2005 overview

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2005 outfall monitoring overview 
Massachusetts Water Resources Authority
Environmental Quality Department
Report ENQUAD 2006-18

Citation:
Werme C, Hunt CD. 2006. 2005 outfall monitoring overview . Boston: Massachusetts Water
Resources Authority. Report ENQUAD 2006-18. 105p.

2005
Outfall Monitoring Overview 
submitted to
Massachusetts Water Resources Authority
Environmental Quality Department
100 First Avenue
Charlestown Navy Yard
Boston, MA 02129
prepared by
Christine Werme
Berkeley, CA 94705
and
Carlton D. Hunt
Battelle
397 Washington Street
Duxbury, MA 02332
October 30, 2006

2005 OUTFALL MONITORING OVERVIEW I
Table of Contents 
List of Figures .................................................................................................................... iii
List of Tables ...................................................................................................................... v
Summary ........................................................................................................................... vii
1. Introduction..................................................................................................................... 1
Background ..................................................................................................................... 1
Outfall Permit.................................................................................................................. 4
Monitoring Program........................................................................................................ 6
Contingency Plan ............................................................................................................ 9
Data Management ......................................................................................................... 11
Reporting....................................................................................................................... 11
Outfall Monitoring Overview ....................................................................................... 12
2. Effluent ......................................................................................................................... 13
Background ................................................................................................................... 13
Pollution Prevention and Wastewater Treatment ..................................................... 13
Environmental Concerns........................................................................................... 13
Monitoring Design ........................................................................................................ 15
Results........................................................................................................................... 18
Contingency Plan Thresholds ....................................................................................... 21
3. Water Column............................................................................................................... 22
Background ................................................................................................................... 22
Circulation and Water Properties.............................................................................. 22
Environmental Concerns........................................................................................... 24
Monitoring Design ........................................................................................................ 26
Results........................................................................................................................... 30
Physical Conditions .................................................................................................. 30
Water Quality............................................................................................................ 33
Phytoplankton Communities..................................................................................... 37
Zooplankton Communities........................................................................................ 40
Contingency Plan Thresholds ....................................................................................... 42
4. Sea Floor ....................................................................................................................... 44
Background ................................................................................................................... 44
Bottom Characteristics and Sediment Transport ...................................................... 44
Environmental Concerns........................................................................................... 44
Monitoring Design ........................................................................................................ 45
Results........................................................................................................................... 50
Sediment Characteristics, Tracers, and Contaminants.............................................. 50
Sediment-Profile Imaging......................................................................................... 51
Soft-bottom Communities......................................................................................... 52
Hard-bottom Communities ....................................................................................... 54
Contingency Plan Thresholds ....................................................................................... 55

2005 OUTFALL MONITORING OVERVIEW II 
5. Fish and Shellfish.......................................................................................................... 57
Background ................................................................................................................... 57
Monitoring Design ........................................................................................................ 58
Results........................................................................................................................... 60
Contingency Plan Thresholds ....................................................................................... 61
6. Special Studies .............................................................................................................. 62
Background ................................................................................................................... 62
Effluent Analysis .......................................................................................................... 62
Nutrient Flux................................................................................................................. 65
Marine Mammal Observations ..................................................................................... 67
Model Results ............................................................................................................... 68
2005 Alexandrium Bloom ............................................................................................. 69
Toxic Contaminants Review......................................................................................... 71
USGS Studies ............................................................................................................... 72
7. Boston Harbor Monitoring............................................................................................ 75
Background ................................................................................................................... 75
Wastewater Loads and Eutrophication ......................................................................... 75
Water Quality Monitoring: Tributary Rivers................................................................ 77
Effects of Rain on Bacteria: Boston Harbor Beaches................................................... 80
Changes in the Sediments ............................................................................................. 82
Changes in the Benthic Community ............................................................................. 83
8. Stellwagen Bank National Marine Sanctuary ............................................................... 89
Background ................................................................................................................... 89
Monitoring Design ........................................................................................................ 89
Results........................................................................................................................... 91
Water Column........................................................................................................... 91
Sea Floor ................................................................................................................... 96
References......................................................................................................................... 98
List of Acronyms ............................................................................................................ 104

2005 OUTFALL MONITORING OVERVIEW III
List of Figures 
Figure 1-1. Map of Massachusetts and Cape Cod bays ...................................................... 2
Figure 2-1. Annual effluent flows, 1990-2005 ................................................................ 18
Figure 2-2. Annual solids and nitrogen discharges........................................................... 19
Figure 2-3. Annual metals discharges............................................................................... 20
Figure 3-1 (a) General circulation within Massachusetts Bay, (b) General circulation
within the Gulf of Maine................................................................................................... 23
Figure 3-2. Water-column sampling stations and regions ................................................ 28
Figure 3-3. Charles River discharge, 1992-early 2006 ..................................................... 30
Figure 3-4. 2005 Charles River discharge compared to observations since 1992 ............ 30
Figure 3-5. Nearfield surface and bottom water temperature ........................................... 31
Figure 3-6. Hourly near-surface temperature for 2005 superimposed on the data from
1989-2004 ......................................................................................................................... 32
Figure 3-7. Nearfield surface and bottom water salinity .................................................. 32
Figure 3-8. Post-transfer nearfield ammonium concentrations compared to baseline...... 34
Figure 3-9. Annual mean ammonium concentrations in Massachusetts Bay regions ...... 34
Figure 3-10. Post-transfer nearfield nitrate concentrations compared to baseline........... 35
Figure 3-11. Annual mean nitrate concentrations in Massachusetts Bay regions ............ 35
Figure 3-12. Post-transfer nearfield chlorophyll compared to baseline............................ 36
Figure 3-13. Post-transfer nearfield dissolved oxygen concentrations compared to
baseline ............................................................................................................................. 37
Figure 3-14. Post-transfer nearfield phytoplankton abundance compared to baseline..... 38
Figure 3-15. Abundance of Phaeocystis pouchetii in the nearfield, 1992-2005............... 39
Figure 3-16. Abundance of Alexandrium species in the nearfield, 1992-2005 ................ 39
Figure 3-17. Post-transfer nearfield zooplankton abundance compared to baseline ........ 40
Figure 3-18. Total zooplankton abundance by region ..................................................... 41
Figure 4-1. Locations of nearfield soft-bottom stations.................................................... 46
Figure 4-2. Locations of farfield soft-bottom stations ...................................................... 47
Figure 4-3. Locations of hard-bottom stations.................................................................. 48
Figure 4-4. Apparent color RPD for all data from nearfield stations ............................... 51
Figure 4-5. Community parameters in the nearfield, 1992-2005...................................... 53
Figure 4-6. Cod and flounder in a 2005 transect .............................................................. 54
Figure 5-1. Prevalence of centrotubular hydropic vacuolation......................................... 60
Figure 6-1. Sediment oxygen demand in Boston Harbor and the nearfield of
Massachusetts Bay during pre- and post-diversion periods compared to other coastal
ecosystems ........................................................................................................................ 67
Figure 6-2. Humpback whale sighted near the Deer Island Treatment Plant in April 2005
........................................................................................................................................... 68
Figure 6-3. Geographic extent of shellfish bed closures in July 2005.............................. 70
Figure 6-4. USGS map of the topography of Massachusetts Bay ................................... 73
Figure 7-1. Relationships between total annual loads and nitrogen concentrations in the
water column in Boston Harbor........................................................................................ 76

2005 OUTFALL MONITORING OVERVIEW IV 
Figure 7-2. Relationships between total loads and chlorophyll concentrations in the water
column in Boston Harbor.................................................................................................. 77
Figure 7-3. Impact of CSO control plan on system-wide CSOs....................................... 78
Figure 7-4. Average fecal coliform counts in different weather conditions and during
phases of MWRA’s CSO control plan at four locations in the lower Charles River........ 79
Figure 7-5. Average monthly Charles River chlorophyll levels ...................................... 80
Figure 7-6. Average monthly Mystic River chlorophyll levels, 1998-2003..................... 80
Figure 7-7. Boston Harbor beach monitoring stations..................................................... 81
Figure 7-8. Yearly mean abundance of Clostridium perfringens spores in Boston Harbor
........................................................................................................................................... 83
Figure 7-9. Locations of benthic stations within Boston Harbor...................................... 85
Figure 7-10. Benthic community parameters in Boston Harbor, 1991-2005 ................... 86
Figure 7-11. Total number of Ampelisca per sample, 1991-2005 .................................... 87
Figure 7-12. Photographs from the same station in Hingham Harbor in 2004 and 2005 . 88
Figure 8-1. Water column stations, including the additional Stellwagen Bank National
Marine Sanctuary stations................................................................................................. 90
Figure 8-2. Annual mean ammonium and nitrate in the Stellwagen Bank National Marine
Sanctuary, the nearfield, and Cape Cod Bay .................................................................... 92
Figure 8-3. Top: Annual mean dissolved inorganic nitrogen; Middle: total dissolved
nitrogen; Bottom: total nitrogen in Stellwagen Bank National Marine Sanctuary, the
nearfield, and Cape Cod Bay ............................................................................................ 93
Figure 8-4. Nitrite in October surface and bottom waters at individual stations in
Stellwagen Bank National Marine Sanctuary ................................................................... 94
Figure 8-5. Total nitrite plus nitrate in bottom waters at individual stations in Stellwagen
Bank National Marine Sanctuary...................................................................................... 95
Figure 8-6. Annual mean chlorophyll in Stellwagen Bank National Marine Sanctuary and
other regions...................................................................................................................... 95
Figure 8-7. Benthic community parameters at stations in or near the Stellwagen Bank
National Marine Sanctuary, 1992-2005............................................................................ 97

2005 OUTFALL MONITORING OVERVIEW V
List of Tables 
Table 1. Summary of monitoring questions and status as of the end of 2005 ................... ix
Table 2. Summary of contingency plan thresholds and exceedances as of 2005. ............ xii
Table 1-1. Rosters of panel and committee members......................................................... 5
Table 1-2. Public concerns and environmental responses presented in the monitoring
plan...................................................................................................................................... 7
Table 1-3. Monitoring program objectives and analyses.................................................... 8
Table 1-4. Contingency Plan threshold parameters .......................................................... 10
Table 1-5. Monitoring reports submitted to OMSAP ....................................................... 12
Table 2-1. Monitoring questions related to the effluent ................................................. 14
Table 2-2. Reporting requirements of the outfall permit .................................................. 16
Table 2-3. Monitoring plan parameters for effluent ......................................................... 18
Table 2-4. Contingency Plan threshold values and 2005 results for effluent monitoring 21
Table 3-1. Monitoring questions related to the water column ......................................... 25
Table 3-2. Components of water-column monitoring....................................................... 27
Table 3-3. Nearfield water-column monitoring parameters ............................................. 29
Table 3-4. Farfield water-column monitoring parameters................................................ 29
Table 3-5. Contingency plan threshold values and 2005 results for water-column
monitoring......................................................................................................................... 43
Table 4-1. Monitoring questions related to the sea floor .................................................. 45
Table 4-2. Contingency Plan threshold values and 2005 results for sea-floor monitoring56
Table 5-1. Monitoring questions related to fish and shellfish .......................................... 57
Table 5-2. Chemical analyses of fish and shellfish........................................................... 59
Table 5-3. Contingency Plan threshold values and 2005 results for fish and shellfish
monitoring......................................................................................................................... 61
Table 6-1. Metals in final effluent from Deer Island Treatment Plant ............................. 63
Table 6-2. Pesticides, PAHs, and PCBs in final effluent from Deer Island Treatment Plant
........................................................................................................................................... 63
Table 6-3. Annual loading estimates (kilograms per year)............................................... 64
Table 6-4. Monitoring questions related to nutrient flux.................................................. 66

2005 OUTFALL MONITORING OVERVIEW VII
Summary 
In September 2005, the Massachusetts Water Resources Authority (MWRA) marked five
years of effluent discharge from the Massachusetts Bay outfall. During the year, the Deer
Island Treatment Plant continued to operate as designed, and there were no unexpected
effects on the ecosystems of Massachusetts and Cape Cod bays. Total loads of many
parameters measured within the effluent, including solids and metals, remain low.
After nine years of baseline monitoring and five years of discharge monitoring, the
MWRA has been able to answer many of the questions that were posed when the
program began (Table 1). As expected, monitoring has been able to detect minimal
environmental responses in the immediate vicinity of the outfall. However, overall
conditions within the bays have not changed from the baseline as a result of the offshore
outfall.
There were three Contingency Plan exceedances during the year (Table 2). One of four
monthly toxicity tests, the sea urchin chronic fertilization test, did not meet the
Contingency Plan warning threshold for a sample collected on September 15. Effluent
from the sample did meet the requirements of other toxicity tests, all other permit
requirements were met, and there were no operational upsets that would have caused any
violations of permit conditions.
As in 2002 through 2004, summer concentrations of the nuisance algal species 
Phaeocystis pouchetii exceeded the caution level. The wide geographical extent of the
blooms suggest that regional processes, rather than the outfall, have been responsible for
the increasing frequency of Phaeocystis blooms.
In May and June 2005, the largest large bloom of toxic dinoflagellates in the genus 
Alexandrium since 1972 occurred, triggering an exceedance of the caution threshold. The
bloom originated in Maine and extended south of Martha’s Vineyard. Concentrations of
cells were orders of magnitude higher than in previous years. The MWRA outfall is not
suspected to be a factor in the size or extent of this bloom.
While conditions in Massachusetts and Cape Cod bays have not changed from the
baseline, MWRA has documented significant improvements in Boston Harbor.
Concentrations of nutrients responsible for eutrophic conditions in the water column,
chlorophyll levels, and pathogen-indicator bacteria level have decreased, while dissolved
oxygen concentrations have increased. Concentrations of many PAHs, PCBs, pesticides,
and some metals in the surface sediments have declined by 20 to 75%, and improvements
in the benthic communities have been observed at some stations.

2005 OUTFALL MONITORING OVERVIEW VIII 
As in other years, no effects of the outfall on the Stellwagen Bank National Marine
Sanctuary have been detected. Plume tracking, water column, and sea floor studies
suggested that no effects of the outfall on the sanctuary were likely, and none have been
measured.

2005 OUTFALL MONITORING OVERVIEW IX 
Table 1. Summary of monitoring questions and status as of the end of 2005 
Monitoring Question Status
Do effluent pathogens exceed the permit limits? Pathogenic viruses detectable in the final effluent
but at very low numbers: secondary treatment and
disinfection effectively remove pathogens.
Does acute or chronic toxicity of effluent exceed
the permit limit?
General compliance with permit limits.
Do effluent contaminant concentrations exceed
permit limits?
Compliance with permit limits. Discharges of
priority pollutants well below SEIS predictions and
in most cases meet receiving water quality criteria
even before dilution.
Do conventional pollutants in the effluent
exceed permit limits?
General compliance: discharges of solids and BOD
have decreased by 80% compared to the old
treatment plant.
What are the concentrations of contaminants in
the influent and effluent and their associated
variability?
High removal by treatment system with consistently
low concentrations since secondary treatment
brought on line. 
Do levels of contaminants in water outside the
mixing zone exceed water quality standards?
Water quality standards not exceeded, confirmed
by plume studies conducted in 2001 and ongoing
effluent monitoring.
Are pathogens transported to shellfish beds at
levels that might affect shellfish consumer
health?
Dilution is sufficient for pathogens to reach
background concentrations before reaching
shellfish beds, confirmed by plume studies
conducted in 2001. Indicator bacteria surveys in
Massachusetts Bay did not detect appreciable
levels of indicator bacteria in the region of the
outfall.
Are pathogens transported to beaches at levels
that might affect swimmer health?
Dilution is sufficient for pathogens to reach
background concentrations before reaching
beaches, confirmed by plume studies conducted in
2001. Pathogen and indicator bacteria sampling in
Massachusetts Bay did not detect appreciable
levels of indicator bacteria in the region of the
outfall.
Has the clarity and/or color of the water around
the outfall changed?
Although clarity and color have not changed, there
are occasional observations of tiny bits of grease,
similar to samples collected at the treatment plant.
Has the amount of floatable debris around the
outfall changed?
Floatable debris of concern is rare in the effluent.
Signs of effluent can occasionally be detected in
the field.
Are the model estimates of short-term (less
than 1 day) effluent dilution and transport
accurate?
Model estimates accurate, confirmed by plume
studies conducted in 2001.
What are the nearfield and farfield water
circulation patterns?
Flow is controlled by general circulation in the Gulf
of Maine, affected by tides and local wind. Bottom
currents around the outfall can flow in any direction
with no mean flow.
What is the farfield fate of dissolved,
conservative, or long-lived effluent
constituents?
Changes in farfield concentrations of salinity and
dissolved components not detected within tens of
meters of outfall and not observed in farfield water
or sediments.
Have nutrient concentrations changed in the
water near the outfall; have they changed at
farfield stations in Massachusetts Bay or Cape
Cod Bay, and, if so, are they correlated with
changes in the nearfield?
Changes consistent with model predictions. The
effluent signature is clearly observed in the vicinity
or the outfall but is diluted over a few days and 10s
of kilometers.
Do the concentrations (or percent saturation) of
dissolved oxygen in the water column meet the
state water quality standards?
Conditions unchanged from background.

2005 OUTFALL MONITORING OVERVIEW X 
Monitoring Question Status
Have the concentrations (or percent saturation)
of dissolved oxygen in the vicinity of the outfall
or at selected farfield stations in Massachusetts
Bay or Cape Cod Bay changed relative to pre-
discharge baseline or a reference area? If so,
can changes be correlated with effluent or
ambient water nutrient concentrations, or can
farfield changes be correlated with nearfield
changes?
Conditions not changed from background.
Has the phytoplankton biomass changed in the
vicinity of the outfall or at selected farfield
stations in Massachusetts Bay or Cape Cod
Bay, and, if so, can these changes be
correlated with effluent or ambient water
nutrient concentrations, or can farfield changes
be correlated with nearfield changes?
No substantial change detected.
Have the phytoplankton production rates
changed in the vicinity of the outfall or at
selected farfield stations, and, if so, can these
changes be correlated with effluent or ambient
water nutrient concentrations, or can farfield
changes be correlated with nearfield changes?
Timing of the fall blooms in the nearfield appears to
be different, but this change may not be associated
with the discharge. Productivity patterns in Boston
Harbor may be changing, as the area transitions
from eutrophic conditions to a more typical coastal
regime.
Has the abundance of nuisance or noxious
phytoplankton changed in the vicinity of the
outfall?
Frequency of Phaeocystis blooms has increased,
but the phenomenon is regional in nature. The
large Alexandrium bloom in 2005 was also regional
and has not been attributed to the outfall.
Has the species composition of phytoplankton
or zooplankton changed in the vicinity of the
outfall or at selected farfield stations in
Massachusetts Bay or Cape Cod Bay? If so,
can these changes be correlated with effluent of
ambient water nutrient concentrations, or can
farfield changes be correlated with nearfield
changes?
No change detected.
What is the level of sewage contamination and
its spatial distribution in Massachusetts and
Cape Cod bays sediments before discharge
through the new outfall?
Effects of historic inputs from Boston Harbor and
other sources detected.
Has the level of sewage contamination or its
spatial distribution in Massachusetts and Cape
Cod bays sediments changed after discharge
through the new outfall?
Effluent signal detected as Clostridium perfringens 
spores, the most sensitive sewage tracer, within a
few kilometers of the outfall.
Has the concentration of contaminants in
sediments changed?
No general increase in contaminants. Effluent
signal can be detected as silver, a sensitive
sewage tracer, in sediment traps and as 
Clostridium perfringens spores in sediments within
2 km of the diffuser.
Has the soft-bottom community changed? All observed changes appear to result from natural
cycles/
Have the sediments become more anoxic; that
is, has the thickness of the sediment oxic layer
decreased?
No increase in total organic carbon or change in
sediment RPD detected.
Are any benthic community changes correlated
with changes in levels of toxic contaminants (or
sewage tracers) in sediments?
No change detected.
Has the hard-bottom community changed? No substantial changes detected. Decreases in
coralline algae detected at some stations; not yet
known whether these changes are related to the
outfall.

2005 OUTFALL MONITORING OVERVIEW XI 
Monitoring Question Status
How do the sediment oxygen demand, the flux
of nutrients from the sediment to the water
column, and denitrification influence the levels
of oxygen and nitrogen in the water near the
outfall?
Described by baseline monitoring; conditions do
not suggest adverse changes have resulted from
moving outfall offshore.
Have the rates of these processes changed? No changes over 5 years.
Has the level of contaminants in the tissues of
fish and shellfish around the outfall changed
since discharge began?
No in flounder or lobster contaminant body
burdens. Detectable increases in PAHs and
chlordane in mussels deployed at the outfall.
Mercury concentrations in flounder tissue have
been elevated.
Do the levels of contaminants in the edible
tissue of fish and shellfish around the outfall
represent a risk to human health?
No changes that would pose a threat to human
health. Regional patterns have persisted since the
baseline period, and there appears to be a general
long-term downward trend for most contaminant
levels.
Are the contaminant levels in fish and shellfish
different between the outfall, Boston Harbor,
and a reference site?
Differences documented during baseline
monitoring. Regional patterns have persisted since
the diversion.
Has the incidence of disease and/or
abnormalities in fish or shellfish changed?
Blind-side skin lesions found on flounder from
western Massachusetts Bay. Appear to be
seasonal manifestations, and their cause has not
been attributed to the outfall. Long-term downward
trend in liver disease.

2005 OUTFALL MONITORING OVERVIEW XII 
Table 2. Summary of contingency plan thresholds and exceedances as of 2005. (NA = not
applicable, D = no exceedance, C = caution level exceedance, W = warning level exceedance) 
Location/
Parameter
Type
Parameter 2000 2001 2002 2003 2004 2005 
Effluent 
pH W D D D D D 
Fecal coliform bacteria,
monthly D D D D D D 
Fecal coliform bacteria,
weekly D D D D D D 
Fecal coliform bacteria,
daily D W D D W D 
Fecal coliform bacteria,
3 consecutive days D D D D D D 
Chlorine residual, daily W D D D D D 
Chlorine residual,
monthly D D D D D D 
Total suspended solids,
weekly D D W D D D 
Total suspended solids,
monthly D D W D D D 
cBOD, weekly D D D D D D 
cBOD, monthly D D D D D D 
Acute toxicity, mysid
shrimp D D D D D D 
Acute toxicity, fish D D D D D D 
Chronic toxicity, fish D W D D D D 
Chronic toxicity, sea
urchin D W D D D W 
PCBs D D D D D D 
Plant performance D D D D D D 
Flow NA D D D D D 
Total nitrogen load NA D D D D D 
Floatables NA NA NA NA NA NA 
Oil and grease D D D D D D

2005 OUTFALL MONITORING OVERVIEW XIII 
Location/
Parameter
Type
Parameter 2000 2001 2002 2003 2004 2005 
Water Column 
Dissolved oxygen
concentration C D D D D D Nearfield
bottom water Dissolved oxygen
saturation C D D D D D 
Dissolved oxygen
concentration D D D D D D Stellwagen
Basin
bottom water Dissolved oxygen
saturation D D D D D D 
Nearfield
bottom water
Dissolved oxygen
depletion rate (June-
October) 
NA D D D D D 
Annual NA D D D D D 
Winter/spring NA D D D D D 
Summer NA D D D D D 
Nearfield
chlorophyll
Autumn C D D D D D 
Winter/spring NA D D D C D 
Summer NA D C C C C 
Nearfield
nuisance algae 
Phaeocystis
pouchetii Autumn D D D D D D 
Winter/spring NA D D D D D 
Summer NA D D D D D 
Nearfield
nuisance algae 
Pseudonitzchia Autumn D D D D D D 
Nearfield
nuisance algae 
Alexandrium
fundyense 
Any sample D D D D D C 
Farfield
shellfish PSP toxin extent D D D D D D 
Plume Initial dilution NA D Completed Completed Completed Completed

2005 OUTFALL MONITORING OVERVIEW XIV 
Location/
Parameter
Type
Parameter 2000 2001 2002 2003 2004 2005 
Sea Floor 
Acenaphthene NA D D NA NA D 
Acenaphylene NA D D NA NA D 
Anthracene NA D D NA NA D 
Benzo(a)anthracene NA D D NA NA D 
Benzo(a)pyrene NA D D NA NA D 
Cadmium NA D D NA NA D 
Chromium NA D D NA NA D 
Chrysene NA D D NA NA D 
Copper NA D D NA NA D 
Dibenzo(a,h)anthracene NA D D NA NA D 
Fluoranthene NA D D NA NA D 
Fluorene NA D D NA NA D 
Lead NA D D NA NA D 
Mercury NA D D NA NA D 
Naphthalene NA D D NA NA D 
Nickel NA D D NA NA D 
p,p’-DDE NA D D NA NA D 
Phenanthrene NA D D NA NA D 
Pyrene NA D D NA NA D 
Silver NA D D NA NA D 
Total DDTs NA D D NA NA D 
Total HMW PAH NA D D NA NA D 
Total LMW PAH NA D D NA NA D 
Total PAHs NA D D NA NA D 
Total PCBs NA D D NA NA D 
Nearfield
sediment
contaminants
Zinc NA D D NA NA D 
Nearfield
sediment RPD depth NA D D D D D 
Species per sample NA D D D D D 
Fisher’s log-series
alpha NA D D D D D 
Shannon diversity NA D D D D D 
Nearfield
benthic
diversity
Pielou’s evenness NA D D D D D 
Nearfield
species
composition
Percent opportunists NA D D D D D

2005 OUTFALL MONITORING OVERVIEW XV 
Location/
Parameter
Type
Parameter 2000 2001 2002 2003 2004 2005 
Fish and Shellfish 
Total PCBs NA D D D NA NA 
Mercury NA D D D D NA 
Chlordane NA D D D NA NA 
Dieldrin NA D D D NA NA 
Nearfield
flounder tissue
Total DDTs NA D D D NA NA 
Nearfield
flounder Liver disease (CHV) NA D D D D D 
Total PCBs NA D D D NA NA 
Mercury NA D D D NA NA 
Chlordane NA D D D NA NA 
Dieldrin NA D D D NA NA 
Nearfield
lobster tissue
Total DDTs NA D D D NA NA 
Total PCBs NA D D D NA NA 
Lead NA D D D NA NA 
Mercury NA D D D NA NA 
Chlordane NA C C D NA NA 
Dieldrin NA D D D NA NA 
Total DDTs NA D D D NA NA 
Nearfield
mussel tissue
Total PAHs NA C C C NA NA

2005 OUTFALL MONITORING OVERVIEW 1
1. Introduction
Background 
For more than 20 years, the Massachusetts Water Resources Authority
(MWRA) has worked to minimize the effects of wastewater discharge on
the marine environment. MWRA was created by an act of the
Massachusetts State Legislature in December 1984 and in 1985 embarked
upon what has become known as the Boston Harbor Project. Before then,
the Boston metropolitan area discharged both sewage sludge and
inadequately treated sewage effluent into the confined waters of Boston
Harbor, from outfalls located at Deer Island in the northern part of the
harbor and Nut Island, in southern Quincy Bay. MWRA ended discharge
of municipal sludge into Boston Harbor in 1991, when sludge from both
treatment plants began to be barged to a processing plant in Quincy and
made into fertilizer. Steps to minimize effects of effluent discharge have
included: 
• Source reduction to prevent pollutants from entering the waste
stream. 
• Improved treatment before discharge. 
• Better dilution once the effluent enters the marine environment. 
Source reduction has included projects to lessen household hazardous
waste disposal and minimize mercury discharges from hospitals and
dentists. An industrial pretreatment/pollution prevention program ensures
that toxic contaminants are removed before they reach the sewer system.
In addition, best management practices are employed at sewer facilities to
mitigate accidental discharge of pollutants. 
Improved treatment was implemented in a series of steps carried out
during 1995-2001. In 1995, a new primary treatment plant at Deer Island
was brought on line, and disinfection facilities were completed. (Primary
treatment is a physical treatment process, which involves removal of
solids through settling followed by disinfection.) Batteries of secondary
treatment (which includes bacterial decomposition as well as settling
followed by disinfection) went on line in 1997, 1998, and 2001. Also
during 1998, discharge from the Nut Island Treatment Plant into Quincy
Bay ceased, and all wastewater was conveyed to Deer Island for treatment,
ending effluent discharge to the southern part of the harbor.
Efforts to improve treatment continued in 2005. MWRA initiated studies
aimed at maximizing flow through the secondary treatment systems,

2005 OUTFALL MONITORING OVERVIEW 2 
achieving significant results by the end of the year. In April 2005 a tunnel
connection opened between the Deer Island Treatment Plant and the Fore
River Pelletizing Facility, where sludge is processed into fertilizer. Prior
to opening the tunnel, sludge was centrifuged at Deer Island and barged to
Fore River. The liquid removed by the centrifuge, known as centrate, was
then sporadically added back at the head of the plant. With the opening of
the tunnel, sludge is centrifuged at Fore River, and the centrate is returned
to Deer Island by tunnel, resulting in a more stable treatment process. 
Better dilution was achieved in 2000, by diverting the effluent discharge
from Boston Harbor to the new 9.5-mile-long outfall and diffuser system,
located offshore in Massachusetts Bay (Figure 1-1). 
Figure 1-1. Map of Massachusetts and Cape Cod bays

2005 OUTFALL MONITORING OVERVIEW 3 
The outfall site was selected because it had a water depth and current
patterns that would promote effective dilution, it was the least likely of the
alternative sites to affect sensitive resources, and it was feasible to
construct an outfall tunnel to the location.
The outfall tunnel is bored through bedrock and has a diffuser system
made up of 53 risers, each with five or six open ports, along its final 1.25
miles. Discharge from the diffuser heads is at the sea floor, at water
depths of about 100 feet. Initial dilution at the outfall is about five times
that of the Boston Harbor outfall, which was shallower, in 50 feet of
water. The offshore location of the outfall ensures that effluent will not
reach beaches or shellfish beds within a tidal cycle, even if currents are
shoreward.
For many of the components of MWRA’s work, there was little or no
argument that the project benefited the marine environment and the people
of the region. Moving the effluent outfall from the harbor to
Massachusetts Bay did raise some concerns, which were expressed as
general, continuing questions: 
• Is it safe to eat fish and shellfish? 
• Are natural/living resources protected? 
• Is it safe to swim? 
• Are aesthetics being maintained?
These concerns were recognized by MWRA and by the permit for the
outfall issued jointly by the U.S. Environmental Protection Agency (EPA)
and the Massachusetts Department of Environmental Protection
(MADEP).

2005 OUTFALL MONITORING OVERVIEW 4
Outfall Permit 
The permit issued by EPA and MADEP under the National Pollutant
Discharge Elimination System (NPDES) became effective on August 9,
2000 and continued until August 9, 2005. (Since expiration, MWRA
continues to operate under the conditions of the permit until a new one is
issued.) It limits discharges of pollutants and requires reporting on the
treatment plant operation and maintenance. The permit requires MWRA
to continue its ongoing pollution prevention program and to employ best
management practices aimed at preventing accidental discharge of
pollutants to the sewer system.
The permit requires MWRA to monitor the effluent and the ambient
receiving waters for compliance with permit limits and in accordance with
a monitoring plan (MWRA 1991, 1997a, 2004) developed in response to
the EPA Supplemental Environmental Impact Statement (SEIS) prepared
as part of the outfall-siting process (EPA 1988). It requires that MWRA
implement a Contingency Plan (MWRA 1997b, 2001), which identifies
relevant environmental quality parameters and thresholds that, if
exceeded, would require a response.
In 1998, in anticipation of the permit, EPA and MADEP established an
independent panel of scientists to review monitoring data and provide
advice on key scientific issues related to the permit. This panel, the
Outfall Monitoring Science Advisory Panel (OMSAP, Table 1-1),
conducts peer reviews of monitoring reports, evaluates the data, and
advises EPA and MADEP on scientific implications. OMSAP also
provides advice concerning any proposed modifications to the monitoring
or contingency plans.
OMSAP may form specialized focus groups when specific technical issues
require expanded depth or breadth of expertise. Two standing sub-
committees also advise OMSAP. The Public Interest Advisory Committee
(PIAC) represents local, non-governmental organizations and
environmental groups and advises OMSAP on values and uses of the
harbor and the bays. The Inter-agency Advisory Committee (IAAC)
represents state and federal agencies and provides OMSAP with advice
concerning environmental regulations.

2005 OUTFALL MONITORING OVERVIEW 5 
Table 1-1. Rosters of panel and committee members 
OMSAP as of December 2005 
Andrew Solow, Woods Hole Oceanographic Institution (chair)
Robert Beardsley, Woods Hole Oceanographic Institution
Norbert Jaworski, retired
Robert Kenney, University of Rhode Island
Scott Nixon, University of Rhode Island
Judy Pederson, MIT Sea Grant
Michael Shiaris, University of Massachusetts, Boston
James Shine, Harvard School of Public Health
Juanita Urban-Rich, University of Massachusetts, Boston
Catherine Coniaris Vakalopoulos,
MA Department of Environmental Protection (OMSAP staff) 
IAAC as of December 2005 
MA Coastal Zone Management
Todd Callaghan
Jan Smith (alternate)
MA Department of Environmental Protection
Catherine Coniaris Vakalopoulos
MA Division of Marine Fisheries
Jack Schwartz
National Marine Fisheries Service
David Dow
Stellwagen Bank National Marine Sanctuary
Ben Haskell
US Army Corps of Engineers
Thomas Fredette
US Environmental Protection Agency
Matthew Liebman
US Geological Survey
Michael Bothner 
PIAC as of December 2005 
Patty Foley (chair, representative of Save the
Harbor/Save the Bay)
Association for the Preservation of Cape Cod
Maggie Geist
Tara Nye (alternate)
Bays Legal Fund
Wayne Bergeron
The Boston Harbor Association
Vivian Li
Cape Cod Commission
John Lipman
Steve Tucker (alternate)
Center for Coastal Studies
Peter Borrelli
Conservation Law Foundation
Priscilla Brooks
New England Aquarium
Marianne Farrington
Massachusetts Audubon Society
Robert Buchsbaum
MWRA Advisory Board
Joseph Favaloro
Safer Waters in Massachusetts
Salvatore Genovese
Polly Bradley (alternate)
Save the Harbor/Save the Bay
Bruce Berman (alternate)
Wastewater Advisory Committee
Edward Bretschneider

2005 OUTFALL MONITORING OVERVIEW 6
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 some
studies during 1989-1991 and implemented a broad baseline-monitoring
program in 1992. Outfall ambient monitoring plans were originally
developed and refined under the direction of an Outfall Monitoring Task
Force (OMTF), made up of scientists, regulators, and environmental
advocacy groups (MWRA 1991, 1997a). (The OMTF was disbanded
upon creation of OMSAP.) Because the first years of monitoring
following diversion of effluent to the bay found no unexpected changes to
the system, changes to the monitoring program were approved by EPA
and MADEP, and a new plan (MWRA 2004) was implemented in the
2004 monitoring year.
The outfall ambient monitoring plan expands the general questions of
public concern by translating them into possible “environmental
responses,” which are more specific questions directly related to the
outfall (Table 1-2). To answer those questions, the monitoring program
focuses on critical constituents of treatment plant effluent, such as
nutrients, organic material, toxic contaminants, 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).
The basic program is augmented by special studies, which are conducted
in response to specific permit requirements, scientific questions, and
environmental concerns. The monitoring program is designed to compare
environmental quality of the Massachusetts Bay system, including Boston
Harbor and Cape Cod Bay, before and after the outfall location moved
from the harbor to the bay.

2005 OUTFALL MONITORING OVERVIEW 7 
Table 1-2. Public concerns and environmental responses presented in the
monitoring plan (MWRA 1991) 
Public Concern: Is it safe to eat fish and shellfish? 
ƒ Will toxic chemicals accumulate in the edible tissues of fish and shellfish,
and thereby contribute to human health problems? 
ƒ Will pathogens in the effluent be transported to shellfishing areas where
they could accumulate in the edible tissues of shellfish and contribute to
human health problems? 
Public Concern: Are natural/living resources protected? 
ƒ Will nutrient enrichment in the water column contribute to an increase in
primary production? 
ƒ Will enrichment of organic matter contribute to an increase in benthic
respiration and nutrient flux to the water column? 
ƒ Will increased water-column and benthic respiration contribute to
depressed oxygen levels in the water? 
ƒ Will increased water-column and benthic respiration contribute to
depressed oxygen levels in the sediment? 
ƒ Will nutrient enrichment in the water column contribute to changes in
plankton community structure? (Such changes could include stimulation
of nuisance or noxious algal blooms and could affect fisheries.) 
ƒ Will benthic enrichment contribute to changes in community structure of
soft-bottom and hard-bottom macrofauna, possibly also affecting
fisheries? 
ƒ Will the water column near the diffuser mixing zone have elevated levels
of some contaminants? 
ƒ Will contaminants affect some size classes or species of plankton and
thereby contribute to changes in community structure and/or the marine
food web? 
ƒ Will finfish and shellfish that live near or migrate by the diffuser be
exposed to elevated levels of some contaminants, potentially contributing
to adverse health in some populations? 
ƒ Will the benthos near the outfall mixing zone and in depositional areas
farther away accumulate some contaminants? 
ƒ Will benthic macrofauna near the outfall mixing zone be exposed to
some contaminants, potentially contributing to changes in community
structure? 
Public Concern: Is it safe to swim? 
ƒ Will pathogens in the effluent be transported to waters near swimming
beaches, contributing to human health problems? 
Public Concern: Are aesthetics being maintained? 
ƒ Will changes in water clarity and/or color result from the direct input of
effluent particles or other colored constituents, or indirectly through
nutrient stimulation of nuisance plankton species? 
ƒ Will the loading of floatable debris increase, contributing to visible
degradation?

2005 OUTFALL MONITORING OVERVIEW 8 
Table 1-3. Monitoring program objectives and analyses 
Task Objective Analyses 
Effluent 
Effluent sampling
Characterize wastewater
discharge from Deer Island
Treatment Plant
Flow
Organic material (cBOD)
Solids
pH
Bacterial indicators
Total residual chlorine
Toxicity
Nutrients
Toxic contaminants
Floatables 
Water Column 
Nearfield surveys Collect water quality data near
outfall location
Farfield surveys
Collect water quality data
throughout Massachusetts and
Cape Cod bays
Temperature
Salinity
Dissolved oxygen
Nutrients
Solids
Chlorophyll
Water clarity
Photosynthesis
Respiration
Phytoplankton
Zooplankton
Moorings (GoMOOS
and USGS)
GoMOOS near Cape Ann and
USGS near outfall provide
continuous oceanographic
data
Currents
Temperature
Salinity
Water clarity
Chlorophyll
Remote sensing
Provides oceanographic data
on a regional scale through
satellite imagery
Surface temperature
Chlorophyll 
Sea Floor 
Soft-bottom studies
Evaluate sediment quality and
benthos in Boston Harbor and
Massachusetts Bay
Sediment chemistry
Sediment profile imagery
Community composition
Hard-bottom studies
Characterize marine benthic
communities in rock and
cobble areas
Topography
Substrate
Community composition 
Fish and Shellfish 
Winter flounder Determine contaminant body
burden and population health
Tissue contaminant
concentrations
Physical abnormalities,
including liver histopathology
American lobster Determine contaminant body
burden
Tissue contaminant
concentrations
Physical abnormalities
Blue mussel
Evaluate biological condition
and potential contaminant
bioaccumulation
Tissue contaminant
concentrations

2005 OUTFALL MONITORING OVERVIEW 9 
Baseline monitoring was initially planned to last for a minimum of three
years, as the outfall was originally planned for completion in 1995.
Delays in construction allowed a relatively long period for baseline
studies. Consequently, MWRA was able to document greater natural
variability and develop a better understanding of the system than would
have been possible in a briefer baseline period. MWRA was also able to
evaluate the environmental response in Boston Harbor to other facilities
improvements ( e.g. , Leo et al. 1995, Pawlowski et al. 1996, Rex and
Connor 1997, Rex 2000, Rex et al. 2002, Taylor 2002, 2003, 2004, 2006).
The extended period also meant that the discharge to Massachusetts Bay,
when it did begin, had the benefit of nearly complete implementation of
secondary treatment.
The monitoring plan is a “living document.” That is, every effort is made
to incorporate new scientific information and improved understanding
resulting from the monitoring program into appropriate continued
measurements. MWRA’s NPDES permit allows an annual list of
proposed changes to the monitoring plan. 
Contingency Plan 
The MWRA Contingency Plan (MWRA 1997b, 2001) describes how, if
monitoring results indicate a possible environmental problem, MWRA and
the regulatory agencies will respond to determine the cause of the problem
and to specify the corrective actions that should be taken if the problem
appears to be related to the discharge. The Contingency Plan identifies
parameters that represent environmentally significant components of the
effluent or the ecosystem and that, if specific threshold levels are
exceeded, indicate a potential for environmental risk (Table 1-4). The
plan provides a process for evaluating parameters that exceed thresholds
and formulating appropriate responses.

2005 OUTFALL MONITORING OVERVIEW 10 
Table 1-4. Contingency Plan threshold parameters 
Measurement
Area Parameter
pH
Fecal coliform bacteria
Residual chlorine
Total suspended solids
Biochemical oxygen demand
Toxicity
PCBs
Plant performance
Flow
Effluent
Total nitrogen load
Floatables
Oil and grease
Dissolved oxygen concentration and saturation
Dissolved oxygen depletion rate
Chlorophyll
Nuisance and noxious algae
Water Column
Effluent dilution
Sea Floor
Sediment contaminants
Redox potential discontinuity depth
Benthic community structure
PCBs, mercury, chlordanes, dieldrin, and DDTs in
mussels and flounder and lobster tissue
Lead in 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, some parameters have more
conservative “caution” as well as “warning” thresholds. Exceeding
caution or warning thresholds could indicate a need for increased attention
or study. If a caution threshold is exceeded, MWRA, with guidance from
OMSAP and the regulatory agencies, may expand the monitoring to track
effluent quality and environmental conditions. The data are examined to
determine whether it is likely that an unacceptable effect resulting from
the outfall has occurred.
Exceeding warning levels could, in some circumstances, indicate a need
for a response to avoid potential adverse environmental effects. If a
threshold is exceeded at a warning level, the response includes early
notification of EPA and MADEP and, if the outfall has contributed to
adverse environmental effects, the quick development of a response plan.
Response plans include a schedule for implementing actions, such as
making adjustments in plant operations or undertaking an engineering
feasibility study regarding specific potential corrective activities.
Every effort is made to incorporate new scientific information and
improved understanding resulting from the monitoring program into
appropriate thresholds. A process for modifying the Contingency Plan is

2005 OUTFALL MONITORING OVERVIEW 11 
set forth in MWRA’s NPDES permit, and Revision 1 was approved during
2001. 
Data Management 
The monitoring program has generated extensive data sets. Data quality is
maintained through program-wide quality assurance and quality control
procedures. After validation, data from field surveys and laboratory
analyses are loaded into a centralized project database. Data handling
procedures are automated to the maximum extent possible to reduce
errors, ensure comparability, and minimize reporting time. Data that are
outside the expected ranges are flagged for review. Data reported by the
laboratory as suspect (for example, because the sample bottle was cracked
in transit) are marked as such and not used in interpretation or threshold
calculations, although they are retained in the database and included in
raw data reports. Any corrections are documented. Each data report notes
any special data quality considerations associated with the data set.
As monitoring results become available, they are compared with
Contingency Plan thresholds. Computer programs calculate each
threshold parameter value from the data, compare it to the threshold, and
notify the project staff if any caution or warning levels are exceeded. 
Reporting 
MWRA’s NPDES permit requires regular reports on effluent quality and
extensive reporting on the monitoring program. A variety of reports are
submitted to OMSAP for review (Table 1-5). Changes to the monitoring
program or the Contingency Plan must be reviewed by regulators and
published in the Environmental Monitor . Data that exceed Contingency
Plan thresholds and corrective actions must also be reported. Data that
exceed thresholds must be reported within five days after the results
become available, and MWRA must make all reasonable efforts to report
all data on thresholds within 90 days of each sampling event.
Reports are posted on MWRA’s web site (www.mwra.com), with copies
placed in repository libraries in Boston and on Cape Cod. OMSAP also
holds public workshops where outfall monitoring results are presented.

2005 OUTFALL MONITORING OVERVIEW 12 
Table 1-5. Monitoring reports submitted to OMSAP 
Report Description/Objectives
Outfall Monitoring Plan
Phase I—Baseline Studies (MWRA
1991)
Phase II—Discharge Ambient
Monitoring (MWRA 1997a, 2004)
Discusses goals, strategy, and design of
baseline and discharge monitoring programs.
Contingency Plan (MWRA 1997b,
2001)
Describes development of threshold
parameters and values and MWRA’s planned
contingency measures.
Program Area Synthesis Reports
Summarize, interpret, and explain annual
results for effluent, water column, benthos,
and fish and shellfish monitoring areas.
Special Studies Reports
Discuss, analyze, and cross-synthesize data
related to specific issues in Massachusetts
and Cape Cod bays.
Outfall Monitoring Overviews Summarize monitoring data and include
information relevant to the contingency plan. 
Outfall Monitoring Overview 
Among the many reports that MWRA completes, this report, the outfall
monitoring overview, has been prepared for most baseline-monitoring
years and for each year that the permit has been in place (Gayla et al. 
1996, 1997a, 1997b, Werme and Hunt 2000a, 2000b, 2001, 2002, 2003,
2004, 2005). The report includes a scientific summary for the year of
monitoring. Overviews for 1995-1999 included only baseline information.
With the outfall operational, subsequent reports have included information
relevant to the Contingency Plan, such as threshold exceedances,
responses, and corrective actions. When data suggest that monitoring
activities, parameters, or thresholds should be changed, the report
summarizes those recommendations.
This year’s outfall monitoring overview, the eleventh completed, presents
monitoring program results for effluent and field data for 2005, marking
five years of post-discharge monitoring. It compares all results to
Contingency Plan thresholds. The overview also includes sections on
special studies, Boston Harbor, and the Stellwagen Bank National Marine
Sanctuary.

2005 OUTFALL MONITORING OVERVIEW 13
2. Effluent
Background
Pollution Prevention and Wastewater Treatment 
Ensuring that the final effluent is clean is the most important element in
MWRA’s strategy to improve the environmental quality of Boston Harbor
without degrading Massachusetts and Cape Cod bays. MWRA ensures
clean effluent through a vigorous pretreatment program and by
maintaining and operating the treatment plant well.
The MWRA Toxic Reduction and Control (TRAC) program sets and
enforces limits on the types and amounts of pollutants that industries can
discharge into the sewer system and works with industries to encourage
voluntary reductions in their use of toxic chemicals. TRAC has also
implemented programs to reduce mercury from dental facilities and to
educate the public about proper disposal of hazardous wastes. A booklet, 
A Healthy Environment Starts at Home (available at www.mwra.com),
identifies household products that could be hazardous and recommends
alternatives.
Secondary treatment further reduces the concentrations of contaminants of
concern, except for nutrients. The Deer Island Treatment Plant removes
approximately 85-90% of the suspended solids and biochemical oxygen
demand (BOD), 50-90% of the toxic chemicals, and about 20% of the
nitrogen from the influent.
To prevent accidental discharge of pollutants and mitigate effects should
an accident occur, MWRA has implemented best management practice
plans at the treatment plant, its headworks facilities, the combined sewer
overflow facilities, its pumping stations, and the sludge-to-fertilizer plant.
The plans include daily visual inspections and immediate corrective
actions. Effectiveness of best management practices is assessed by non-
facility staff. 
Environmental Concerns 
Sewage effluent contains a variety of contaminants that can, at too high
levels, affect the marine environment, public health, and aesthetics. The
MWRA permit sets limits on these contaminants so as to ensure that these
attributes will be protected. Several specific questions in the MWRA
ambient monitoring plan respond to public concerns and possible
environmental responses by addressing whether the effluent is meeting

2005 OUTFALL MONITORING OVERVIEW 14 
permit limits (Table 2-1). Other questions require the use of effluent data
in conjunction with plume studies, which were completed in 2001, and
water-column monitoring (see Section 3, Water Column). 
Table 2-1. Monitoring questions related to the effluent 
Is it safe to eat fish and shellfish? 
Will pathogens in the effluent be transported to shellfishing areas where they could
accumulate in the edible tissues of shellfish and contribute to human health problems? 
ƒ Do effluent pathogens exceed the permit limit? 
ƒ Are pathogens transported to shellfish beds at levels that might affect shellfish
consumer health? 
Are natural/living resources protected? 
Will the water column near the diffuser-mixing zone have elevated levels of some
contaminants? 
ƒ Do effluent contaminant concentrations exceed permit limits? 
ƒ What are the concentrations of contaminants and characteristic tracers of
sewage in the influent and effluent and their associated variability? 
Will finfish and shellfish that live near or migrate by the diffuser be exposed to elevated
levels of some contaminants, potentially contributing to adverse health in some
populations? 
ƒ Does acute or chronic toxicity of effluent exceed permit limits? 
ƒ Do levels of contaminants in water outside the mixing zone exceed state water
quality standards? 
Is it safe to swim? 
Will pathogens in the effluent be transported to waters near swimming beaches,
contributing to human health problems? 
ƒ Do effluent pathogens exceed the permit limit? 
ƒ Are pathogens transported to beaches at levels that might affect swimmer
health? 
Are aesthetics being maintained? 
Will changes in water clarity and/or color result from the direct input of effluent particles or
other colored constituents, or indirectly through nutrient stimulation of nuisance plankton
species?
Will the loading of floatable debris increase, contributing to visible degradation? 
ƒ Do conventional pollutants in the effluent exceed permit limits? 
ƒ Has the clarity and/or color of the water around the outfall changed? 
ƒ Has the amount of floatable debris around the outfall changed? 
The effluent constituents of greatest concern include pathogens, toxic
contaminants, organic material, solid material, nutrients, oil and grease,
and “floatables,” including plastic and other debris. The MWRA permit
also sets limits for chlorine and pH: 
• Pathogens , including bacteria, viruses, and protozoa, are found in
human and animal waste and can cause disease. Human exposure
to water-borne pathogens can occur through consumption of
contaminated shellfish or through ingestion or physical contact
while swimming. 
• Toxic contaminants include heavy metals, such as copper and
lead, polychlorinated biphenyls (PCBs), pesticides, polycyclic
aromatic hydrocarbons (PAHs), and petroleum hydrocarbons.
Toxic contaminants can lower survival and reproduction rates of
marine organisms. Some toxic contaminants can accumulate in

2005 OUTFALL MONITORING OVERVIEW 15 
marine life, potentially affecting human health through seafood
consumption. 
• Organic material , a major constituent of sewage, consumes
oxygen as it decays. Even under natural conditions, oxygen levels
decline in bottom waters during the late summer, so any effluent
component that might further decrease oxygen levels is a concern.
Too much organic material could also disrupt animal communities
on the sea floor. 
• Suspended solids , small particles in the water column, decrease
water clarity and consequently affect growth and productivity of
algae and other marine plants. Excess suspended solids also
detract from people’s aesthetic perception of the environment. 
• In marine waters, nitrogen is the limiting nutrient that controls
growth of algae and other aquatic plants. Excess nitrogen can be
detrimental, leading to eutrophication and low levels of dissolved
oxygen, excess turbidity, and nuisance algal blooms. Nutrients,
particularly dissolved forms, are the only components of sewage
entering the treatment plant that are not substantially reduced by
secondary treatment. 
• Oil and grease slicks and floating debris known as floatables pose
aesthetic concerns. Plastic debris can also be harmful to marine
life, as plastic bags are sometimes mistaken for food and clog the
digestive systems of turtles and marine mammals. Plastic and
other debris can also entangle animals and cause them to drown. 
• Sewage effluent is disinfected by addition of a form of chlorine ,
sodium hypochlorite, which is the active ingredient in bleach.
While sodium hypochlorite is effective in destroying pathogens, at
high enough concentrations, it is harmful to marine life.
Consequently, MWRA dechlorinates the effluent with sodium
bisulfite before discharge. 
• Seawater is noted for its buffering capacity, that is, its ability to
neutralize acids and bases. However, state water quality standards
dictate that effluent discharges not change the pH of the ambient
seawater more than 0.5 standard units on a scale of 1 to 14.
Consequently, the outfall permit sets both upper and lower values
for pH of the effluent. 
Monitoring Design 
Effluent monitoring measures the concentrations of constituents of the
effluent and variability in those concentrations to assess compliance with
NPDES permit limits, which are based on state and federal water quality
standards and criteria and on ambient conditions. Effluent monitoring also
provides measurements of mass loads of effluent constituents, so that fate,
transport, and risk of contaminants can be assessed.

2005 OUTFALL MONITORING OVERVIEW 16 
The permit includes numeric limits (Table 2-2) for suspended solids, fecal
coliform bacteria, pH, chlorine, PCBs, and carbonaceous biochemical
oxygen demand (cBOD). In addition, state water quality standards
establish limits for 158 pollutants, and the permit prohibits any discharge
that would cause or contribute to exceeding any of those limits. 
Table 2-2. Reporting requirements of the outfall permit 
Parameter Sample Type Frequency Limit 
Permit-required monitoring 
Flow Flow meter Continuous Report only
Flow dry day Flow meter Continuous 436 MGD annual
average
cBOD 24-hr composite 1/day 40 mg/l weekly
25 mg/l monthly
TSS 24-hr composite 1/day 45 mg/l weekly
30 mg/l monthly
pH Grab 1/day Not <6 or >9
Fecal coliform bacteria Grab 3/day 14,000 col/100ml
Total residual chlorine Grab 3/day 631 μg/l daily
456 μg/l monthly
PCB, Aroclors 24-hr composite 1/month 0.045 ng/l
Toxicity LC50 24-hr composite 2/month 50%
Toxicity C-NOEC 24-hr composite 2/month 1.5%
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
Ammonium-nitrogen 24-hr composite 1/month
Total Kjeldahl nitrogen 24-hr composite 1/month
Total nitrate 24-hr composite 1/month
Total nitrite 24-hr composite 1/month
Cyanide, total Grab 1/month
Copper, total 24-hr composite 1/month
Total arsenic 24-hr composite 1/month
Hexachlorobenzene 24-hr composite 1/month
Aldrin 24-hr composite 1/month
Heptachlor epoxide 24-hr composite 1/month
Total PCBs 24-hr composite 1/month
Volatile organic
compounds Grab 1/month
Report only 
Contingency Plan-required monitoring 
Oil and grease, as
petroleum
hydrocarbons
Grab Weekly Warning
threshold/ 15 mg/l
Floatables Continuous Under development
Plant performance Ongoing 5 violations/year

2005 OUTFALL MONITORING OVERVIEW 17 
The permit prohibits discharge of nutrients in amounts that would cause
eutrophication. It requires MWRA to test the toxicity of the effluent as a
whole on sensitive organisms and establishes limits based on the tests.
Allowable concentrations of contaminants were based on the predicted
dilution at the outfall and verified by field studies of outfall plumes in
2001.
Most parameters are measured in 24-hour composite samples, and some
must meet daily, weekly, or monthly limits. Flow is measured
continuously. Nutrient measurements include total nitrogen, ammonium,
nitrate, and nitrite. Organic material is monitored by measuring the
cBOD. Monitoring for toxic contaminants includes analyses for heavy
metals of concern, chlorinated pesticides, PCBs, volatile organic
compounds, PAHs, total residual chlorine, and cyanide. Toxicity is tested
using whole effluent samples. Tests for acute toxicity include 48-hour
survival of mysid shrimp ( Americamysis bahia , formerly known as 
Mysidopsis bahia ) and inland silverside fish ( Menidia beryllina ). Chronic
toxicity is assessed through inland silverside growth-and-survival and sea
urchin ( Arbacia punctulata ) one-hour-fertilization tests. Pathogen
monitoring consists of enumeration of fecal coliform bacteria. Total
suspended solids (TSS) and settleable solids are also measured.
The contingency plan also sets limits for overall plant performance, annual
nitrogen load, floatables, and oil and grease. Floatables are measured;
threshold limits are under development.
Beyond the requirements of ordinary discharge monitoring, the MWRA
monitoring plan requires additional nutrient measurements and non-
standard, low-detection methods to measure toxic contaminants (Table 2-
3). These measurements are made to better interpret field-monitoring
results.
The monitoring plan also calls for an evaluation of indicators of human
pathogens. To date, MWRA has collected data on anthropogenic viruses,
viral indicators, and Enterococcus bacteria in the influent and effluent.

2005 OUTFALL MONITORING OVERVIEW 18 
Table 2-3. Monitoring plan parameters for effluent 
Parameter Sample Type Frequency
Total Kjeldahl nitrogen Composite Weekly
Ammonium Composite Weekly
Nitrate Composite Weekly
Nitrite Composite Weekly
Total phosphorus Composite Weekly
Total phosphate Composite Weekly
Acid base neutrals Composite Bimonthly
Volatile organic compounds Grab Bimonthly
Cadmium 24-hour composite Weekly
Copper 24-hour composite Weekly
Chromium 24-hour composite Weekly
Mercury 24-hour composite Weekly
Lead 24-hour composite Weekly
Molybdenum 24-hour composite Weekly
Nickel 24-hour composite Weekly
Silver 24-hour composite Weekly
Zinc 24-hour composite Weekly
17 chlorinated pesticides 24-hour composite Weekly
Extended list of PAHs 24-hour composite Weekly
20 PCB congeners 24-hour composite Weekly 
Results 
Average daily flow to the Deer Island Treatment Plant in 2005 was higher
than any year since 1996 (Figure 2-1). Approximately 93% of the flow
received secondary treatment, with a higher degree of secondary treatment
as the year progressed, a result of studies designed to maximize flow
through secondary treatment. 
MWRA Primary and Secondary Flows 1990-2005
0
50
100
150
200
250
300
350
400
450
90 91 92 93 94 95 96 97 98 99 00 01 02 03 04 05
Million Gallons per Day
Primary-treated Flows Secondary-treated Flows 
Figure 2-1. Annual effluent flows, 1990-2005

2005 OUTFALL MONITORING OVERVIEW 19 
Solids discharges decreased slightly to the lowest level recorded in the
monitoring program, while nitrogen discharges remained about the same
as 2004 (Figure 2-2). Some metals loads were slightly lower (Figure 2-3,
top). There was a decrease in load of total PAHs from 2.1 pounds per day
in 2004 to 1.5 pounds per day in 2005 (not shown). 
Solids in MWRA Treatment Plant Discharges 1988-2005
0
20
40
60
80
100
120
140
160
180
88 89 90 91 92 93 94 95 96 97 98 99 00 01 02 03 04 05
Tons per Day
Deer Island Nut Island Sludge 
Deer Island Treatment Plant Nitrogen Discharges 1996-2005
0
2000
4000
6000
8000
10000
12000
14000
1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 
*M ethod change for TKN April 2003 
Metric Tons per Year
Ammonium Nitrite/Nitrate Other Nitrogen Species* Caution Level 
Figure 2-2. Annual solids (top) and nitrogen (bottom) discharges

2005 OUTFALL MONITORING OVERVIEW 20 
Metals in MWRA Treatment Plant Discharges 1989-
2005
0
200
400
600
800
1000
1200
89 90 91 92 93 94 95 96 97 98 99 00 01 02 03 04 05
Year
Average pounds per day discharged Silver
Nickel
Chromium
Lead
Copper
Zinc 
Figure 2-3. Annual metals discharges 
Additional benefits can be expected from completion of the digested
sludge pipeline that runs under the harbor from the Deer Island Treatment
Plant to the Fore River sludge-to-fertilizer pelletizing plant. Prior to
completion of the pipeline, sludge had to be thickened at Deer Island
before being barged to the pelletizing plant. The nutrient-rich water
remaining after thickening, called centrate, was added to the influent at
irregular intervals. In addition, nutrient-rich centrate from the pelletizing
plant was returned to Deer Island by barge and added to the influent in
batches. Thus, the biological secondary process had to deal with relatively
large fluctuations in nutrients. Since the pipeline was completed in 2005,
liquid sludge is pumped to Fore River through the pipeline, and all
centrifuging occurs at the pelletizing plant. The resulting centrate is
returned to Deer Island via the tunnel as a more steady stream. This has
had a stabilizing effect on the biological process and enabled more
efficient operation.

2005 OUTFALL MONITORING OVERVIEW 21
Contingency Plan Thresholds 
The Deer Island Treatment Plant had one permit violation during 2005
(Table 2-4). The Contingency Plan requires that four tests for effluent
toxicity be conducted each month. One of the tests, the sea urchin chronic
fertilization test, did not meet the Contingency Plan warning threshold for
a sample collected on September 15. Effluent from the sample did meet
the requirements of other toxicity tests, all other permit requirements were
met, and there were no operational upsets that would have caused any
violations of permit conditions.
MWRA is currently completing a special study of trace contaminants,
including metals, pesticides, PCBs, and PAHs. Those results are
presented in Section 6, Special Studies. 
Table 2-4. Contingency Plan threshold values and 2005 results for effluent monitoring 
Parameter Caution Level Warning Level 2005 Results
pH None <6 or >9 Not exceeded
Fecal coliform bacteria None
14,000 fecal coliforms/100
ml (monthly 90 th percentile,
weekly geometric mean,
maximum daily geometric
mean, and minimum of 3
consecutive samples)
Not exceeded
Chlorine, residual None 631 ug/l daily,
456 ug/l monthly Not exceeded
Total suspended solids None 45 mg/l weekly
30 mg/l monthly Not exceeded
cBOD None 40 mg/l weekly,
25 mg/l monthly Not exceeded
Toxicity None
Acute: effluent LC50<50%
for shrimp and fish
Chronic: effluent NOEC for
fish survival and growth and
sea urchin fertilization
<1.5% effluent
One exceedance of sea
urchin fertilization test in
September
PCBs Aroclor=0.045 ng/l Not exceeded
Plant performance 5 violations/year Noncompliance >5% of the
time Not exceeded
Flow None Flow >436 for annual
average of dry days Not exceeded
Total nitrogen load 12,500 mtons/year 14,000 mtons/year Not exceeded
Floatables Threshold pending
Oil and grease None 15 mg/l weekly Not exceeded

2005 OUTFALL MONITORING OVERVIEW 22
3. Water Column
Background
Circulation and Water Properties 
Circulation, water properties, and consequently, the biology of
Massachusetts and Cape Cod bays are driven by the larger pattern of water
flow in the Gulf of Maine (Figure 3-1) and by regional and local winds.
A coastal current flows southwestward along the Maine and New
Hampshire coasts; it may enter the bays by Cape Ann to the north of
Boston. This current drives an average counterclockwise circulation in
Massachusetts Bay and (sometimes) Cape Cod Bay. Water flows back out
of the bays to the north of Race Point at the tip of Cape Cod. Whether the
coastal current enters the bays and whether it continues south into Cape
Cod Bay depends on the strength of the current and the direction and
speed of the wind. Because the coastal current is strongest during the
spring period of high runoff from rivers and streams, the spring circulation
pattern is more consistent than that of the summer and fall (Geyer et al. 
1992, Jiang et al. 2006).
During the summer and fall, freshwater inflow is less, and so the wind and
water density interact in a different, more complex way, with alternating
periods of upwelling and downwelling in various locations, depending
primarily on the wind direction and strength (Lermusiaux 2001). Water
flow is variable, as the weather patterns change from week to week. Flow
at any particular time depends on the wind speed and direction relative to
the topography of the sea floor. At times, flow can “reverse,” with flow
northward along the coast. Transient gyres in Massachusetts and Cape
Cod bays spin in either direction.
As in many coastal waters, during the winter the water is well-mixed from
top to bottom, and nutrient levels are high. As light levels increase in the
early spring, phytoplankton populations often begin a period of rapid
growth known as a spring bloom. Contrary to popular wisdom, however,
strong spring blooms do not occur every year. During the years in which
they occur, spring blooms begin in the shallowest waters of Cape Cod
Bay. Blooms in the deeper Massachusetts Bay waters follow two to three
weeks later. Spring phytoplankton blooms are typically followed by an
increase in zooplankton abundance. These zooplankton populations are
food for many animals, including the endangered right whale.

2005 OUTFALL MONITORING OVERVIEW 23 
Figure 3-1. (a) General circulation within Massachusetts Bay. Reprinted from
Journal of Marine Systems, Vol. 29, Author: PFJ Lermusiaux, "Evolving the
subspace of the three-dimensional multiscale ocean variability: Massachusetts
Bay", pp 385-422 © 2001 with permission from Elsevier. (b) General circulation
within the Gulf of Maine (from Beardsley et al. 1997). 
(b)

2005 OUTFALL MONITORING OVERVIEW 24 
Later in the spring, the surface waters warm, and the water column
stratifies. Inputs of freshwater from rivers contribute to the stratification,
with lighter, less saline water remaining at the surface. Stratification
effectively separates the surface and bottom waters, preventing
replenishment of nutrients to the surface and oxygen to the bottom.
Phytoplankton in the surface waters deplete the available nutrients and
then undergo senescence, sinking through the pycnocline to the bottom.
While oxygen levels remain high in the surface waters throughout the
year, levels fall in the bottom waters, as bottom-dwelling animals respire,
and bacteria use up oxygen as the phytoplankton decompose. Bottom-
water oxygen levels are typically lowest during the late summer or early
fall.
Cooling surface waters and strong winds during the autumn months
promote mixing of the water column. Oxygen is replenished in the bottom
waters, and nutrients brought to the surface can stimulate a fall
phytoplankton bloom. Similar to the spring, varying meteorological and
oceanographic conditions greatly influence the timing, magnitude, and
spatial extents of the blooms, and fall blooms do not always occur. When
they do occur, the fall blooms typically end in the early winter, when
declining light levels limit photosynthesis. Plankton die and decay,
replenishing nutrients in the water column. 
Environmental Concerns 
Water-column monitoring questions focus on the possible effects of
nutrients, organic matter, pathogens, and floatable debris from wastewater
on the water quality of Massachusetts Bay (MWRA 1991, Table 3-1).
Due to source reduction and treatment, toxic contaminants discharged in
the MWRA effluent are so low in concentrations that it is impractical to
measure them in the water column. Because organic material, pathogens,
and floatables are effectively removed by treatment at the Deer Island
plant, but nutrients are not, nutrient issues cause the greatest concern.
The monitoring program looks extensively at possible effects of
discharging nutrient-rich effluent into Massachusetts Bay. One concern is
that excess nutrients, particularly nitrogen, could over-stimulate algal
blooms, which would be followed by low levels of dissolved oxygen in
the bottom waters when the phytoplankton organisms die, sink, and
decompose. Another concern is that changes in the relative levels of
nutrients could stimulate growth of undesirable algae. Three nuisance or
noxious species or species groups are of particular concern: the
dinoflagellate Alexandrium fundyense ( A. fundyense and A. tamarense are
now considered to be varieties of the same species), the diatom Pseudo-
nitzschia multiseries , and the colonial flagellate Phaeocystis pouchetii . 
Alexandrium fundyense blooms are known in New England as red tides.

2005 OUTFALL MONITORING OVERVIEW 25 
Table 3-1. Monitoring questions related to the water column 
Is it safe to eat fish and shellfish? 
Will pathogens in the effluent be transported to shellfishing areas where they could
accumulate in the edible tissues of shellfish and contribute to human health
problems? 
ƒ Are pathogens transported to shellfish beds at levels that might affect
shellfish consumer health? 
Are natural/living resources protected? 
Will nutrient enrichment in the water column contribute to an increase in primary
production?
Will nutrient enrichment in the water column contribute to changes in plankton
community structure? 
ƒ Have nutrient concentrations changed in the water near the outfall; have
they changed at farfield stations in Massachusetts Bay or Cape Cod Bay,
and, if so, are they correlated with changes in the nearfield? 
ƒ Has the phytoplankton biomass changed in the vicinity of the outfall or at
selected farfield stations in Massachusetts Bay or Cape Cod Bay, and, if so,
can changes be correlated with effluent or ambient water nutrient
concentrations, or can farfield changes be correlated with nearfield
changes? 
ƒ Have the phytoplankton production rates changed in the vicinity of the outfall
or at selected farfield stations, and, if so, can these changes be correlated
with effluent or ambient water nutrient concentrations, or can farfield
changes be correlated with nearfield changes? 
ƒ Has the abundance of nuisance or noxious phytoplankton species changed
in the vicinity of the outfall? 
ƒ Has the species composition of phytoplankton or zooplankton changed in
the vicinity of the outfall or at selected farfield stations in Massachusetts Bay
or Cape Cod Bay? If so, can these changes be correlated with effluent or
ambient water nutrient concentrations, or can farfield changes be correlated
with nearfield changes? 
Will increased water-column and benthic respiration contribute to depressed oxygen
levels in the water? 
ƒ Do the concentrations (or percent saturation) of dissolved oxygen in the
vicinity of the outfall and at selected farfield stations meet the state water
quality standard? 
ƒ Have the concentrations (or percent saturation) of dissolved oxygen in the
vicinity of the outfall or at selected farfield stations in Massachusetts Bay or
Cape Cod Bay changed relative to pre-discharge baseline or a reference
area? If so, can changes correlated with effluent or ambient water nutrient
concentrations, or can farfield changes be correlated with nearfield
changes? 
Is it safe to swim? 
Will pathogens in the effluent be transported to waters near swimming beaches,
contributing to human health problems? 
ƒ Are pathogens transported to beaches at levels that might affect swimmer
health? 
Are aesthetics being maintained? 
Will changes in water clarity and/or color result from the direct input of effluent
particles or other colored constituents, or indirectly through nutrient stimulation of
nuisance plankton species?
Will the loading of floatable debris increase, contributing to visible degradation? 
ƒ Has the clarity and/or color of the water around the outfall changed? 
ƒ Has the amount of floatable debris around the outfall changed? 
Information on transport and fate necessary to answer all the questions 
ƒ Are model estimates of short-term (less than 1 day) effluent dilution and
transport accurate? 
ƒ What are the nearfield and farfield water circulation patterns? 
ƒ What is the farfield fate of dissolved, conservative, or long-lived effluent
constituents?

2005 OUTFALL MONITORING OVERVIEW 26 
They produce a toxin, which when sufficiently concentrated, causes
paralytic shellfish poisoning (PSP), a condition that can be fatal to marine
mammals, fish, and humans. At high concentrations (more than 1 million
cells per liter), some diatoms in the genus Pseudo-nitzschia may produce
sufficient quantities of toxic domoic acid to cause a condition known as
amnesic shellfish poisoning, which is marked by gastrointestinal and
neurological symptoms, including dementia. Phaeocystis pouchetii is not
toxic, but individual cells can aggregate in gelatinous colonies that may be
aesthetically displeasing or provide poor food for zooplankton.
Dissolved oxygen concentrations in bottom waters naturally decrease
during the stratified period as part of the natural seasonal pattern. If
discharged nutrients were to stimulate large phytoplankton blooms, the
conditions could lead to lower levels of dissolved oxygen when the cells
sink to the bottom and decay.
Because of the concern that lowered levels of dissolved oxygen could
affect animals in the vicinity of the outfall, it was important during the
baseline-monitoring period to develop an understanding of the natural
fluctuations of oxygen levels within the system. Modeling and
measurements showed that the typical periods of low oxygen in bottom
waters correlate with warmer and saltier bottom waters. Ongoing
monitoring assesses potential diversions from the natural conditions. 
Monitoring Design 
Water-column monitoring includes assessments of water quality,
phytoplankton, and zooplankton in Massachusetts and Cape Cod bays.
Regular monitoring includes four components: nearfield surveys, farfield
surveys, continuous recording, and remote sensing (Table 3-2). Plume-
tracking studies, conducted in 2001, qualitatively verified the expected
dilution at the outfall and confirmed predictions that bacteria and toxic
contaminant concentrations in the discharged effluent are very low.

2005 OUTFALL MONITORING OVERVIEW 27 
Table 3-2. Components of water-column monitoring 
Task Objective
Nearfield surveys Collect water quality data near the outfall
Farfield surveys Collect water quality data throughout Massachusetts
and Cape Cod bays
Moorings (GoMOOS
and USGS)
GoMOOS near Cape Ann and USGS near outfall
provide continuous oceanographic data near outfall
location
Remote sensing Provides oceanographic data on a regional scale
through satellite imagery 
Nearfield surveys provide vertical and horizontal profiles of physical,
chemical, and biological characteristics of the water column in the area
around the outfall where some effects of the effluent are expected and
have been observed. Farfield surveys assess differences across the bays
and seasonal changes over a large area. Several farfield stations mark the
boundary of the monitoring area and are in or near the Stellwagen Bank
National Marine Sanctuary. Two of those stations denote the “northern
boundary,” representing water entering Massachusetts Bay from the Gulf
of Maine. Other stations are in Boston Harbor, coastal and offshore
regions, and in Cape Cod Bay (Figure 3-2). Twelve surveys of seven
nearfield stations and six surveys of 25 farfield stations were conducted in
2005, with two additional stations sampled in February and April.
Parameters measured are listed in Tables 3-3 and 3-4. Parameters
measured in the water column include dissolved inorganic and organic
nutrients, particulate forms of nutrients, chlorophyll, total suspended
solids, dissolved oxygen, productivity, respiration, phytoplankton
abundance and species composition, and zooplankton abundance and
species composition. Nutrients measured include the major forms of
nitrogen, phosphorus, and silica. The measurements focus on the
dissolved inorganic forms, which are most readily used by phytoplankton.
The surveys also include observations and net tows in the outfall area to
assess the presence of floatable debris.
The continuous recording components of the program, the U.S. Geological
Survey (USGS) and Gulf of Maine Ocean Observing System (GoMOOS)
moorings, capture temporal variations in water quality between nearfield
surveys. Remote sensing by satellite captures spatial variations in water
quality on a larger, regional scale.

2005 OUTFALL MONITORING OVERVIEW 28 
Figure 3-2. Water-column sampling stations and regions

2005 OUTFALL MONITORING OVERVIEW 29 
Table 3-3. Nearfield water-column monitoring parameters 
Parameter Measurement details
Temperature
Salinity
Dissolved oxygen
Chlorophyll fluorescence
Transmissometry
Irradiance
Depth of sensors
In-situ sensor measurements
Boat surveys of seven stations
Every half meter depth
Ammonium
Nitrate
Nitrite
Phosphate
Silicate
Inorganic nutrients sampling
Seven stations
Five depths
Dissolved inorganic carbon
Dissolved nitrogen
Dissolved phosphorus
Particulate carbon
Particulate nitrogen
Particulate phosphorus
Particulate biogenic silica
Total suspended solids
Additional nutrients sampling
Seven stations
Three depths
Primary productivity
Respiration
Phytoplankton
Zooplankton
Rates and plankton sampling
Two stations
Variable depths
Floatables Net tows 
Table 3-4. Farfield water-column monitoring parameters 
Parameter Measurement details
Temperature
Salinity
Dissolved oxygen
Chlorophyll fluorescence
Transmissometry
Irradiance
Depth of sensors
In-situ sensor measurements
Boat surveys of 25 stations
Every half meter depth
Ammonium
Nitrate
Nitrite
Phosphate
Silicate
Inorganic nutrients sampling
23 stations at five depths
Two shallow stations at three depths
Dissolved inorganic carbon
Dissolved nitrogen
Dissolved phosphorus
Particulate carbon
Particulate nitrogen
Particulate phosphorus
Particulate biogenic silica
Total suspended solids
Phytoplankton
Zooplankton
Additional nutrients and plankton sampling
Ten stations
Variable depths
Primary productivity Rates sampling
One station
Five depths
Respiration Rates sampling
Two stations
Three depths

2005 OUTFALL MONITORING OVERVIEW 30 
Results
Physical Conditions 
The Massachusetts Bay region was wetter in 2005 than in many other
years, particularly during the late spring and late fall. There were three
significant storms during April through June and unusually wet conditions
in October (Libby et al. 2006a). Flow of the Merrimack River in the late
spring was the greatest measured throughout the duration of the
monitoring program, a direct result of the storms and also the result of
accelerated melting of a deeper-than-average winter snowpack. Similarly,
flow through the Charles River was higher than average (Figures 3-3, 3-4). 
Figure 3-3. Charles River discharge, 1992-early 2006 (data from a gauge at Waltham
and 3-month moving average) 
Figure 3-4. 2005 Charles River discharge compared to observations since 1992

2005 OUTFALL MONITORING OVERVIEW 31 
May 2005 was particularly unusual. In most years, May is a transitional
period between winter downwelling and summer upwelling conditions. In
2005, two large storms with winds from the northeast resulted in
continued downwelling and wave heights greater than five meters, the
roughest May conditions observed throughout the monitoring program.
Figure 3-5 shows annual surface and bottom water temperatures in the
outfall nearfield since 1992. In 2005, winter air and water temperatures
were average, but May was unusually cold, another consequence of the
storms from the northeast. The May near-surface water temperature near
the outfall was the coldest measured during the monitoring program
(Figure 3-6). At the same time, bottom temperatures warmed, as the
warmer surface waters mixed into the bottom waters during the storms.
Usually, stratified conditions are established by May, but the storms broke
down the stratification. Similarly, a late October storm broke down the
summer stratified conditions, warming the bottom waters and cooling the
surface waters. This breakdown of stratified conditions usually occurs
later in the season. 
Figure 3-5. Nearfield surface and bottom water temperature (Surface measurements are
the upper line.)

2005 OUTFALL MONITORING OVERVIEW 32 
Figure 3-6. Hourly near-surface temperature for 2005 superimposed on the data from
1989-2004 
In response to the runoff from the spring storms, salinities reached low
levels, particularly in the bottom waters (Figure 3-7). Spring bottom-
water salinities were among the lowest measured for the monitoring
program. 
Figure 3-7. Nearfield surface and bottom water salinity (Surface measurements are the
lower line.)

2005 OUTFALL MONITORING OVERVIEW 33
Water Quality 
As in every year since the Massachusetts Bay outfall began operation,
water quality measurements in 2005 continued to confirm predictions that
it would be possible to detect localized effects of the discharge for some
parameters, but that there would be no adverse effects on the farfield
(Libby et al. 2006a). Trends in water quality parameters, including
nutrients, phytoplankton biomass, and dissolved oxygen were generally
similar to previous years. However, there were some differences in the
timing and magnitude of events.
Ammonium is the form of nitrogen most readily taken up by
phytoplankton, and localized, elevated concentrations have been observed
in the nearfield since the outfall began operation (Figure 3-8). These
elevated levels had been anticipated, because a large portion of the
dissolved inorganic nitrogen in treated effluent is ammonium.
In 2005, there was some difference from the anticipated pattern. As
expected, nearfield ammonium concentrations in early February were
higher than the baseline range. However, by late February, concentrations
dropped to less than the baseline mean, the result of nutrient uptake during
the spring phytoplankton bloom. In mid May, concentrations of
ammonium in the nearfield were 0.3 μM below the baseline range.
Consequently, the annual average concentration of ammonium in the
nearfield was the lowest measured since outfall diversion and not
significantly different from the baseline period (Figure 3-9). These low
levels were probably due to dilution caused by the stormy conditions that
were prevalent during the year. The concentrations of ammonium in
Boston Harbor, which had dropped dramatically following effluent
diversion to Massachusetts Bay, remained low. Ammonium
concentrations in the other regions were the lowest measured in nearly ten
years.

2005 OUTFALL MONITORING OVERVIEW 34 
0
2
4
6
8
10
12
14
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
NH4 ( μ M)
Baseline Mean
Post Transfer Mean 
Figure 3-8. Post-transfer nearfield ammonium concentrations compared to
baseline (Error bars represent one standard deviation.) 
0
2
4
6
8
10
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
NH4 ( μ M)
Boston Harbor Nearfield N. Boundary Cape Cod Coastal Offshore 
Figure 3-9. Annual mean ammonium concentrations in Massachusetts Bay
regions 
Concentrations of nitrate, another form of nitrogen readily used by
phytoplankton and present in the effluent, continued to fall within the
baseline range for most surveys and showed the same seasonal pattern as
seen in baseline monitoring (Figure 3-10), and there have been no changes
in the variable regional pattern (Figure 3-11). Nitrate concentrations in the

2005 OUTFALL MONITORING OVERVIEW 35 
nearfield were slightly elevated above the baseline range during one fall
survey, as stratification broke down during the earlier-than-usual October
storm, and nutrients from the bottom waters mixed throughout the water
column. 
0
2
4
6
8
10
12
14
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
NO3 ( μ M)
Baseline Mean
Post Transfer Mean 
Figure 3-10. Post-transfer nearfield nitrate concentrations compared to baseline
(Error bars represent one standard deviation.) 
0
2
4
6
8
10
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
NO3 ( μ M)
Nearfield Boston Harbor N. Boundary Cape Cod Coastal Offshore 
Figure 3-11. Annual mean nitrate concentrations in Massachusetts Bay regions

2005 OUTFALL MONITORING OVERVIEW 36 
Phytoplankton biomass, as measured by chlorophyll and particulate
organic carbon, showed similar trends as in previous years. Chlorophyll
(mg per square meter) has shown no systematic response to nutrient
enrichment of the outfall (Figure 3-12), although the data are marked by
large variability in timing and magnitude of spring and fall peaks.
Concentrations during the winter and spring of 2005 were in the upper end
of the baseline range, and concentrations in the late spring and summer
were close to the baseline mean. The annual average was at the low end
of the baseline range, reflecting a lack of a fall bloom in 2005. Nearfield
concentrations of particulate organic matter generally followed the
baseline means and trends. 
0
50
100
150
200
250
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Chlorophyll (mg m -2 )
Baseline Mean
Post Transfer Mean 
Figure 3-12. Post-transfer nearfield chlorophyll compared to baseline (Error
bars represent one standard deviation.) 
Measurements of concentrations (Figure 3-13) and percent saturation (not
shown) of dissolved oxygen in the bottom waters have shown no response
to nutrient enrichment or addition of organic matter from the outfall. As
in other post-baseline years, the seasonal cycle of higher concentrations
during the winter and spring and lower concentrations in the summer and
fall, returning to higher concentrations following a fall overturn continued.
Like 2004, near-bottom oxygen concentrations in the fall were higher than
average, a result of strong mixing during the October storm.

2005 OUTFALL MONITORING OVERVIEW 37 
6
7
8
9
10
11
12
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
DO (mg L -1 )
Baseline Mean
Post Transfer Mean 
Figure 3-13. Post-transfer nearfield dissolved oxygen concentrations compared
to baseline (Error bars represent one standard deviation.) 
Phytoplankton Communities 
Seasonal abundance of phytoplankton in the post-outfall diversion years
has remained similar to the baseline mean for most survey dates (Libby et
al. 2006a; Figure 3-14), and the taxonomic composition of the
phytoplankton community has been relatively consistent. The year was
marked, however, by an April bloom of the nuisance species Phaeocystis
pouchetii and by a major May and June bloom of toxic dinoflagellates in
the genus Alexandrium , producing the largest red tide in New England
since 1972.
The usual species assemblage in Massachusetts Bay includes small
microflagellates and cryptomonads, which are numerically dominant
throughout the year, peaking in abundance during the warm summer
months. Diatoms are usually abundant during the winter, spring, and fall.
In some years, there are major blooms of a single species, such as 
Asterionellopsis glacialis in the fall or Phaeocystis pouchetii in the spring.
The blooms tend to occur on broad regional scales, and the reasons they
occur are not well understood.

2005 OUTFALL MONITORING OVERVIEW 38 
0
1
2
3
4
5
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
10 6 cells L -1
Baseline Mean
Post Transfer Mean 
Figure 3-14. Post-transfer nearfield phytoplankton abundance compared to
baseline (Error bars represent one standard deviation.) 
The most pronounced change in the phytoplankton community over the
course of the monitoring program has been an increase in the frequency of 
Phaeocystis pouchetii blooms (Figure 3-15). During the baseline period,
there were spring Phaeocystis blooms approximately every three years, in
1992, 1994 (only recorded in the farfield), 1997, and 2000. Since the
outfall began operation, the blooms have occurred annually and have
increased in duration. In earlier years, Phaeocystis blooms occurred
primarily in late March and April. Since 2002, they have begun earlier in
March persisted until early May.
Reasons for the increases in occurrence and duration remain unknown.
Because the Phaeocystis blooms occurred over such a broad geographic
area, it is unlikely that the outfall is a cause. The blooms have occurred
well beyond the boundaries of Massachusetts and Cape Cod bays, and
there have been no obvious spatial associations with the outfall. A
detailed discussion of the blooms will be presented in a review of issues
related to nutrients in the region, currently in preparation.
In May and June, a large bloom of toxic dinoflagellates in the genus 
Alexandrium occurred (Figure 3-16), the largest since 1972. The bloom
extended from Maine to south of Cape Cod and Martha’s Vineyard.
Concentrations of cells were orders-of-magnitude higher than in previous
years. It is now understood that a high abundance of Alexandrium cysts
in the western Gulf of Maine sediments was the main cause of the bloom.
Wind conditions, particularly the northeast storms that occurred in May,

2005 OUTFALL MONITORING OVERVIEW 39 
accelerated flow along the coast and into Massachusetts Bay, contributing
to the timing of the bloom, however even without the northeast winds, a
major red tide would have occurred. The bloom is discussed further in
Section 6, Special Studies. 
Phaeocystis
0
2
4
6
8
10
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
Abundance (millions of cells L
-1 ) Outfall Startup 
Figure 3-15. Abundance of Phaeocystis pouchetii in the nearfield, 1992-2005 
Alexandrium
1
10
100
1,000
10,000
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
Abundance (cells L -1 ) 
Figure 3-16. Abundance of Alexandrium species in the nearfield, 1992-2005

2005 OUTFALL MONITORING OVERVIEW 40 
Zooplankton Communities 
The structure of the zooplankton community in 2005 was similar to many
earlier years and continued to show no effects of the outfall (Libby et al. 
2006a). Abundance was dominated by copepod nauplii and copepodites
and adults of the small copepods Oithona similis and Pseudocalanus spp.
Other, less dominant, copepods typically include Calanus finmarchicus , 
Paracalanus parvus , Centropages typicus , and C. hamatus . The
planktonic early life stages of bivalves, gastropods, barnacles, and
polychaetes occur in sporadic pulses.
There has, however, been a measurable decrease in total zooplankton
abundance during 2001 through 2005 in comparison to the baseline period
(Figure 3-17). Total abundance has been lower during the late spring and
early summer and during the fall. 
0
25,000
50,000
75,000
100,000
125,000
150,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Animals m -3
Baseline Mean
Post Transfer Mean 
Figure 3-17. Post-transfer nearfield zooplankton abundance compared to
baseline (Error bars represent one standard deviation.) 
Similar decreases have been observed across Massachusetts Bay,
including the northern boundary to the Gulf of Maine, the offshore, and
the coastal stations, but not in the shallower, more inshore waters of
Boston Harbor or Cape Cod Bay (Figure 3-18). This difference is not
surprising: circulation modeling has found that Cape Cod Bay is generally
isolated from Massachusetts Bay during the summer stratified season
(Geyer et al. 1992, Lermusiaux 2001, Jiang et al. 2006).

2005 OUTFALL MONITORING OVERVIEW 41 
Boundary (F27)
0
25,000
50,000
75,000
100,000
125,000
150,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Animals m -3
Baseline Mean
Post Transfer Mean 
Boston Harbor
0
25,000
50,000
75,000
100,000
125,000
150,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Animals m -3
Baseline Mean
Post Transfer Mean 
Nearfield
0
25,000
50,000
75,000
100,000
125,000
150,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Animals m -3
Baseline Mean
Post Transfer Mean 
Coastal
0
25,000
50,000
75,000
100,000
125,000
150,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Animals m -3
Baseline Mean
Post Transfer Mean 
Offshore (F06)
0
25,000
50,000
75,000
100,000
125,000
150,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Animals m -3
Baseline Mean
Post Transfer Mean 
Cape Cod Bay
0
25,000
50,000
75,000
100,000
125,000
150,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Animals m -3
Baseline Mean
Post Transfer Mean 
Boundary (F27)
0
25,000
50,000
75,000
100,000
125,000
150,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Animals m -3
Baseline Mean
Post Transfer Mean 
Boston Harbor
0
25,000
50,000
75,000
100,000
125,000
150,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Animals m -3
Baseline Mean
Post Transfer Mean 
Nearfield
0
25,000
50,000
75,000
100,000
125,000
150,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Animals m -3
Baseline Mean
Post Transfer Mean 
Coastal
0
25,000
50,000
75,000
100,000
125,000
150,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Animals m -3
Baseline Mean
Post Transfer Mean 
Offshore (F06)
0
25,000
50,000
75,000
100,000
125,000
150,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Animals m -3
Baseline Mean
Post Transfer Mean 
Cape Cod Bay
0
25,000
50,000
75,000
100,000
125,000
150,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Animals m -3
Baseline Mean
Post Transfer Mean 
Figure 3-18. Total zooplankton abundance by region. The placement of the individual figures
approximates their geographic positions; for example, the Boundary station is farthest to the
north and east, and the Cape Cod Bay stations are farthest to the south.

2005 OUTFALL MONITORING OVERVIEW 42 
Analysis of nearfield data has suggested that the low mean abundance
during the late spring and summer can be attributed to low abundance of
the small, dominant, Oithona similis ; abundance of other species, such as
the larger Calanus finmarchicus , a forage species for right whales, has
remained at or above the baseline mean. The decline may be due to
normal, large variability, but may also be a response to the consecutive 
Phaeocystis pouchetii blooms that have occurred throughout
Massachusetts Bay. Some investigators have suggested that Phaeocystis 
is unpalatable to certain animals, such as right whales, but the effects on
various zooplankton species are poorly understood. Regression analysis
indicates that there is decreased abundance of Oithona but increased
abundance of Calanus finmarchicus with increases in Phaeocystis 
abundance.
The mean decrease in total zooplankton abundance during the fall months
may have resulted from the lack of substantial fall phytoplankton blooms,
and in some years, may also be a response to late summer and fall blooms
of the ctenophore Mnemiopsis leidyi , a zooplankton predator, which first
appeared in the region in October 2000. Subsequent Mnemiopsis blooms,
when they have occurred, have spanned geographically large areas,
beginning in August and persisting until November. 
Contingency Plan Thresholds 
Threshold parameters for water-column monitoring include minimum
dissolved oxygen concentrations and percent saturation in nearfield and
Stellwagen Bank bottom waters, dissolved oxygen depletion rate in
nearfield bottom waters, chlorophyll levels, abundance of nuisance algal
species, geographic extent of PSP toxin, and initial dilution.
There were two exceedances of thresholds in 2005—the summer 
Phaeocystis threshold and the Alexandrium threshold. The summer 
Phaeocystis threshold has been exceeded each year since 2001, due to the
extended duration of the blooms that have occurred in recent years and to
the extremely low summer threshold. The Alexandrium threshold of 100
cells per liter was exceeded during the red tide, with more than 10,000
cells per liter measured during a regular nearfield survey and more than
36,000 cells per liter being measured during a rapid-response Alexandrium 
full (AF) survey undertaken in response to the bloom. The threshold for
PSP toxin extent was not exceeded, because the spatio-temporal pattern of
the red tide was consistent with past blooms, beginning in the north and
progressing to the south. All other monitoring results were within ranges
that met the thresholds.

2005 OUTFALL MONITORING OVERVIEW 43 
Table 3-5. Contingency plan threshold values and 2005 results for water-column monitoring 
Location/
Parameter
Specific
Parameter Baseline Caution Level Warning
Level
2005
Results
Dissolved
oxygen
concentration
Background 5 th
percentile
5.75 mg/l
Lower than 6.5
mg/l for any
survey (June-
October) unless
background
conditions are
lower
Lower than 6.0
mg/l for any
survey (June-
October) unless
background
conditions are
lower
Lowest survey
mean = 7.98 mg/l
Bottom water
nearfield
Dissolved
oxygen percent
saturation
Background 5 th
percentile
64.3%
Lower than 80%
for any survey
(June-October)
unless
background
conditions are
lower
Lower than 75%
for any survey
(June-October)
unless
background
conditions are
lower
Lowest survey
mean = 80.7%
Dissolved
oxygen
concentration
Background 5 th
percentile
6.2 mg/l
6.5 mg/l for any
survey (June-
October) unless
background
conditions lower
Lower than 6.0
mg/l for any
survey (June-
October) unless
background
conditions are
lower
Lowest survey
mean =
7.6 mg/l
Bottom water
Stellwagen
Basin
Dissolved
oxygen percent
saturation
Background 5 th
percentile
66.3%
Lower than 80%
for any survey
(June-October)
unless
background
conditions
Lower than 75%
for any survey
(June-October)
unless
background
conditions are
lower
Lowest survey
mean = 76.5%
Bottom water
nearfield
DO depletion
rate (June-
October)
0.024 mg/l/d 0.037 mg/l/d 0.049 mg/l/d 0.013 mg/l/d
Annual 79 mg/m 2 118 mg/m 2 158 mg/m 2 79.22 mg/m 2
Winter/spring 62 mgml 2 238 mg/m 2 None 133 mg/m 2
Summer 51 mg/m 2 93 mg/m 2 None 61.2 mg/m 2
Chlorophyll
nearfield
Autumn 97 mg/m 2 212 mg/m 2 None 43 mg/m 2
Winter/spring 468,000 cells/l 2,020,000 cells/l None 438,481
cells/l
Summer 72 cells/l 357 cells/l None 517 cells/l, caution
exceedance
Nuisance
algae
nearfield 
Phaeocystis
pouchetii Autumn 317 cells/l 2,540 cells/l None 0 cells/l
Winter/spring 6,200 cells/l 21,000 cells/l None 147 cells/l
Summer 14,600 cells/l 43,100 cells/l None 3,317 cells/l
Nuisance
algae
nearfield 
Pseudo-
nitzschia 
Autumn 9,940 cells/l 24,700 cells/l None 45 cells/l
Nuisance
algae
nearfield 
Alexandrium
fundyense 
Any nearfield
sample
Baseline
maximum =
163 cells/l
100 cells/l None
10,919 cells/l (NF
surveys); 36,830
(AF surveys),
caution
exceedance
Farfield PSP toxin
extent Not applicable New incidence None
Closures from
Maine to south of
Cape Cod

2005 OUTFALL MONITORING OVERVIEW 44
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
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 outfall is marked by
underwater drumlins, which are elongated hills about 10 meters high, with
crests covered by gravel and boulders. Long-term sinks for fine-grained
sediments include Boston Harbor, Cape Cod Bay, and Stellwagen Basin.
Long-term monitoring and modeling have confirmed that sediment
transport in the region occurs primarily during storms (Butman et al. 
2005). Typically, waves during storms with winds from the northeast
resuspend sediments, which are transported by shallow currents from
western Massachusetts Bay toward Cape Cod Bay and by deeper currents
to Stellwagen Basin. Cape Cod Bay is partially sheltered from large
waves by the arm of Cape Cod, and storm waves are rarely large enough
to resuspend sediments in Stellwagen Basin, which is the deepest feature
in the region. Tidal currents, wind-driven currents, and currents
associated with spring runoff are insufficient to resuspend sediments. 
Environmental Concerns 
Within Boston Harbor, studies of the sediments have documented
recovery following the cessation of sludge and effluent discharges and
other improvements (see Section 7, Boston Harbor Studies). Conversely,
relocating the outfall raised concerns about potential effects on the
offshore sea floor. Concern has focused on three mechanisms of potential
disruption to the animal communities living on the seafloor:
eutrophication and related low levels of dissolved oxygen, accumulation
of toxic contaminants in depositional areas, and smothering (Table 4-1).

2005 OUTFALL MONITORING OVERVIEW 45 
Table 4-1. Monitoring questions related to the sea floor 
Are natural/living resources protected? 
Will benthic enrichment contribute to changes in community structure of soft-bottom
and hard-bottom macrofauna, possibly affecting fisheries?
Will benthic macrofauna near the outfall mixing zone be exposed to some
contaminants, potentially contributing to changes in the community?
Will the benthos near the outfall mixing zone and in depositional areas farther away
accumulate some contaminants? 
ƒ What is the level of sewage contamination and its spatial distribution in
Massachusetts and Cape Cod bays sediments before discharge through the
new outfall? 
ƒ Has the level of sewage contamination or its spatial distribution in
Massachusetts or Cape Cod bays sediments changed after discharge
through the new outfall? 
ƒ Have the concentrations of contaminants in sediments changed? 
ƒ Has the soft-bottom community changed? 
ƒ Are any benthic community changes correlated with changes in levels of
toxic contaminants (or sewage tracers) in sediments? 
ƒ Has the hard-bottomed community changed? 
Will increased water-column and benthic respiration contribute to depressed oxygen
levels in the sediment? 
ƒ Have the sediments become more anoxic; that is, has the thickness of the
sediment oxic layer decreased? 
If transfer of the nutrient loads to offshore were to cause eutrophication,
the depressed levels of dissolved oxygen that were also a concern in
water-column monitoring could adversely affect bottom-dwelling animals.
An increase in the amounts of particles and organic matter to the bottom
could disrupt normal benthic community structure in the vicinity of the
discharge. Although source control and treatment plant performance are
designed to keep effluent contaminant concentrations too low to affect the
sediments, the location of the outfall in an area of sediment transport
caused concern about accumulation of toxic contaminants in Cape Cod
Bay and Stellwagen Basin. Similarly, concentrations of particulate matter
were expected to be low, but there remained some concern that bottom
communities near the outfall could be affected by deposition. 
Monitoring Design 
Sea-floor monitoring includes several components: measurements of
sediment characteristics, sewage effluent tracers, and contaminant
concentrations in sediments; sediment-profile imaging to provide a rapid
assessment of benthic communities and sediment quality; studies of
nearfield and farfield soft-bottom communities (sampling sites in Figures
4-1 and 4-2); and study of hard-bottom communities (sampling sites in
Figure 4-3).

2005 OUTFALL MONITORING OVERVIEW 46 
Figure 4-1. Locations of nearfield soft-bottom stations

2005 OUTFALL MONITORING OVERVIEW 47 
Figure 4-2. Locations of farfield soft-bottom stations

2005 OUTFALL MONITORING OVERVIEW 48 
Figure 4-3. Locations of hard-bottom stations

2005 OUTFALL MONITORING OVERVIEW 49 
Measurements of sediment characteristics, tracers, and contaminants
include analyses of grain size, total organic carbon (TOC), Clostridium
perfringens spores, PAHs, PCBs, chlorinated pesticides, and metals.
Sediment-contaminant monitoring has been complemented by special
studies, primarily in association with USGS (Bothner and Butman 2005).
The USGS program is discussed in Section 6, Special Studies.
Sediment-profile image monitoring is conducted each August to give area-
wide assessments of sediment quality and benthic community status. The
sediment-profile images provide more rapid assessments 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 to which oxygen penetrates,
known as the oxidation-reduction (redox) potential discontinuity (RPD).
Later, complete analyses of films provide information on prism
penetration, surface relief, apparent color RPD depth, sediment grain size,
sediment layering, fauna and structures, and successional stage of the soft-
bottom animal communities.
Monitoring the soft-bottom benthic infauna also includes annual surveys
conducted in August. Samples are collected with a 0.04-m 2 Young-Van
Veen benthic grab, sieved on 300-μm mesh, and fixed in formalin in the
field, then transferred to alcohol and stained with Rose Bengal in the
laboratory. Animals are sorted, identified, and counted.
Most pollutant-effect monitoring studies of benthic communities,
including the MWRA monitoring program, focus on the soft-bottom areas
with finer-grained sediments, but such depositional areas are few in the
vicinity of the outfall. Therefore, MWRA also conducts video and
photographic surveys of the hard-bottom habitats found on the tops and
flanks of drumlins in western Massachusetts Bay. Video and still
photographs are taken at a series of stations or waypoints, including
diffuser head #44 of the outfall (which was not opened) and diffuser head
#2. These annual surveys are conducted in June. Photographs are
examined for substrate type (top or flank of the drumlin, with relief
defined by presence of boulders and cobbles), amount of sediment drape
(the degree to which a layer of fine material covers the hard surface), and
biota (taxa identified to species or species groups and counted).
Beginning in 2003 and 2004, the existing 23 nearfield and 8 farfield soft-
bottom stations were split into two subgroups. This division was made
randomly after accounting for regional representation and level of
replication, with two stations (NF12 and NF17, which are also sampled by

2005 OUTFALL MONITORING OVERVIEW 50 
USGS) being included in both groups. The program includes the
following: 
• Sediment characteristics and tracers, such as TOC, sediment grain
size, and Clostridium perfringens spore counts, are sampled in one
subset in alternate years, such that each station is sampled at least
once every two years. 
• Chemical constituents, including PAHs, PCBs, pesticides, and
metals, are measured annually at the two stations included in both
groups and once every three years at stations being sampled for
other parameters, with sampling occurring in 2005. 
• Sediment-profile images for the measurement of RPD depth
continue to be taken at all 23 nearfield stations each year. 
• Benthic infauna is studied at the same stations as are sampled for
sediment characteristics. Species composition and abundance are
assessed for all stations sampled. 
• Hard-bottom monitoring continues as previously, except that two
stations were discontinued and two stations were added in 2003. 
Results
Sediment Characteristics, Tracers, and Contaminants 
Baseline sampling at nearfield stations found that the area around the
outfall was composed of heterogeneous sediments that had received
historic inputs of contaminants from Boston Harbor, the atmosphere, and
other sources. In the nearfield, contaminant concentrations have been
correlated with grain size, with the muddier stations having more organic
carbon and higher concentrations of contaminants.
Sampling and analysis for chemical constituents in 2005 was the most
comprehensive since 2002. At several stations in 2005, sediments were
coarser than they had been in prior years, presumably a result of the spring
northeast storms. Concentrations of total organic carbon at some nearfield
and farfield stations were among the lowest measured in the monitoring
program. For many contaminants, including PCBs, DDT, aluminum,
chromium, iron, nickel, and silver, the concentrations were low in
comparison to other years since the outfall began operation. The decrease
in concentrations of PCBs and DDT may reflect changes in analytic
methods as well as the expected slow declines since PCBs and DDT were
banned in the 1970s and 1980s. Decreases in concentrations of aluminum,
chromium, iron, and nickel reflect the coarsening of the sediments. There
was clear evidence of the discharge in concentrations of the sewage tracer 
Clostridium perfringens spores at stations located within two kilometers of
the outfall, but no widespread detectable accumulation of any
contaminant. Concentrations of Clostridium perfringens spores were

2005 OUTFALL MONITORING OVERVIEW 51 
lower than baseline levels at stations located between the mouth of Boston
Harbor and the outfall and at farfield stations. 
Sediment-Profile Imaging 
Sediment-profile imaging measurements in 2005 showed no changes from
the baseline to the post-baseline period (Maciolek et al. 2006; Figure 4-4).
The mean RPD depth prior to outfall startup was 2.3 cm, while the post-
diversion mean is 2.4 cm. No relationship between RPD depth and outfall
operation has been detected, and no regional trends have appeared during
the years that the outfall has been operating. 
0.0
1.0
2.0
3.0
4.0
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Year
RPD (cm)
Mean RPD Depth +/- 1SD
Outfall Startup
Baseline Mean
Threshold 
Figure 4-4. Apparent color RPD for all data from nearfield stations 
Some sediment-profile images showed evidence of increased physical
processes, probably a result of the 2005 storms. Sediments were coarser,
and there were fewer biological structures, such as worm tubes. These
effects were more obvious in Boston Harbor, where amphipod mats,
which had predominated, were no longer evident. The changes in Boston
Harbor sediments are discussed further in Section 7, Boston Harbor
Studies.

2005 OUTFALL MONITORING OVERVIEW 52
Soft-bottom Communities 
The soft-bottom communities have also shown no response to the outfall
(Maciolek et al. 2006). During the baseline period, multivariate analyses
indicated that sediment grain size was the dominant factor in structuring
the benthic communities. In the nearfield, stations with fine sediments
have been dominated by polychaete worms, such as Prionospio
steenstrupi , Spio limicola , Mediomastus californiensis , and Aricidea
catherinae . Sandier stations have been inhabited by the sand dollar 
Echinarachnius parma , polychaetes Exogenes hebes , E. verugera , 
Spiophanes bombyx , and Owenia fusiformis , and the amphipod 
Crassicorophium crassicorne .
The benthic communities of the farfield have differed from those in the
nearfield, as the farfield stations span a greater depth range, are
geographically widespread, and generally have finer sediments than those
in the nearfield. Polychaete worms, including Eucone incolor , Aricidea
quadrilobata , and Levinsenia gracilus , have predominated at most
stations. Prionospio steenstrupi has also been common at some of the
farfield stations. Another polychaete, Cossura longicirrata , has
dominated at a station in Cape Cod Bay.
The nine years of baseline monitoring provided a broad base for
understanding the potential responses of the benthic communities to the
discharge. During the baseline period, some stations were severely
affected by winter storms, while other, deeper stations exhibited more
stability over time. The years of post-discharge-transfer monitoring have
detected some statistical differences in community parameters, such as
increased numbers and dominance of some species at some stations.
These changes are considered to be natural fluctuations rather than
patterns that can be related to the discharge.
In 2005, mean total abundance fell in both the nearfield (Figure 4-5, top)
and the farfield (not shown). Species richness, measured as total number
of species per sample and an index, log-series alpha, also declined (Figure
4-5, middle and bottom). These changes largely appear to result from
natural cycles.

2005 OUTFALL MONITORING OVERVIEW 53 
Nearfield Abundance
0
1000
2000
3000
4000
5000
6000
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 
Year
Total Abundance per Sample Mean +/-1SD
Baseline Mean: 2242
Outfall Startup 
Nearfield Species Richness
30
40
50
60
70
80
90
100
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 
Year
Species per Sample 
Mean +/-1SD
Baseline Mean: 65
Outfall Startup 
Nearfield Log Series Alpha
4
6
8
10
12
14
16
18
20
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005 
Year
Log-Series Alpha 
Mean +/-1SD
Baseline Mean:13.06
Outfall Startup 
Figure 4-5. Community parameters in the nearfield, 1992-2005: Top:
abundance per sample, Middle: species richness (number species per sample),
Bottom: species richness (log-series alpha)

2005 OUTFALL MONITORING OVERVIEW 54 
Hard-bottom Communities 
Rocky environments in the vicinity of MWRA’s outfall support
communities of algae and invertebrates similar to those found throughout
northern New England. Near the outfall, these environments and the
communities they support are stable from year to year but vary over
relatively short distances, on the scale of tens of meters. The habitat
ranges from large boulders to cobbles to gravel pavements.
Some changes in the hard-bottom communities have been detected since
the outfall began operation, but they have been modest, and it is difficult
to attribute them to outfall operation (Maciolek et al. 2006). Other
changes have occurred throughout the course of the monitoring program,
beginning prior to the outfall start-up. For example, there has been a
slight decrease in the number of upright algae at many stations, but these
decreases began in the 1990s before the outfall went on-line, and the trend
appears to be reversing. Other species, such as Cancer crabs, also appear
to exhibit cycles of abundance. There have been steady increases in the
number of cod throughout the duration of the program (Figure 4-6). 
Figure 4-6. Cod and flounder in a 2005 transect

2005 OUTFALL MONITORING OVERVIEW 55 
There have been increases in the amount of sediment drape and concurrent
decreases in the percent cover of coralline algae at some stations,
including the northernmost reference sites. In 2005, the decline in
coralline algae was more pronounced and extended to additional sites that
did not show any increase in sediment drape. Degree of coralline algae
cover was hypothesized as a possible indicator of outfall effects. The
geographic patterns observed in the declines, which include stations
distant from the outfall, do not suggest that the outfall has been
responsible. 
Contingency Plan Thresholds 
No Contingency Plan thresholds for sea-floor monitoring were exceeded
in 2005 (Table 4-2). RPD depth was deeper than the baseline mean, soft-
bottom community parameters were within normal ranges, and the percent
of the soft-bottom community composed of opportunistic species
remained low.

2005 OUTFALL MONITORING OVERVIEW 56 
Table 4-2. Contingency Plan threshold values and 2005 results for sea-floor monitoring 
Location Parameter Caution Level Warning Level 2005 Results
Acenaphthene None 500 ppb dry 17.72 ppb dry
Acenaphylene None 640 ppb dry 26.88 ppb dry
Anthracene None 1100 ppb dry 92.24 ppb dry
Benzo(a)anthracene None 1600 ppb dry 250.4 ppb dry
Benzo(a)pyrene None 1600 ppb dry 245.39 ppb dry
Cadmium None 9.6 ppm dry 0.14 ppm dry
Chromium None 370 ppm dry 49.08 ppm dry
Chrysene None 2800 ppb dry 221.39 ppb dry
Copper None 270 ppm dry 18.39 ppm dry
Dibenzo(a,h)anthracene None 260 ppb dry 29.36 ppb dry
Fluoranthene None 5100 ppb dry 424.17 ppb dry
Fluorene None 540 ppb dry 28.26 ppb dry
Lead None 218 ppm dry 42.21 ppm dry
Mercury None 0.71 ppm dry 0.21 ppm dry
Naphthalene None 2100 ppb dry 31.3 ppb dry
Nickel None 51.6 ppb dry 7.09 ppb dry
p,p’-DDE None 27 ppm dry 0.48 ppm dry
Phenanthrene None 1500 ppb dry 238.73 ppb dry
Pyrene None 2600 ppb dry 383.94 ppb dry
Silver None 3.7 ppm dry 0.23 ppm dry
Total DDTs None 46.1 ppb dry 1.01 ppb dry
Total HMW PAH None 9600 ppb dry 3223.98 ppb dry
Total LMW PAH None 3160 ppb dry 961.31 ppb dry
Total PAHs None 44792 ppb dry 4185.29 ppb dry
Total PCBs None 180 ppb dry 6.88 ppb dry
Sediment toxic
contaminants,
nearfield
Zinc None 410 ppm dry 59.26 ppm dry
Sediments,
nearfield RPD depth 1.18 cm None 2.6 cm
Species per sample <46.52 or >79.95 None 58.75
Fisher’s log-series
alpha <9.95 or >15.17 None 12.03
Shannon diversity <3.30 or >3.91 None 3.5
Odd years,
Benthic
diversity,
nearfield Pielou’s evenness <0.56 or >0.66 None 0.6
Benthic
opportunists % opportunists >10% >25% 0.24%

2005 OUTFALL MONITORING OVERVIEW 57
5. Fish and Shellfish
Background 
MWRA monitors fish and shellfish because of concerns for public health
and because some fish and shellfish species are good indicators of effects
of pollutants on overall marine health (Table 5-1). The fish and shellfish
industry is an important part of the regional identity and economy of
Massachusetts. There were concerns that the discharge of sewage effluent
into the relatively clean waters of Massachusetts Bay could result in
chemical contamination of the fisheries and that contaminants could cause
direct damage to the fishery stocks. 
Table 5-1. Monitoring questions related to fish and shellfish 
Is it safe to eat fish and shellfish? 
Will toxic chemicals accumulate in the edible tissues of fish and shellfish, and thereby
contribute to human health problems? 
ƒ Has the level of contaminants in the tissues of fish and shellfish around the
outfall changed since discharge began? 
ƒ Do the levels of contaminants in the edible tissue of fish and shellfish around
the outfall represent a risk to human health? 
ƒ Are the contaminant levels in fish and shellfish different between outfall,
Boston Harbor, and a reference site? 
Are natural/living resources protected? 
Will fish and shellfish that live near or migrate by the diffuser be exposed to elevated
levels of some contaminants, potentially contributing to adverse health in some
populations? 
ƒ Has the level of contaminants in the tissues of fish and shellfish around the
outfall changed since discharge began? 
ƒ Are the contaminant levels in fish and shellfish different between the outfall,
Boston Harbor, and a reference site? 
ƒ Are the contaminant levels in fish and shellfish different between outfall,
Boston Harbor, and a reference site? 
ƒ Has the incidence of disease and/or abnormalities in fish or shellfish
changed? 
Because many toxic contaminants adhere to particles, which settle,
animals that live on the bottom, in contact with sediments, and animals
that eat bottom-dwelling organisms are most likely to be affected.
Exposure to contaminated sediments could result in fin erosion, disease, or
other, subtler, abnormalities in flounder, lobster, or other bottom-dwelling
animals. Shellfish that feed by filtering suspended matter from large
volumes of water are also potential bioaccumulators of toxic
contaminants. Consumption of filter-feeding animals by predators could
result in transferring contaminants up the food chain and ultimately to
humans.

2005 OUTFALL MONITORING OVERVIEW 58
Monitoring Design 
The monitoring program focuses on three indicator species: winter
flounder ( Pseudopleuronectes americanus ), lobster ( Homarus
americanus ), and blue mussel ( Mytilus edulis ). Winter flounder and
lobster are important resource species in the region. The blue mussel is
also a fishery species and is a common biomonitoring organism.
Like all flatfish, winter flounder live and feed on the bottom, often lying
partially buried in the sediments. Consequently, flounder can be exposed
to contaminants directly, through contact with the sediments, or indirectly,
by ingesting contaminated prey. Flounder livers are examined to quantify
disease, including three types of vacuolation (centrotubular, tubular, and
focal, representing increasing severity), microphage aggregation, biliary
duct proliferation, and neoplasia or tumors. Neoplasia and vacuolation
have been associated with chronic exposure to contaminants. Chemical
analyses of winter flounder tissues are also made to determine tissue
burden and to evaluate whether contaminant burdens approach human
health consumption limits. Chemical analyses (Table 5-2) of composite
samples of fillets and livers include PCBs, pesticides, mercury, and lipids.
Liver samples are also analyzed for PAHs, lead, silver, cadmium,
chromium, copper, nickel, and zinc.
Lobsters live on a variety of surfaces within the region, including mud,
sand, gravel, and rock outcrops. Commercial lobstermen collect lobsters
for the monitoring program. Chemical analyses are performed on
composite samples. Meat (from the tail and claw) and hepatopancreas are
analyzed for lipids, PCBs, pesticides, and mercury. Hepatopancreas
samples are also analyzed for PAHs, lead, silver, cadmium, chromium,
copper, nickel, and zinc.
Like other filter feeders, blue mussels process large volumes of water and
can concentrate toxic metals and organic compounds in their tissues.
Mussels can be readily maintained in fixed cages, so they are convenient
monitoring tools. Mussels are collected from clean reference sites (which
have included Rockport, Gloucester, and Sandwich, Massachusetts, and
Stover’s Point, Maine). They are placed in cages and deployed in
replicate arrays. After a minimum deployment of 40 days or a preferred
deployment of 60 days, chemical analyses are performed on composite
samples of mussel tissue. Tissues are analyzed for PCBs, pesticides,
PAHs, lipids, mercury, and lead.

2005 OUTFALL MONITORING OVERVIEW 59 
Table 5-2. Chemical analyses of fish and shellfish 
Parameter Measurement details 
Flounder fillet 
Mercury
PCBs
Chlorinated pesticides
Lipids
Three composites of fillets from five flounder 
Flounder liver 
Trace metals
PAHs
PCBs
Chlorinated pesticides
Lipids
Three composites of livers from five flounder 
Lobster meat 
Mercury
PCBs
Chlorinated pesticides
Lipids
Three composites of meat from five lobsters 
Lobster hepatopancreas 
Trace metals
PAHs
PCBs
Chlorinated pesticides
Lipids
Three composites of hepatopancreas from five
lobsters 
Mussel 
Mercury
Lead
PAHs
PCBs
Chlorinated pesticides
Lipids
Six composites of soft tissue from ten mussels 
Flounder and lobster are sampled from Deer Island Flats, the outfall site,
and eastern Cape Cod Bay. Flounder are also taken near Nantasket Beach
and Broad Sound. (No fish were collected at Broad Sound in 2005.)
Flounder and lobster are examined for external lesions. Since 2004,
histology analyses for flounder are made every year; chemical analyses for
lobsters and flounder are completed every third year. Mussels are
deployed every three years at five locations: at the edge of the mixing
zone, one kilometer south of the diffuser line, in Cape Cod Bay, at at Deer
Island Light, and in the Inner Harbor.
In 2005, only winter flounder were studied. Fifty sexually mature (at least
three years old) winter flounder were taken from each of the four sampling
sites during May. Each of the fish was examined for physical
characteristics. All fish were used for histological and age analyses. As
part of an ongoing investigation of external ulcers that have been observed
on the blind sides of winter flounder since 2003, additional surveys were
also conducted in the January and March.

2005 OUTFALL MONITORING OVERVIEW 60
Results 
As in previous years, the mild centrotubular hydropic vacuolation (CHV)
was the most common form of vacuolation noted in histological analyses
(Moore 2006). Incidence of CHV was low, less than 20%, at all sites and
less than five when the percentage was corrected for age (Figure 5-1). No
neoplasia was observed in any fish from any site.
Ulcer prevalence followed the same spatial and temporal pattern that had
been observed in previous years. The syndrome appears in the early
spring and apparently diminishes by the early summer. The etiology
remains unknown.
MWRA has also noted that a biogeographic assessment of Stellwagen
Bank, currently being conducted by NOAA, will report an increase in
kidney disease in flounder from the area near Deer Island in 2004 as
compared to fish collected in the same area in the 1980s. No similar
disease was seen in fish collected near the outfall, and there was no
consistent indication that incidence of the disease was correlated with
chemical exposure. MWRA will evaluate these data as they become
available. 
0
2
4
6
8
10
12
14
16
18
1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Year
Hydropic Vacuolation/ Mean Age
DIF
NB
BS
OS
ECCB
Outfall Startup 
Figure 5-1. Prevalence of centrotubular hydropic vacuolation (CHV), corrected
for age. (DIF = Deer Island Flats, OS = Outfall Site, ECCB = Eastern Cape Cod
Bay, NB = Nantasket Beach, and BS = Broad Sound)

2005 OUTFALL MONITORING OVERVIEW 61 
Contingency Plan Thresholds 
Threshold parameters for fish and shellfish include levels of toxic
contaminants in flounder, lobster, and mussels and liver disease in
flounder; during 2005, only liver disease in flounder was tested (Table 5-
3). Some thresholds are based on U.S. Food and Drug Administration
(FDA) limits for maximum concentrations of specific contaminants in
edible portions of food. Others are based on the baseline monitoring.
Liver disease in flounder, measured as the percentage of fish exhibiting
CHV, remained well below the baseline mean as well as caution and
warning thresholds. 
Table 5-3. Contingency Plan threshold values and 2005 results for fish and shellfish monitoring 
Parameter
Type/
Location
Parameter Baseline Caution
Level
Warning
Level
2005
Results
Flounder
Nearfield
Liver disease
(CHV) 24.4% 44.9% None 8%

2005 OUTFALL MONITORING OVERVIEW 62
6. Special Studies
Background 
Besides monitoring the effluent and the water column, sea floor, and fish
and shellfish in Massachusetts Bay and the surrounding area, MWRA
conducts special studies in response to specific permit requirements,
scientific questions, and public concerns. During 2005, special studies
included detailed analysis of the effluent, studies of nutrient flux at the
sediment-water interface, marine mammal observations, water-quality
modeling, studies related to the Alexandrium bloom or red tide,
completion of a review of issues related to toxic contaminants, and
completion of a summary report by USGS. 
Effluent Analysis 
The MWRA monitoring plan requires intensive monitoring of toxic
contaminants in the final effluent in the Deer Island Treatment Plant, with
lower detection limits than are usually required for NPDES permit
monitoring. These specialized methods have allowed MWRA to detect
relatively subtle changes in concentrations of contaminants in the effluent.
Analysis of samples collected during the first five years of discharge to
Massachusetts Bay have shown that none of the contaminants, with a
possible exception of PCBs, have been present in concentrations that
would result in exceeding water quality standards after 70:1 initial
dilution, the dilution expected under near worst-case conditions of
maximum effluent flow and strong stratification of the receiving waters
(Tables 6-1, 6-2).
PCBs have not been detected in the effluent as Aroclor mixtures, the only
PCB measurement for which the permit has set limits. However, a few
congeners have been detected at low levels, with a median concentration
of 1.4 nanograms per liter (parts per trillion). At an initial dilution of 70:1,
these levels would translate to a concentration of 0.02 nanograms per liter
in the receiving water, lower than but close to the current EPA
recommended national water quality criterion of 0.064 nanograms per liter
(EPA 2004). Interpretation of these PCB results is difficult, as there are
no comparable data from the ambient water.

2005 OUTFALL MONITORING OVERVIEW 63 
Table 6-1. Metals in final effluent from Deer Island Treatment Plant 
Metal Method* Samples Non-
Detects Detects (%) Range (μg/L) Median
(μg/L)
Upper 95%
Percentile
(μg/L)
Lowest EPA
Water Quality
Criterion (μg/L)*
Aluminum ICP 352 118 234 (66%) 24 – 860 78 191 None
Antimony ICP 121 121 0 (0%) <15 - <25 5.6 (HHC)
Arsenic GFAA 124 120 6 (5%) <0.8 – 1.2 <0.8 0.018 (HHC)
Beryllium ICP 121 121 0 (0%) <0.5 None
Boron ICP 121 57 64 (53%) <250 – 432 252 369 None
Cadmium GFAA 417 56 361 (86%) <0.03 – 0.39 0.089 0.198 8.8 (CCC)
Chromium GFAA 417 51 366 (88%) <0.70 – 8.1 1.0 1.96 50 (CCC) as
Cr +6
GFAA 161 1 160(99%) <1 – 25 8.4 14.9 3.1 (CCC)
ICP 458 142 316 (69%) 5.6 – 39.6 11.3 21.4 3.1 (CCC) Copper
ICP/MS 56 0 56 (100%) 5.6 – 21 10.2 16.3 3.1 (CCC)
Iron ICP 144 0 144 (100%) 120 – 1090 355 618 None
GFAA 421 374 47 (11%) <2.4 – 14.8 <2.4 3.52 8.1 (CCC)
Lead ICP/MS 31 1 30 (97%) 0.33 – 4.2 1.3 3.1 8.1 (CCC)
CVAA 418 57 361 (86%) <0.01 – 0.22 0.018 0.051 0.94 (CCC)
Mercury CVAF 54 0 54 (100%) 0.0048 – 0.062 0.018 0.062 0.94 (CCC)
Molybdenum GFAA 310 0 310 (100%) 2.1 – 28 7.2 13.8 None
Nickel GFAA 421 1 429 (100%) <0.7 – 7.3 2.9 4.9 8.2 (CCC)
Selenium GFAA 121 121 0 (0%) <0.9 71 (CCC)
Silver GFAA 413 8 405 (98%) <0.09 – 4.2 0.34 0.72 1.9 (CMC)
Thallium GFAA 121 121 0 (0%) <1 0.24 (HHC)
Zinc ICP 428 0 428 (100%) 12 – 99 27.2 49.7 81 (CCC)
* See List of Acronyms on page 103; criteria from EPA 2004, based on salt water or human health criteria 
Table 6-2. Pesticides, PAHs, and PCBs in final effluent from Deer Island Treatment Plant 
Compound Samples Non-
Detects Detects (%) Range (ng/L) Median
(ng/L)
Upper 95%
Percentile
(ng/L)
Lowest EPA Water
Quality Criterion
(ng/L)*
Total Chlordane 522 32 490 (94%) 0.24 – 58 2.25 8.25 0.80 (HHC) for
Chlordane only
Alpha-Chlordane
(SIM only) 221 0 221 (100%) 0.34 – 7.9 1.04 3.7
Total DDT 510 77 443 (87%) 0.17 – 13 0.78 2.54 0.22 (HHC)
4,4’-DDE (SIM only) 199 0 199 (100%) 0.12 – 3.1 0.56 1.35
4,4’-DDT (SIM only) 220 188 32 (14%) 0.17 – 11 0.40 1.47
Gamma-BHC
(Lindane) 638 386 252 (39%) 0.36 – 37 0.84 4.44 160 (CMC)
Gamma-BHC
(Lindane) (SIM only) 221 175 46 (21%) <0.5 – 37 0.51 4.54 160 (CMC)
Hexachlorobenzene
(HCB) 638 495 143 (22%) 0.04 – 0.76 0.09 0.23 0.28 (HHC)
Hexachlorobenzene
(HCB) (SIM only) 221 85 136 (62%) 0.04 – 0.63 0.09 0.17 0.28 (HHC)
Total PCB (SIM only) 268 0 268 (100%) 0.19 – 17.8 2.07 5.02 0.064 (HHC)
Chrysene 431 22 409 (95%) 3.18 – 334 13.5 52 3.8 (HHC)
Fluorene 431 74 357 (83%) 1.11 – 105 5.93 28 1,100,000 (HHC)
Total NOAA PAH 300 2 298 (99%) 10.8 – 3515 234 903 N/A
* See List of Acronyms on page 103; criteria from EPA 2004, based on salt water or human health criteria

2005 OUTFALL MONITORING OVERVIEW 64 
Because flow from the treatment plant has been lower and the removal
efficiencies of the treatment plant have been greater than had been
projected during planning for the outfall, MWRA has recently updated
loading estimates (Delaney and Hall 2006; Table 6-3). Estimates of
annual loadings from the Deer Island Treatment Plant were first made for
the EPA Supplemental Environmental Impact Statement (SEIS) prepared
as part of the outfall-siting process (EPA 1988). Those estimates were
based on presumed influent concentrations, which were based on the
available analytical techniques at the time, many of which resulted in data
that were “below detection limits.” With better analytical detection limits,
those estimates would have been less. Contaminant concentrations have
also declined, in part because of MWRA’s aggressive source reduction
program, and also because changing technologies have reduced some
contaminant concerns ( e.g., digital cameras have decreased the use of
silver in photography). Sung and Higgins (1998) also projected loadings,
based on limited early results from the treatment plant. The new estimates
correspond to the average flow of 359 million gallons per day and 93%
secondary effluent that have been observed over the first five years of
outfall operation. 
Table 6-3. Annual loading estimates (kilograms per year) 
Parameter Projected
(SEIS 1988)
Projected
(Sung and
Higgins 1998)
Mean Loading
2000-2005
(Delaney and Hall
2006) 
Cadmium 697 21 55
Chromium 3,517 490 648
Copper 11,945 14,000 6,588
Lead 4,961 2,400 850
Mercury 216 50 12
Molybdenum 6,800 3,743
Nickel 8,926 2,400 1,534
Silver 299 620 207
Zinc 14,000 16,318
Total PCB 50 4.8 0.91
Total PAH 1,400 * 112 +
Total DDT 0.67 0.46
4,4’-DDT (only) 28 0.37
Total Chlordanes 0.48 0.86
Heptachlor (only) 10 0.20

2005 OUTFALL MONITORING OVERVIEW 65 
Marine Biological Laboratory scientists collect sediment samples to measure
nutrient flux. 
Nutrient Flux 
One concern about the outfall was that increased loads of organic matter
might enhance benthic respiration and nutrient fluxes between the
sediments and the water column in the nearfield. The resulting higher
rates of benthic respiration or sediment oxygen demand might lead to
lower levels of oxygen in both the sediments and the water column. The
monitoring plan required a special study to measure the organic matter
loads, sediment oxygen demand, denitrification, and the flux of nutrients
in the vicinity of the outfall to assess the importance of these processes
(Table 6-4). Comparable studies take place in Boston Harbor.

2005 OUTFALL MONITORING OVERVIEW 66 
Table 6-4. Monitoring questions related to nutrient flux 
Are natural/living resources protected? 
How do the sediment oxygen demand, the flux of nutrients from the sediment to the
water column, and denitrification influence the levels of oxygen and nitrogen in the
water near the outfall?
Have the rates of these processes changed? 
ƒ Will increased water-column and benthic respiration contribute to depressed
oxygen levels in the water? 
ƒ Will increased water-column and benthic respiration contribute to depressed
oxygen levels in the sediment? 
ƒ Will enrichment of organic matter contribute to an increase in benthic
respiration and nutrient flux to the water column? 
In 2005, monitoring of three sites in the nearfield and one site in
Stellwagen Basin continued to show little or no indication of any effect of
the outfall discharge (Tucker et al. 2006). Rather, the overriding influence
on benthic nutrient cycling was the effect of the May northeast storms and
the late October storm. Total organic carbon levels were lower than usual,
probably because of scouring of surface sediments during the storms.
Inventories of surface pigments also decreased, and rates of sediment
oxygen demand and dissolved inorganic nitrogen flux were low.
Phosphate fluxes were nearly undetectable.
Studies also continued at the four Boston Harbor stations, where the
storms were also the major events affecting the benthos. Physical
disturbance scoured the sediments and flushed porewaters, preventing
formation of the Ampelisca amphipod mats, which had been important to
the biogeochemistry of the harbor. (See Section 7, Boston Harbor Studies,
for additional discussion of the Ampelisca tube mats.) Sediment oxygen
demand and nutrient fluxes were the lowest observed in the monitoring
program. The large variability between stations and years that existed
early in the monitoring program has largely disappeared.
Prior to the outfall diversion, Boston Harbor had high rates of sediment
oxygen demand compared to those in other coastal systems (Figure 6-1).
During the post-diversion years, the rates in the harbor have progressively
declined to levels lower than many estuaries, while the rates in
Massachusetts Bay have not increased. The improvements in Boston
Harbor with corresponding lack of change in Massachusetts Bay is one
measure of the success of the Boston Harbor clean-up.

2005 OUTFALL MONITORING OVERVIEW 67 
0 20 40 60 80 100 120 140 160
Boston Harbor, MA 1995
Pawtuxent River Est, MD
Boston Harbor, MA 2003
Narragansett Bay, RI
South River Est, NC
Buzzards Bay, MA
Boston Harbor, MA 2004
Eel Pond, MA
Vostok Bay, Russia
Loch Ewe, Scotland
New York Bight, NY
Boston Harbor, MA 2005
Massachusetts Bay, MA 1995
Kaneohe Bay, HI
Massachusetts Bay, MA 2005
Site
Summer SOD (mmol O2 m -2 d -1 ) 
Figure 6-1. Sediment oxygen demand in Boston Harbor and the nearfield of Massachusetts Bay
during pre- and post-diversion periods compared to other coastal ecosystems. Data for Boston
Harbor and Massachusetts Bay are July-October averages; data for the other systems are
summer rates from Nixon 1981 
Marine Mammal Observations 
Several endangered or threatened species of whales and turtles visit
Massachusetts and Cape Cod bays, including the right, humpback,
finback, sei, and blue whales. The minke whale, harbor porpoise, gray
seal, harbor seal, and several species of dolphins, which are not
endangered but are protected, also occur.
Since 1995, MWRA has included endangered species observers on
monitoring surveys. In 2005, observers were included on twelve nearfield
water quality surveys and three farfield surveys (Short and Michelin
2006). Besides providing observational data, the presence of trained
marine mammal observers addresses a request by the National Marine
Fisheries Service (NMFS) that MWRA take active steps to minimize the
chances of a collision of one of its survey vessels with a right whale.

2005 OUTFALL MONITORING OVERVIEW 68 
The surveys are not designed to determine possible effects of the outfall
on marine mammals, but do provide some general information. During
the 2005 surveys, about 30 individual whales, about 20 harbor porpoise,
one unidentified porpoise, and a small pod of Atlantic white-sided
dolphins were directly observed by the trained observers and other
members of the monitoring team. Whale sightings were concentrated
within Massachusetts Bay. The total number of whales sighted was higher
than in those seen in 2002 through 2004. Records of the Whale Center of
New England (www.whalecenter.org) also indicated an increase from the
sparse sightings they had reported in 2004. They reported numerous fin
whales and a group of approximately about 15 humpback whales during
the summer months. Sei whales and right whales were reported during late
July and early August.
During April, there were numerous reports of a humpback whale within
Boston Harbor (Figure 6-2). The whale appeared to be feeding on
schooling smelt and herring. 
Figure 6-2. Humpback whale sighted near the Deer Island Treatment Plant in April 2005 
Model Results 
MWRA has used numerical models to simulate and predict the physical
and biological conditions in Massachusetts Bay. A hydrodynamic model
was developed by USGS (Signell et al . 1996) and a water quality model,
known as the Bays Eutrophication Model (BEM), was developed by

2005 OUTFALL MONITORING OVERVIEW 69 
Hydroqual, Inc. (2000) for MWRA. Working now with the University of
Massachusetts Boston, MWRA continues to maintain, enhance, and apply
the models (Jiang and Zhou 2004a, 2004b, 2006a, 2006b).
In September 2005, MWRA and the modeling team met with OMSAP's
Model Evaluation Group (MEG), to present recent results and discuss
future directions for the modeling effort. It was the first time that the
MEG had convened since 2002. Among other findings and
recommendations, the MEG expressed overall satisfaction with the
modeling efforts, finding that the level of agreement between model
results and observations seemed reasonable and typical. A list of
questions, comments, and recommendations concerning future modeling
efforts, improvements to model validity and presentation, and assessment
measures was developed. These recommendations will be used by the
permitting agencies to determine what, if any, continued modeling
requirements will be included in MWRA’s new NPDES permit. (The
existing permit expired in 2005; the conditions of that permit continue
until a new one is issued.) 
2005 Alexandrium Bloom 
During May-July 2005, an extensive bloom of Alexandrium fundyense 
(and Alexandrium tamarense , which scientists consider to be a variant of
the same species) occurred along the coast of southern New England,
eventually closing shellfish beds from central Maine to Massachusetts and
resulting in the closure of 40,000 km 2 of offshore federal waters (Figure 6-
3). Alexandrium is one of the nuisance algae of concern in water column
monitoring, because it produces a toxin that can build up in shellfish to
levels that can cause paralytic shellfish poisoning (PSP) in birds, marine
mammals, and humans that eat the affected shellfish. Alexandrium 
blooms, known as red tides, have sporadically caused shellfish bed
closures in Massachusetts Bay since 1972, when a strong bloom was first
observed. PSP toxicity was not observed in Massachusetts Bay from 1994
to 2004.
The 2005 bloom was exceptional in several ways: high toxin levels were
measured farther south than ever before in New England; levels of toxicity
in many locations were higher than previously observed at those stations;
for some locations, toxicity was above quarantine levels (levels high
enough to close the shellfish beds) for the first time; and cell
concentrations far exceeded those observed in the coastal waters of
southern New England in the past.

2005 OUTFALL MONITORING OVERVIEW 70 
Figure 6-3. Geographic extent of shellfish bed closures in July 2005; initial dates of
closure at each station shown in parentheses (figure courtesy of Don Anderson, Woods
Hole Oceanographic Institution)

2005 OUTFALL MONITORING OVERVIEW 71 
MWRA participated in a region-wide collaborative monitoring effort
intended to help understand the scale and duration and to evaluate the
causes of this unprecedented red tide. The monitoring showed that a large
spring bloom developed in the coastal waters of Maine, where there were
known Alexandrium cyst seedbeds. This bloom moved south with
stronger-than-usual coastal currents, a result of high spring runoff from
large rivers in Maine, and was transported into Massachusetts and Cape
Cod bays and to waters south of the Cape by the two strong northeast
storms that occurred in May.
The causes and effects of the bloom have continued to be evaluated.
OMSAP held a meeting to review the bloom in August 2005, and in April
2006, MIT Sea Grant convened a symposium on the bloom. The high
abundance of newly deposited cysts in the western Gulf of Maine is now
thought to be the main cause of the bloom. A major concern was that the
2005 event could result in formation of similar seedbeds in Massachusetts
Bay or further south in Nantucket Sound. That concern has not been
realized, as sampling after the bloom found that cysts were only sparse in
Massachusetts sediments. Dense seedbeds have persisted in the western
Gulf of Maine.
The MWRA outfall is not suspected to be a factor in the region-wide size
or extent of this bloom. Localized effects of the outfall were possible but
have not been measured; there is no indication of any stimulation or
prolongation of the bloom in the area of the outfall.
MWRA has developed a standing survey plan for monitoring Alexandrium 
(Libby 2006) to respond quickly to rapidly developing red tides. The
survey plan is designed to supplement regular outfall monitoring. It
provides a stepwise approach, with triggers that determine the appropriate
level of response. 
Toxic Contaminants Review 
During 2005, MWRA prepared a review of issues associated with toxic
contaminants in Boston Harbor and Massachusetts Bay (Hunt et al. 2006).
The report made several findings: 
• Contaminants in Boston Harbor and Massachusetts Bay have a
historical legacy dating from the Civil War and subsequent industrial
development that peaked in the post World War II era, but
contaminant levels are decreasing in response to regulatory actions. 
• MWRA actions to reduce sources and improve treatment have
significantly reduced loading to the system. Current annual loads are
significantly less than those that had been projected during the 1980s.

2005 OUTFALL MONITORING OVERVIEW 72 
• MWRA and regulatory actions have substantially reduced
contaminant levels in surface sediments in Boston Harbor, while only
minimally affecting sediments in Massachusetts Bay. 
• There has been decreased incidence of tumors in flounder and
lowered contaminant levels in fish and shellfish for some
contaminants. Levels of mercury and silver in flounder and lobster
taken near the outfall have increased but are still low. 
• Processes related to contaminant transport, fate, and bioavailability
are becoming sufficiently understood to make judgments about future
responses. 
• Emerging contaminants of concern, such as endocrine-disrupter
compounds and brominated flame retardants, are potentially
important and should be understood in anticipation of possible
regulatory actions over the next decade. 
• The current knowledge base is sufficient to allow reduced monitoring
but not to eliminate it. 
USGS Studies 
During 2005, the USGS completed a major review of the processes that
influence transport and fate of contaminated sediments in Boston Harbor
and Massachusetts Bay (Bothner and Butman 2005, available at
http://pubs.usgs.gov/of/2005/1250/). USGS has conducted research in the
region since the 1970s and expanded its program in 1989, with the
beginnings of the Boston Harbor Project. Their focus is on several
components related to sediment contamination and transport: 
• Sea-floor mapping. Using sidescan sonar, high-resolution
multibeam echosounding, seismic reflection profiling, sediment
sampling, and bottom photographs and video, the USGS has
developed fine-resolution maps of the region (Butman et al. 2004;
Figure 6-4). The maps can be used to locate sediment types, define
depositional regions, and study the effects of human activities, such as
waste disposal and bottom trawls. 
• Currents and sediment-transport measurements and modeling. 
USGS has made almost continuous measurements of temperature,
salinity, currents, pressure, light transmission, and bottom
characteristics from arrays of moored instruments. The measurements
have been complemented by major modeling efforts. For example,
USGS has used computer models (Signell and Butman 1992, Signell 
et al. 2000) to study flushing of Boston Harbor, provide input to a
bay-wide water-quality model, and predict the dilution of effluent
discharged from the outfall. Recently, USGS has coupled the
circulation model with a sediment-transport model to examine the
effects of storms on the transport of sediments in Massachusetts Bay.

2005 OUTFALL MONITORING OVERVIEW 73 
• Geochemical measurements and database. Sediment samples
collected three times per year near the outfall have been used to
determine temporal trends in concentrations of metals and spores of
the sewage tracer bacterium Clostridium perfringens . USGS has also
sampled sediments from Boston Harbor and throughout
Massachusetts Bay and has conducted special studies of geochemical
processes. The work has highlighted the importance of erosion and
resuspension of deeply buried particles as a continuing source of
contamination to the region. 
Figure 6-4. USGS map of the topography of Massachusetts Bay in shaded relief
view, colored by water depth

2005 OUTFALL MONITORING OVERVIEW 74 
USGS will continue to interpret and synthesize data and to refine and
expand the application of sediment-transport modeling. Work is also
underway to study the release of metals from the sediments to the
overlying water and to evaluate the potential of using mollusk-shell
growth rings as recorders of historic metals concentrations in the water
column.

2005 OUTFALL MONITORING OVERVIEW 75
7. Boston Harbor Monitoring
Background 
The goal of the Boston Harbor Project was to improve the quality of
Boston Harbor without degrading Massachusetts Bay. This outfall
monitoring overview generally focuses on Massachusetts Bay and the
Contingency Plan thresholds that were established to ensure that there
would be no unanticipated effects of the outfall. There has also been
extensive monitoring in Boston Harbor; this section presents some of the
results that were reported during 2005. 
Wastewater Loads and Eutrophication 
Large changes in the water quality of Boston Harbor have been observed
through the duration of the Boston Harbor Project. Concentrations of the
nutrients most responsible for eutrophication have declined, as have
standing stocks of phytoplankton and concentrations of particulate organic
mater. The harbor has shown increases in concentration of dissolved
oxygen in bottom waters and lowered counts of pathogen-indicator
bacteria (Taylor 2004, 2006).
Recently, MWRA has analyzed historical data to determine whether
relationships exist among these observed changes and the decreases in the
wastewater loadings to the harbor (Taylor 2005a, 2005b, 2006). The
analysis has shown strong relationships between the annual loadings and
the annual average concentrations of the dissolved and non-dissolved
inorganic fractions of total nitrogen in the harbor water samples (Figure 7-
1). During the first four years after the direct wastewater discharges to the
harbor were ended, nitrogen concentrations were the lowest observed
(these four years are indicated by the ellipses on the figure).

2005 OUTFALL MONITORING OVERVIEW 76 
0 500 1000 1500 2000 2500
0
5
10
15
20
25
30
35 
DIN
Non-
DIN 
TOTAL 
N 
TN conc = 15.07 + (0.010 x TN loadings), r 2 = 0.94, p = <0.01
DIN conc = 2.33 + (0.009 x DIN loadings), r 2 = 0.86, p = <0.01
Non-DIN conc = 12.82 + (0.011 x Non-DIN loadings), r 2 = 0.74, p = <0.01 
NITROGEN CONC. VS LOADINGS 
ANNUAL AVERAGE CONC.
( UMOL L -1 )
TOTAL LOADINGS
( KMOL D -1 ) 
Figure 7-1. Relationships between total annual loads and nitrogen
concentrations in the water column in Boston Harbor. Ellipses indicated years
after MWRA treatment plant discharges to the harbor ended. TN=total nitrogen,
DIN=dissolved inorganic nitrogen 
For annual average concentrations of chlorophyll, a measure of
phytoplankton biomass, the relationship was not quite as robust (Figure 7-
2). This result is to be expected for a biological variable. During three of
the four years after the direct treatment plant discharges to the harbor were
ended, however, average chlorophyll concentrations were lower than in
previous years.

2005 OUTFALL MONITORING OVERVIEW 77 
0 500 1000 1500 2000 2500
0
3
6
9
12 
CHL-A
Phaeo
TOTAL
CHL-A 
Total chl-a conc = 4.66 + (0.002 x TN loadings), r 2 = 0.36, p = 0.06
Chl-a conc = 3.32 + (0.001 x TN loadings), r 2 = 0.22, p = 0.18
Phaeophytin conc = 1.20 + (0.001 x TN loadings), r 2 = 0.50, p = 0.02 
CHL-A CONC. VS TN LOADINGS 
ANNUAL AVERAGE CONC.
( UG L -1 )
TOTAL N LOADINGS
( KMOL D -1 ) 
Figure 7-2. Relationships between total loads and chlorophyll. Ellipses indicate
years after MWRA treatment plant discharges to the harbor ended. CHL-A=total
chlorophyll a, “active” or acid-corrected chlorophyll a; Phaeo=“degraded”
chlorophyll or phaeophytin 
Water Quality Monitoring: Tributary Rivers 
MWRA monitors water quality at more than 50 stations in Boston Harbor
and its major tributaries, the Charles, Mystic, and Neponset rivers. One
major goal of the monitoring is to assess the effects of MWRA’s
combined sewer overflow (CSO) control plan (MWRA 1997c) on the
waterbodies affected by CSOs. By the end of 2005, 63 CSOs remained
active within Boston Harbor and its tributaries; 21 have been closed since
the early 1990s. The annual volume of flow has decreased from more than
three billion gallons per year in the late 1980s to about one half billion
gallons per year (Figure 7-3).

2005 OUTFALL MONITORING OVERVIEW 78 
0
0.5
1
1.5
2
2.5
3
3.5
4 
'87 '88 '89 '90 '91 '92 '93 '94 '95 '96 '97 '98 '99 '00 '01 '02 '03 '04 '05 '06 '07 '08 '09 '10 '11 '12 '13 '14 '15 
Annual CSO Overflow Volume
(Billion Gallons)
Phase I:
1989 - 1991 
Begin minimum
controls and
system
optimization 
Phase II:
1992 - 1997 
Full Deer Island
pumping
capacity, system
optimization
projects, and
minimum controls 
Phase III:
1998 - 2015 
Completion of more than 20 long-term
CSO projects, 94% of remaining flow
w ill be treated 
Figure 7-3. Impact of CSO control plan on system-wide CSOs 
Monitoring is conducted year-round with the most intensive sampling
occurring during the spring and summer. Testing focuses on bacteria and
parameters related to eutrophication. A recent report (Coughlin 2006)
summarized information from the Charles River, the Mystic River, and the
major tributary to the Mystic River, Alewife Brook.
MWRA samples in the Charles River from the Watertown Dam
downstream to the New Charles River Dam in Boston. Stations are
located so that they bracket 12 CSO outfalls along the river in Cambridge
and Boston. Contaminants also enter the river from upstream sources, a
brook near Kenmore Square, and illicit connections to storm drains, many
of which have been identified and eliminated. In general, water quality is
poorest at upstream locations, improving as the river widens and slows.
Dissolved oxygen concentrations follow the opposite pattern, worsening
downstream, due to summer stratification. Seawater leaking through the
Charles River locks contributes to the strong seasonal stratification and
consequent low levels of dissolved oxygen in the bottom water.
There have been noticeable improvements in the Charles River since
MWRA implemented the long-term CSO plan. Average bacteria counts
during heavy rain, when the river is affected by contaminated stormwater
and CSO, have decreased substantially; there have also been noticeable
decreases during dry weather and light rain, when illicit connections and
contaminated storm water have the largest effects because the CSOs
typically only discharge in heavy rain (Figure 7-4).

2005 OUTFALL MONITORING OVERVIEW 79 
Fecal coliform counts by phase of CSO Plan, Lower Charles 
Station 012, Watertown Dam
Station 008, downstream of Mass. Ave. bridge
Station 006, downstream of Cottage Farm CSO
Station 011, downstream of Science Museum
0
1
2
3
4
Cell Mean for logfc
1989 to 1991 1992 to 1997 1998 to 2003
0
1
2
3
4
Cell Mean for logfc
1989 to 1991 1992 to 1997 1998 to 2003
0
1
2
3
4
Cell Mean for logfc
1989 to 1991 1992 to 1997 1998 to 2003
0
1
2
3
4
Cell Mean for logfc
1989 to 1991 1992 to 1997 1998 to 2003
1
10
100
1000
10000
1
10
100
1000
10000
1
10
100
1000
10000
1
10
100
1000
10000
1
10
100
1000
10000
1
10
100
1000
10000
1
10
100
1000
10000
1
10
100
1000
10000
1
10
100
1000
10000
1
10
100
1000
10000
1
10
100
1000
10000
1
10
100
1000
10000
Heavy Rain Light Rain Damp Dry Heavy Rain Light Rain Damp Dry Heavy Rain Light Rain Damp Dry 
Figure 7-4. Average fecal coliform counts in different weather conditions and during phases of
MWRA’s CSO control plan at four locations in the lower Charles River. Dotted line indicates 200
fecal coliform/100 ml, the swimming standard. (Note log scale.) 
The Mystic River and Alewife Brook are affected by nine CSOs and
runoff from many storm drains in Cambridge and Somerville. Alewife
Brook is the primary source of bacterial contamination to the lower Mystic
River. Bacteria counts in Alewife Brook frequently fail to meet standards;
water clarity and dissolved oxygen conditions are also poor. In the lower
portions of the Mystic River, however, bacteria counts meet standards
even during heavy rains, an improvement that has occurred since the
1990s.
Nutrients, especially phosphorus, affect the water quality of both the
Charles and Mystic rivers, particularly in the lower reaches where dams
prevent the free flow of water, the rivers broaden, and flow rates decrease.
In the summer, high nutrient loads entering from upstream, combined with
low flow, warm temperatures, and sunlight, contribute to excess levels of
algae (measured as chlorophyll) in the downstream reaches of the rivers
(Figures 7-5, 7-6).

2005 OUTFALL MONITORING OVERVIEW 80 
0
20
40
60
80
J F M A M J J A S O N D 
μg/L 
Figure 7-5. Average monthly Charles River chlorophyll levels at Watertown
Dam (upstream, open circles) and Museum of Science stations (river mouth,
black circles), 1998-2003. Summer chlorophyll levels in the downstream Charles
are typically elevated above 25 
μ g/L, which indicates algal overgrowth. 
0
20
40
60
80
J F M A M J J A S O N D 
μg/L 
Figure 7-6. Average monthly Mystic River chlorophyll levels at (upstream at
Alewife confluence, open circles) river mouth, (black circles) and inner harbor
(gray circles), 1998-2003. Summer chlorophyll levels in the downstream Mystic
River are typically extremely high, well above 25 
μ g/L, which indicates excessive
algal growth. 
Effects of Rain on Bacteria:
Boston Harbor Beaches 
MWRA monitors bacterial indicators not only in the tributaries to Boston
Harbor, but also at harbor beaches (Figure 7-7). During the years of the
Boston Harbor Project, flows of untreated water from CSOs have declined
significantly, yet additional improvements remain to be made. Several
CSO projects are underway, including a storage tunnel to collect
combined sewage and stormwater that would otherwise discharge to South
Boston beaches and elimination of other CSOs in Dorchester Bay by
constructing separate sewers for stormwater and sewage. Beaches
continue to be closed due to increased levels of indicator bacteria after
rainstorms wash contaminated stormwater, sometimes combined with
sewage, into the harbor.

2005 OUTFALL MONITORING OVERVIEW 81 
Figure 7-7. Boston Harbor beach monitoring stations 
These continued improvements to the CSO system and elimination of
sewage contamination of stormwater are the most important actions that
communities and MWRA are taking to ensure that waters are safe for
swimming and boating. Together with the Harvard School of Public
Health, MWRA has also been developing better tools for assessing water
conditions. Bacteria enumeration requires at least 24 hours, but rainfall
can be known in real time. Therefore, a statistical tool called receiver
operating characteristic (ROC) curve analysis has been used to quantify
the relationships between rainfall and bacteria indicators (Morrison 2005,
Morrison and Coughlin 2005) to more accurately assess beach conditions.
ROC curves are generated from “true positive” and “false positive” rates,
with the best indicators having high true positive and low false positive
rates.
ROC curve analysis of rainfall and bacteria monitoring data collected from
Boston Harbor beaches in 1996-2004 enabled the development of rainfall
thresholds for posting swimmers’ advisories (Morrison and Coughlin
2005). Although no rainfall threshold produced an ideal result of 100%
true positive and 0% false positive rates, rainfall was a superior predictor

2005 OUTFALL MONITORING OVERVIEW 82 
of beach water quality than the “previous day’s” bacteria results. The
thresholds are being used by the Department of Conservation and
Recreation to “presumptively” post beaches after rainstorms rather than
waiting a day for the bacteria data.
Similarly, MWRA has characterized the water quality of Alewife Brook
and the Mystic River, which lie at the boundary of Cambridge, Somerville,
and Arlington, and which continue to be affected by stormwater and by
discharge through CSOs. Those studies found a strong relationship
between antecedent rain and increased indicator bacteria levels.
ROC curve analysis indicated that the most downstream station in Alewife
Brook provided the best indicator of bacteria levels following storms
(Morrison 2005). At this station, 0.27 inches of rain occurring within
three days prior to sampling predicted levels of the indicator bacteria E.
coli high enough to exceed the boating standard 75% of the time. The
study found that each sampling location responded to rainfall differently,
so that the ability to use rainfall as a real-time indicator of bacteria levels
varies by location. 
Changes in the Sediments 
At the onset of the Boston Harbor Project, portions of the harbor contained
sediments with high levels of contamination. Some areas of the Inner
Harbor were nearly devoid of life, although the Outer Harbor had areas
with diverse, bottom-dwelling communities.
Sediment samples from Boston Harbor have been regularly collected for
chemical analysis since 1991. Surface sediments have been analyzed for
the sewage tracer bacterium Clostridium perfringens spores and for
contaminants, including PCBs, pesticides, PAHs, linear alkyl benzenes,
and metals. The data have shown significant decreases in concentrations
of the bacteria tracer and of the chemical contaminants. In the early
1990s, concentrations of Clostridium perfringens spores were high and
variable (Figure 7-8, see Figure 7-9 for station locations). There was a
mean of about 3,500 colony-forming units for each percent dry fine-
grained sediment (cfu/g dw/% fines), the standard measurement unit, in
the Outer Harbor. By 1998, concentrations of Clostridium perfringens 
spores throughout the harbor had declined to about 170 cfu/g dw/% fines.
Similarly, concentrations of PAHs, PCBs, DDTs, mercury, cadmium, and
silver in the surface sediments have declined by 20 to 75% since 1994,
depending on the chemical and the location within the harbor.
Concentrations of silver (a sewage tracer) in the Inner Harbor declined
50% between 1994 and 2002, possibly because of a decline in
photographic processes that use silver as well as due to improved

2005 OUTFALL MONITORING OVERVIEW 83 
treatment. In Dorchester Bay, concentrations of the pesticide DDT and its
breakdown products declined 71% during the same period. In contrast,
concentrations of lead and copper have not changed substantially,
suggesting that there are sources other than sewage. 
0
200
400
600
800
1000
1200
1400
1600
1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006
Sampling Year
C. perfringens (cfu/g dw / fines)
Northern Harbor (T01, T03, T05A)
Quincy Bay (T06, T07)
Hingham/Hull Bay (T08)
Fort Point Channel mouth (CO19)
Savin Hill Cove (T04)
Inner Harbor mouth (T02) 
* Outer Harbor, 1991
Mean + Stdev = 3,436 cfu/g dw / fines
Effluent diversion Secondary
treatment
and Nut
Island
transfer
Primary
treatment
Cessation of
sludge
discharge 
* 
Figure 7-8. Yearly mean abundance of Clostridium perfringens spores in Boston
Harbor (Error bars represent one standard deviation.) 
Changes in the Benthic Community 
In New England, the animals comprising a normal, nearshore, soft-
sediment community include a variety of mollusks, arthropods, and
worms. Areas of Boston Harbor that were affected by sewage had
severely reduced numbers and types of animals, often dominated by
pollution-tolerant worms. Changes in the bottom animal communities
have been dramatic, as the communities responded to ending of sludge and
effluent discharges and also to severe storms. These changes have been
documented through collection and analysis of sediment grab samples,
which have been collected during August of each year (from nine stations
in recent years) within the harbor (Figure 7-9). Greater geographic
coverage is achieved by taking sediment-profile images from 61
reconnaissance stations.
The changes in the bottom communities are not always evident from
examining averages of standard community parameters. Since 1991, the
total abundance of organisms has fluctuated (Figure 7-10, top). The
species richness parameters, number of taxa and log-series alpha,

2005 OUTFALL MONITORING OVERVIEW 84 
increased when the Massachusetts Bay outfall went on line, but have since
declined (Figure 7-10, middle and bottom). Dramatic improvements have
been seen at some stations, such as Station T01 near Deer Island, where
diversity is much higher, and Station T05A at the harbor mouth, which
now supports many species that were previously found only in
Massachusetts Bay.

2005 OUTFALL MONITORING OVERVIEW 85 
Figure 7-9. Locations of benthic stations within Boston Harbor

2005 OUTFALL MONITORING OVERVIEW 86 
Figure 7-10. Benthic community parameters in Boston Harbor, 1991-2005.
Parameters calculated from traditional grab stations: Top: abundance per
sample, Middle: species richness (number species per sample), Bottom: species
richness (log-series alpha) 
Boston Harbor 
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Log-series Alpha 
Mean+/- 1SD 
Boston Harbor 
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Number of Taxa 
Mean+/- 1SD 
Boston Harbor 
0
2000
4000
6000
8000
10000
12000
14000
16000
18000
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Total Abundance 
Mean+/- 1SD

2005 OUTFALL MONITORING OVERVIEW 87 
The changes can also be demonstrated by examining the increase and
subsequent decline in tube mats formed by the amphipods in the genus 
Ampelisca . In 1989 and 1990, MWRA found Ampelisca tube mats at
only 24% of the stations sampled in the harbor. In October 1991, a major
storm, immortalized as “The Perfect Storm,” caused the highest storm
surge in Boston Harbor in two decades, scouring soft (and contaminated)
sediments from the sea floor. This scouring, coupled with the ending of
sludge discharges to the harbor in December 1991, was followed by a
surge in Ampelisca . By August 1992, more than 50% of stations in the
harbor had tube mats.
Total number of Ampelisca increased through 1994 (Figure 7-11). The
number of stations with mats increased through 1996, when more than
80% of the stations had tube mats. After the mid-1990s, the numbers of
total Ampelisca appeared to be declining, only to increase again in 2003
and decrease in 2004. It was expected that these fluctuations would
continue, that they were normal successional changes such as would be
expected in the healthier, cleaner environment.
However, the severe storms that occurred in May 2005 interrupted the
usual seasonal pattern of amphipod growth, and only 616 Ampelisca 
individuals were found in the harbor samples (compared to 73,112 in
2003). Existing mats had been broken apart and washed away. Changes
in the surface sediments were observed in the sediment-profile images
(Figure 7-12) and in the benthic grab samples. Scientists are unsure
whether Ampelisca will ever return in high numbers or whether a new
community will be established. 
Ampelisca spp. 
Total number sampled by grab at eight Boston Harbor stations each August
0
10,000
20,000
30,000
40,000
50,000
60,000
70,000
80,000
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Total Number per Sampling Date 
Figure 7-11. Total number of Ampelisca per sample, 1991-2005

2005 OUTFALL MONITORING OVERVIEW 88 
Figure 7-12. Photographs from the same station (R28) in Hingham Harbor in
2004 (top) and 2005 (bottom). Note amphipod tube mats in 2004 photograph.

2005 OUTFALL MONITORING OVERVIEW 89
8. Stellwagen Bank
National Marine Sanctuary
Background 
The Gerry E. Studds Stellwagen Bank National Marine Sanctuary
(SBNMS) comprises 842 square miles located at the boundary between
Massachusetts Bay and the rest of the Gulf of Maine. Its landward
boundaries lie approximately 25 miles east of Boston, three miles north of
Provincetown, and three miles south of Gloucester. Stellwagen Basin,
which is partially within the sanctuary, is the deepest part of
Massachusetts Bay and a long-term sink for fine-grained sediments.
Stellwagen Bank, a sand-and-gravel plateau, lies to the east of Stellwagen
Basin and has water depths of about 65 feet. Tidal mixing of nutrients
throughout the relatively shallow water column creates a rich habitat for
marine life on Stellwagen Bank.
MWRA’s discharge permit recognizes concerns about possible effects of
the outfall on the sanctuary and requires an annual assessment of those
possible effects. 
Monitoring Design 
MWRA’s regular water-column and sea-floor monitoring efforts include
stations within and near the sanctuary. Five water-column stations,
including four within the sanctuary and one just outside its northern
border, are considered “boundary” stations, because they mark the
boundary between Massachusetts Bay and the rest of the Gulf of Maine.
These stations are important to MWRA, not just because of their location
within a marine sanctuary, but also because water-column processes
within Massachusetts Bay are largely driven by the regional processes in
the Gulf of Maine. Eight water-column stations located between the
sanctuary and the coast are considered “offshore” stations by the MWRA
program.
Since 2001, the sanctuary managers, in conjunction with MWRA’s
contractor Battelle, have conducted a monitoring program which added
four stations to the August and October MWRA surveys (Figure 8-1).
These sites were selected to provide a more comprehensive evaluation of
water quality across the sanctuary. The program and results for 2005 are
described in Libby et al. (2006b).

2005 OUTFALL MONITORING OVERVIEW 90 
Figure 8-1. Water column stations, including the additional Stellwagen Bank National Marine
Sanctuary (SBNMS) stations sampled in August and October 2001-2005; F32 and F33 sampled
in February, March, and April; other stations sampled in February, March, April, June, August,
and October

2005 OUTFALL MONITORING OVERVIEW 91 
Two MWRA sea-floor stations are within the sanctuary, one at the
southern boundary and one within Stellwagen Basin (FF04 and FF05, see
Figure 4-2). A third sea-floor station (FF11) is just north of the sanctuary
boundary and a fourth station (FF14) is located outside the sanctuary, but
within Stellwagen Basin. These four stations are the deepest of those
included in the MWRA monitoring program and have similar properties,
with muddy sediments and moderate concentrations of total organic
carbon. The station north of the sanctuary and the one within Stellwagen
Basin are east or northeast of the outfall, outside the general circulation
pattern that transports diluted effluent south and southeastward in
Massachusetts Bay. From 1992 through 2003, these stations were
sampled annually in August. Changes to the benthic monitoring program
implemented in 2004 call for sampling approximately half the stations
each year. Stations FF11 and FF14 were sampled in 2005. 
Results
Water Column 
Overall, water quality within the sanctuary was excellent during 2005.
There was no indication of any effect of the MWRA outfall (Libby et al. 
2006B). While ammonium concentrations rose in the nearfield following
the outfall diversion, there has been no parallel annual increase in
Stellwagen Bank or Cape Cod Bay (Figure 8-2, top). Nitrate
concentrations (Figure 8-2, bottom) continue to show an upward trend in
offshore Massachusetts Bay and in the nearfield, a regional phenomenon
that predates the outfall diversion and is not well understood. Other
measurements of nitrogen (Figure 8-3) and dissolved phosphate (not
shown) also show these long-term trends. Concentrations of nitrate,
dissolved inorganic nitrogen, and total dissolved nitrogen have
consistently been higher in samples from the sanctuary than those
measured at other stations. In contrast, concentrations of total nitrogen
have been similar in all regions.

2005 OUTFALL MONITORING OVERVIEW 92 
0.0
0.5
1.0
1.5
2.0
2.5
3.0
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
Year
NH4 ( μ M)
SBNMS
Nearfield
Cape Cod
Outfall Startup 
0
1
2
3
4
5
6
7
8
9
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
Year
NO3 ( μ M)
SBNMS
Nearfield
Cape Cod
Outfall Startup 
Figure 8-2. Annual mean ammonium (top) and nitrate (bottom) in the Stellwagen
Bank National Marine Sanctuary, the nearfield, and Cape Cod Bay

2005 OUTFALL MONITORING OVERVIEW 93 
0
2
4
6
8
10
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
Year
DIN ( μ M)
SBNMS
Nearfield
Cape Cod
Outfall Startup 
0
5
10
15
20
25
30
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
Year
TDN ( μ M)
SBNMS
Nearfield
Cape Cod
Outfall Startup 
0
5
10
15
20
25
30
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
Year
TN ( μ M)
SBNMS
Nearfield
Cape Cod
Outfall Startup 
Figure 8-3. Top: Annual mean dissolved inorganic nitrogen (DIN); Middle: total
dissolved nitrogen (TDN); Bottom: total nitrogen (TN) in Stellwagen Bank
National Marine Sanctuary, the nearfield, and Cape Cod Bay

2005 OUTFALL MONITORING OVERVIEW 94 
The five years of August and October sampling by the sanctuary have
shown that within stations and depths, levels of nitrogen species, such as
nitrite, are generally similar to one another, although there is some
variation among stations and by year, as shown for nitrite (Figure 8-4).
One feature that stands out is the lower concentrations of nitrite plus
nitrate in the bottom waters of Station F28, which is located on Stellwagen
Bank (Figure 8-5). This difference appears to reflect the station’s shallow
depth. 
August - Surface
0.00
0.05
0.10
0.15
0.20
0.25
0.30
0.35
0.40
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Year
NO2 ( μ M)
SW1
F12
F28
F27
SW4
SW2
SW3
Outfall Startup 
August - Bottom
0.00
0.05
0.10
0.15
0.20
0.25
0.30
0.35
0.40
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Year
NO2 ( μ M)
SW1
F12
F28
F27
SW4
SW2
SW3
Outfall Startup 
Figure 8-4. Nitrite in October surface (top) and bottom (bottom) waters at
individual stations in Stellwagen Bank National Marine Sanctuary

2005 OUTFALL MONITORING OVERVIEW 95 
October - Bottom
0
2
4
6
8
10
12
14
16
18
20
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Year
NO2 + NO3 ( μ M)
SW1
F12
F28
F27
SW4
SW2
SW3
Outfall Startup 
Figure 8-5. Total nitrite plus nitrate in bottom waters at individual stations in
Stellwagen Bank National Marine Sanctuary 
The mean annual chlorophyll levels have not changed in response to the
outfall discharge (Figure 8-6). Annual chlorophyll levels were similar in
the nearfield, Cape Cod Bay, and Stellwagen Bank. 
0
20
40
60
80
100
120
140
160
180
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Year
Chlorophyll (mg m -2 )
SBNMS
Nearfield
Cape Cod
Outfall Startup 
Figure 8-6. Annual mean chlorophyll in Stellwagen Bank National Marine
Sanctuary and other regions

2005 OUTFALL MONITORING OVERVIEW 96 
As in other years, the MWRA monitoring program documented a spring 
Phaeocystis pouchetii bloom throughout Massachusetts and Cape Cod
bays (Libby et al. 2006a; disussed in Section 3, Water Column). The
major Alexandrium bloom (discussed in Section 3, Water Column, and
Section 6, Special Studies) occurred in May and June. By August, no
evidence of the bloom remained within the waters of the sanctuary.
Concentrations of dissolved oxygen and percent saturation have not
declined in the Stellwagen Basin or in the nearfield (data not shown).
Rather than showing a decline, levels in 2005 were slightly high compared
to the baseline years. 
Sea Floor 
No changes in concentrations of sewage tracers or sewage-related
contaminants were observed in the sediment samples from stations within
the sanctuary, and there were no changes in community parameters in
2005 (Maciolek et al. 2006).
The deep-water stations (see Figure 4-2) continued to support a distinct
infaunal community with recognizable differences from communities in
the nearfield and Cape Cod Bay. Benthic community parameters at
individual stations showed no pattern of change following start-up of the
outfall in 2000 (Figure 8-7). Overall, the numbers of individual organisms
and species per sample have increased, paralleling results from throughout
Massachusetts Bay. No consistent pattern has been found that relates to
outfall operation.

2005 OUTFALL MONITORING OVERVIEW 97 
0
1000
2000
3000
4000
5000
6000
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Year
Abundance (individuals/ sample)
FF05
FF04
FF14
FF11
Outfall startup 
0
10
20
30
40
50
60
70
80
90
100
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Year
Total Species per Sample
FF05
FF04
FF14
FF11
Outfall startup 
0
2
4
6
8
10
12
14
16
18
20
22
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005
Year
Log Series Alpha
FF05
FF04
FF14
FF11
Outfall startup 
Figure 8-7. Benthic community parameters at stations in or near the Stellwagen
Bank National Marine Sanctuary, 1992-2005

2005 OUTFALL MONITORING OVERVIEW 98
References 
Bothner MH, Butman B. (editors) 2005. Processes influencing the
transport and fate of contaminated sediments in the coastal ocean—Boston
Harbor and Massachusetts Bay. Woods Hole: U.S. Geological Survey
Open-File Report 2005-1250.
Butman B, Valentine PC, Danforth WW, Hayes L, Serrett LA, Middleton
TJ. 2004. Shaded relief, backscatter intensity and sea floor topography of
Massachusetts Bay and Stellwagen Bank region, offshore of Boston,
Massachusetts. U.S. Geological Survey Geologic Investigation Map I-
2734, scale 1:125,000. 2 sheets.
Butman B, Warner JC, Bothner MH, Alexander PS. 2005. Section 6:
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Coughlin K. 2006. Summary of CSO receiving water quality monitoring
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2006-07 38p.
Delaney MF, Hall MP. 2006 Contaminant monitoring of Deer Island
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Resources Authority. Report ENQUAD. Draft.
EPA. 1988. Boston Harbor Wastewater Conveyance System.
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Environmental Protection Agency Region 1.
EPA. 2004. National recommended water quality criteria. Office of Water,
Office of Science and Technology. 24p.
Gayla DP, Bleiler J, Hickey K. 1996. Outfall monitoring overview report:
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List of Acronyms 
AF Alexandrium fundyense targeted survey
BEM Bays Eutrophication Model
BOD Biochemical oxygen demand
BS Broad Sound
cBOD Carbonaceous biochemical oxygen demand
CCB Cape Cod Bay
CCC Criterion continuous concentration
CHV Centrotubular hydropic vacuolation
CMC Criterion maximum concentration
C-NOEC Chronic test, no observable effect concentration
CSO Combined sewer overflow
DDE Dichlorodiphenylethylene
DDT Dichlorodiphenyltrichloroethane
DIF Deer Island Flats
DIN Dissolved inorganic nitrogen
DO Dissolved oxygen
ECCB Eastern Cape Cod Bay
EPA U.S. Environmental Protection Agency
FDA U.S. Food and Drug Administration
FA Foul Area
FF Farfield
GFAA Graphite furnace

The text goes on. The rest is in the file.