lobster nursery. Therefore, in 1998 a study of cobble-
boulder habitats in the vicinity of the new outfall was conducted to
determine the density of the early benthic-phase lobsters, particularly
new recruits and yearlings. The assessment found that the area around
the outfall is not significant lobster habitat. The distinct pycnocline
that develops at the sites and the depth of the water probably keep
lobsters from settling in great numbers. The relatively few lobsters
that do settle near the new outfall may be at a disadvantage compared
to lobsters at inshore sites, because the lower water temperatures may
slow growth and prevent the juveniles from outgrowing predators.
MWRA will continue to conduct special studies as they are required
by the permit or warranted by monitoring results, scientific questions,
or public concerns. The primary mechanism for initiating special
studies is expected to be the regular review of monitoring data by
OMSAP and their committees.

1998 OUTFALL MONITORING OVERVIEW 63
References 
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Braasch E, editors. Proceedings of the Gulf of Maine ecosystem
dynamics: a scientific symposium and workshop: RARGOM. p 352.
EPA. 1988. Boston Harbor Wastewater Conveyance System.
Supplemental Environmental Impact Statement (SEIS). Boston:
Environmental Protection Agency Region I.
Geyer WR, Gardner GB, Brown WS, Irish J, Butman B, Loder T,
Signell RP. 1992. Final report: Physical oceanographic investigation of
Massachusetts and Cape Cod bays. Boston: Massachusetts Bays
Program. Report MBP-92-03. 497p.
Hunt CD, Kropp RK, Fitzpatrick JJ, Yodzis P, Ulanowicz RE. 1999. A
review of issues related to the development of a food web model for
important prey of endangered species in Massachusetts and Cape Cod
Bays. Boston: Massachusetts Water Resources Authority. Report
ENQUAD 99-14. 62p.
HydroQual. 2000. Bays Eutrophication Model (BEM): modeling
analysis for the period 1992-1994. Boston: Massachusetts Water
Resources Authority. Report ENQUAD 00-02. 158 p.
HydroQual, Normandeau. 1995. A water quality model for
Massachusetts and Cape Cod bays: calibration of the Bays
Eutrophication Model (BEM). Boston: Massachusetts Water
Resources Authority. Report ENQUAD 95-8. 403p.
Kropp RK, Dahlen D, Boyle JD, Diaz. 1999. 1998 outfall benthic
monitoring report. Boston: Massachusetts Water Resources Authority.
Report ENQUAD 99-15. 320 p.
Lavalli KL, Kropp RK. 1998. Abundance of juvenile lobsters at the
new outfall site: comparisons with inshore abundances and discussion
of potential outfall impacts on lobster populations. Boston:
Massachusetts Water Resources Authority. Report ENQUAD 98-14.
26p.
Lefkovitz L, McLeod LA, Moore M. 1999. 1998 Annual fish and
shellfish report. Boston: Massachusetts Water Resources Authority.
Report ENQUAD 99-11. 200 p.

1998 OUTFALL MONITORING OVERVIEW 64 
Leo WS, Rex AC, Carroll SR, Connor MS. 1995. The state of Boston
Harbor 1994: connecting the Harbor to its watersheds. Boston:
Massachusetts Water Resources Authority. Report ENQUAD 95-12.
37 p.
Libby PS, Albro CS, Hunt CD, Keller AA, Oviatt CA, Turner J. 1999.
1998 Annual water column monitoring report. Boston: Massachusetts
Water Resources Authority. Report ENQUAD 99-16. 180 p.
McLeod LA. 1999. Summary of marine mammal observations during
1998 surveys. Boston: Massachusetts Water Resources Authority.
Report ENQUAD 99-01. 9p.
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fish and shellfish report. Boston: Massachusetts Water Resources
Authority. Report ENQUAD 98-12.
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outfall monitoring plan Phase I: baseline studies. Boston:
Massachusetts Water Resources Authority. Report ENQUAD ms-2.
95p.
MWRA. 1997a. Massachusetts Water Resources Authority effluent
outfall monitoring plan: Phase II post discharge monitoring. Boston:
Massachusetts Water Resources Authority. Report ENQUAD ms-44.
61p.
MWRA. 1997b. Contingency plan. Boston: Massachusetts Water
Resources Authority. 41p.
Pawlowski C, Keay KE, Graham E, Taylor DI, Rex AC, Connor MS.
1996. The state of Boston Harbor 1995: the new treatment plant makes
its mark. Boston: Massachusetts Water Resources Authority. Report
ENQUAD 96-06. 22 p.
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questions and answers about the new outfall. Boston: Massachusetts
Water Resources Authority. Report ENQUAD 97-05. 32 p.

1998 OUTFALL MONITORING OVERVIEW 65 
Townsend D, Cammen LM, Christensen JP, Ackelson SG, Keller MD,
Haugen, EM, Corwin S, Bellows WK, Brown JF. 1991. Seasonality of
oceanographic conditions in Massachusetts Bay. Boston:
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114p.
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Boston: Massachusetts Water Resources Authority. Report ENQUAD
99-08. 33.p.
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U.S. Geological Survey. USGS Fact Sheet 078-98. 2p.

1998 OUTFALL MONITORING OVERVIEW 66
List of Acronyms 
BOD Biological oxygen demand
cBOD Carbonaceous biological oxygen demand
CHV Centrotubular hydropic vacuolation
C-NOEC No observable effect concentration
CSO Combined sewer overflow
DIF Deer Island Flats
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
MGD Million gallons per day
MWRA Massachusetts Water Resources Authority
NPDES National Pollutant Discharge Elimination System
OMSAP Outfall Monitoring Science Advisory Panel
OMTF Outfall Monitoring Task Force
PAH Polyaromatic hydrocarbon
PCB Polychlorinated biphenyl
PIAC Public Interest Advisory Committee
RPD Redox potential discontinuity
SEIS Supplemental Environmental Impact Statement
USGS U.S. Geological Survey
TOC Total organic carbon
TSS Total suspended solids

67 
Massachusetts Water Resources Authority
Charlestown Navy Yard
100 First Avenue
Boston, MA 02129
(617) 242-6000
http://www.mwra.state.ma.us

68

1998 OUTFALL MONITORING OVERVIEW

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