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2004 overview

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2004 outfall monitoring overview 
Massachusetts Water Resources Authority 
Environmental Quality Department 
Report ENQUAD 2005-16

Citation: 
Werme C, Hunt CD. 2005. 2004 Outfall monitoring overview. Boston: Massachusetts Water
Resources Authority. Report ENQUAD 2005-16. 88p.

2004 
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 
November 2, 2005

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2004 OUTFALL MONITORING OVERVIEW I 
Table of Contents 
List of Figures .................................................................................................................... iii 
List of Tables ...................................................................................................................... v 
Summary ........................................................................................................................... vii 
1. Introduction ..................................................................................................................... 1 
Background ..................................................................................................................... 1 
Outfall Permit .................................................................................................................. 3 
Monitoring Program ........................................................................................................ 5 
Contingency Plan ............................................................................................................ 8 
Data Management ........................................................................................................... 9 
Reporting ......................................................................................................................... 9 
Outfall Monitoring Overview ....................................................................................... 10 
2. Effluent ......................................................................................................................... 11 
Background ................................................................................................................... 11 
Pollution Prevention and Wastewater Treatment ..................................................... 11 
Environmental Concerns ........................................................................................... 11 
Monitoring Design ........................................................................................................ 13 
Results ........................................................................................................................... 16 
Contingency Plan Thresholds ....................................................................................... 19 
3. Water Column ............................................................................................................... 20 
Background ................................................................................................................... 20 
Circulation and Water Properties .............................................................................. 20 
Environmental Concerns ........................................................................................... 22 
Monitoring Design ........................................................................................................ 24 
Results ........................................................................................................................... 27 
Physical Conditions .................................................................................................. 27 
Water Quality ............................................................................................................ 30 
Phytoplankton Communities ..................................................................................... 35 
Zooplankton Communities ........................................................................................ 38 
Contingency Plan Thresholds ....................................................................................... 39 
4. Sea Floor ....................................................................................................................... 41 
Background ................................................................................................................... 41 
Bottom Characteristics and Sediment Transport ...................................................... 41 
Environmental Concerns ........................................................................................... 41 
Monitoring Design ........................................................................................................ 42 
Results ........................................................................................................................... 47 
Sediment Characteristics, Tracers, and Contaminants .............................................. 47 
Sediment-Profile Imaging ......................................................................................... 48 
Soft-bottom Communities ......................................................................................... 51 
Hard-bottom Communities ....................................................................................... 53 
Contingency Plan Thresholds ....................................................................................... 54 
5. Fish and Shellfish .......................................................................................................... 55 
Background ................................................................................................................... 55

2004 OUTFALL MONITORING OVERVIEW II 
Monitoring Design ........................................................................................................ 56 
Results ........................................................................................................................... 58 
Contingency Plan Thresholds ....................................................................................... 62 
6. Special Studies .............................................................................................................. 63 
Background ................................................................................................................... 63 
Nutrient Flux ................................................................................................................. 63 
Marine Mammal Observations ..................................................................................... 65 
Model Results ............................................................................................................... 67 
Virus Monitoring in Boston Harbor and the Charles River .......................................... 69 
Recent Trends in Solids and Nutrient Loadings to Boston Harbor .............................. 70 
2005 Alexandrium Bloom ............................................................................................. 72 
7. Stellwagen Bank ........................................................................................................... 75 
National Marine Sanctuary ............................................................................................... 75 
Background ................................................................................................................... 75 
Monitoring Design ........................................................................................................ 75 
Results ........................................................................................................................... 77 
Water Column ........................................................................................................... 77 
Sea Floor ................................................................................................................... 79 
References ......................................................................................................................... 81 
List of Acronyms .............................................................................................................. 87

2004 OUTFALL MONITORING OVERVIEW III 
List of Figures 
Figure 1-1. Map of Massachusetts and Cape Cod bays ...................................................... 2 
Figure 2-1. Annual effluent flows, 1990-2004 ................................................................ 16 
Figure 2-2. Annual nitrogen and solids discharges ........................................................... 17 
Figure 2-3. Top: Annual metals discharges; Bottom: mercury loads as a function of
amount of secondary treatment. ........................................................................................ 18 
Figure 3-1. General circulation within Massachusetts Bay .............................................. 20 
Figure 3-2. Water column sampling stations and regions ................................................. 25 
Figure 3-3. Top: Charles River discharge, 1992-early 2005; Bottom: 2004 Charles River
discharge compared to observations since 1992 ............................................................... 28 
Figure 3-4. Nearfield surface and bottom water temperature, salinity, and stratification 30 
Figure 3-5. Post-diversion winter concentrations of ammonia and nitrate expressed as
change from the baseline in micromoles .......................................................................... 31 
Figure 3-6. Post-transfer nearfield ammonia concentrations compared to baseline ......... 32 
Figure 3-7. Annual mean ammonia concentrations in Massachusetts Bay regions .......... 32 
Figure 3-8. Post-transfer nearfield nitrate concentrations compared to baseline ............. 33 
Figure 3-9. Annual mean nitrate concentrations in Massachusetts Bay regions .............. 33 
Figure 3-10. Post-transfer nearfield chlorophyll compared to baseline ............................ 34 
Figure 3-11. Post-transfer nearfield dissolved oxygen concentrations compared to
baseline ............................................................................................................................. 35 
Figure 3-12. Post-transfer nearfield phytoplankton abundance compared to baseline ..... 36 
Figure 3-13. Top: Abundance of Phaeocystis pouchetii in the nearfield, 1992-2004;
Middle: Duration of blooms by year; Bottom: duration of blooms vs. day of the year that
water temperatures reached 14°C ..................................................................................... 37 
Figure 3-14. Post-transfer nearfield zooplankton abundance compared to baseline ........ 38 
Figure 4-1. Locations of nearfield soft-bottom stations sampled in August 2004 ............ 43 
Figure 4-2. Locations of farfield soft-bottom stations sampled in August 2004 .............. 44 
Figure 4-3. Locations of hard-bottom stations monitored in June 2004 ........................... 45 
Figure 4-4. Apparent color RPD for all data from nearfield stations ............................... 49 
Figure 4-5. Top: Sediment profile image from Station NF23, showing physically
structured sediment surface; Bottom: Image from Station NF08, showing biologically
structured surface .............................................................................................................. 50 
Figure 4-6. Community parameters in the nearfield, 1992-2004: abundance per sample,
species richness ................................................................................................................. 52 
Figure 4-7. Head of active diffuser #2, with frilly anemones surrounding the discharge
port. ................................................................................................................................... 53 
Figure 5-1. Prevalence of centrotubular hydropic vacuolation normalized for age ........ 58 
Figure 5-2. Blind-side flounder ulcers .............................................................................. 59 
Figure 5-3. Percent of flounder with ulcers ...................................................................... 60 
Figure 5-4. Mercury in flounder fillets and livers, 1992-2004 ......................................... 61 
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 ........................................................................................................................ 65

2004 OUTFALL MONITORING OVERVIEW IV 
Figure 6-2. Beluga whale interacts with diver during MWRA survey in April 2004 ...... 66 
Figure 6-3. Time series of modeled and observed temperature, salinity, dissolved
inorganic nitrogen, chlorophyll, oxygen, and productivity at station N04 near the outfall
in 2002. ............................................................................................................................. 68 
Figure 6-4. Changes in annual freshwater flow and loading to Boston Harbor, 1994-2003 
........................................................................................................................................... 71 
Figure 6-5. Alexandrium cell counts measured during MWRA monitoring surveys in
response to the red tide ..................................................................................................... 73 
Figure 6-6. Geographic extent of shellfish bed closures in July 2005 .............................. 74 
Figure 7-1. Water column stations, including the additional Stellwagen Bank National
Marine Sanctuary stations sampled in August and October 2001-2004 ........................... 76 
Figure 7-2. Annual mean ammonia and nitrate in the Stellwagen Bank National Marine
Sanctuary and other regions of Massachusetts and Cape Cod bays ................................. 78 
Figure 7-3. Annual mean chlorophyll in Stellwagen Bank National Marine Sanctuary and
other regions ...................................................................................................................... 79 
Figure 7-4. Benthic community parameters at stations within the boundary region,
1992-2004 ......................................................................................................................... 80

2004 OUTFALL MONITORING OVERVIEW V 
List of Tables 
Table 1. Summary of monitoring questions and status as of the end of 2004 ................. viii 
Table 2. Summary of Contingency Plan thresholds and exceedances as of 2004 ............. xi 
Table 1-1. Roster of panel and committee members .......................................................... 4 
Table 1-2. Public concerns and environmental responses presented in the monitoring plan 
............................................................................................................................................. 6 
Table 1-3. Summary of the monitoring program ................................................................ 7 
Table 1-4. Contingency Plan threshold parameters ............................................................ 8 
Table 1-5. List of monitoring reports submitted to OMSAP ............................................ 10 
Table 2-1. Monitoring questions related to effluent monitoring ...................................... 12 
Table 2-2. Reporting requirements of the outfall permit .................................................. 14 
Table 2-3. Monitoring plan parameters for effluent ......................................................... 16 
Table 2-4. Contingency Plan threshold values and 2004 results for effluent monitoring 19 
Table 3-1. Monitoring questions related to the water column ......................................... 23 
Table 3-2. Components of water-column monitoring ....................................................... 24 
Table 3-3. Nearfield water column monitoring parameters .............................................. 26 
Table 3-4. Farfield water column monitoring parameters ................................................ 26 
Table 3-5. Contingency Plan threshold values for water-column monitoring .................. 40 
Table 4-1. Monitoring questions related to the sea floor .................................................. 42 
Table 4-2. No Contingency Plan baseline and threshold values for sea-floor monitoring
were exceeded in 2004. ..................................................................................................... 54 
Table 5-1. Monitoring questions related to fish and shellfish .......................................... 55 
Table 5-2. Chemical analyses of fish and shellfish ........................................................... 57 
Table 5-3. Contingency Plan baseline, threshold, and 2004 values for fish and shellfish
monitoring ......................................................................................................................... 62 
Table 6-1. Monitoring questions related to nutrient flux .................................................. 63

2004 OUTFALL MONITORING OVERVIEW VI 
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2004 OUTFALL MONITORING OVERVIEW VII 
Summary 
During 2004, the fourth full year of discharge from the Massachusetts Bay outfall, the
Deer Island Treatment Plant operated as designed, with no detectable negative effects on
the ecosystem 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 four years of post-discharge monitoring, the
Massachusetts Water Resources Authority (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. 
There were three Contingency Plan exceedances during the year (Table 2). On one day
in April, the daily mean effluent fecal coliform bacteria count was slightly higher than the
permit allowance. This excursion took place during a period of rough weather, so no
field measurements could be taken; however, the rough weather also increased mixing,
minimizing a chance for any environmental effect. As in 2002 and 2003, summer
concentrations of the nuisance algal species Phaeocystis pouchetii exceeded the caution
level. In 2004, the winter/spring concentration of Phaeocystis pouchetii also exceeded
the caution level. As in 2002 and 2003, the wide geographical extent of the bloom
suggests that regional processes, rather than the outfall, have been responsible for
increasing frequency of Phaeocystis blooms. 
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. 
During 2004, MWRA implemented several changes to the monitoring program,
following a revised monitoring plan, which focuses on the potential for long-term chronic
effects. Effluent monitoring remained unchanged. Nearfield water column sampling was
reduced from 17 surveys of 21 stations to 12 surveys of 7 stations. Soft-bottom sampling
began a rotation, in which approximately half the stations were sampled for identification
and enumeration of animals, with the remainder of the stations to be sampled and
analyzed in alternate years. Fish and shellfish sampling also began a rotation, in which
samples will be analyzed for chemical constituents once every three years. These
measurements of chemical constituents were not made during 2004.

2004 OUTFALL MONITORING OVERVIEW VIII 
Table 1. Summary of monitoring questions and status as of the end of 2004 
Monitoring Question Status 
Do effluent pathogens exceed the permit limits? Pathogenic viruses detectable in the final effluent
but at very low numbers: secondary treatment
effectively removes 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 and
adverse condition 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 surveys and adverse condition
surveys 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.

2004 OUTFALL MONITORING OVERVIEW IX 
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? 
No outfall-related change detected. Frequency of 
Phaeocystis blooms has increased, but the
phenomenon is regional in nature. 
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? Possible localized change reflected by high number
of animals in the nearfield in 2002 (decrease in
2004). 
Have the sediments become more anoxic; that
is, has the thickness of the sediment oxic layer
decreased? 
No change in total organic carbon or 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? Small increase in sediment drape on hard-bottom
surfaces detected at a subset of stations; not yet
known whether these changes are related to the
outfall.

2004 OUTFALL MONITORING OVERVIEW X 
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 short-term changes. 
Has the level of contaminants in the tissues of
fish and shellfish around the outfall changed
since discharge began? 
No short-term changes 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 in 2003 and 2004. 
Do the levels of contaminants in the edible
tissue of fish and shellfish around the outfall
represent a risk to human health? 
No short-term 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.

2004 OUTFALL MONITORING OVERVIEW XI 
Table 2. Summary of Contingency Plan thresholds and exceedances as of 2004. (NA = not
applicable, D = no exceedance, C = caution level exceedance, W = warning level exceedance) 
Location/ 
Parameter 
Type 
Parameter 2000 2001 2002 2003 2004 
Effluent 
pH W D D D D 
Fecal coliform
bacteria, monthly D D D D D 
Fecal coliform
bacteria, weekly D D D D D 
Fecal coliform
bacteria, daily D W D D W 
Fecal coliform
bacteria, 
3 consecutive days 
D D D D D 
Chlorine residual,
daily W D D D D 
Chlorine residual,
monthly D D D D D 
Total suspended
solids, weekly D D W D D 
Total suspended
solids, 
monthly 
D D W D D 
cBOD, weekly D D D D D 
cBOD, monthly D D D D D 
Acute toxicity,
mysid shrimp D D D D D 
Acute toxicity, fish D D D D D 
Chronic toxicity,
fish D W D D D 
Chronic toxicity,
sea urchin D W D D D 
PCBs D D D D D 
Plant performance D D D D D 
Flow NA D D D D 
Total nitrogen load NA D D D D 
Floatables NA NA NA NA NA 
Oil and grease D D D D D 
Water Column 
Dissolved oxygen
concentration C D D D D Nearfield 
bottom water Dissolved oxygen
saturation C D D D D 
Dissolved oxygen
concentration D D D D D Stellwagen
Basin 
bottom water Dissolved oxygen
saturation D D D D D 
Nearfield 
bottom water 
Dissolved oxygen
depletion rate
(June-October) 
NA D D D D 
Annual NA D D D D 
Winter/spring NA D D D D 
Summer NA D D D D 
Nearfield
chlorophyll 
Autumn C D D D D

2004 OUTFALL MONITORING OVERVIEW XII 
Location/ 
Parameter 
Type 
Parameter 2000 2001 2002 2003 2004 
Winter/spring NA D D D C 
Summer NA D C C C 
Nearfield
nuisance algae 
Phaeocystis
pouchetii Autumn D D D D D 
Winter/spring NA D D D D 
Summer NA D D D D 
Nearfield
nuisance algae 
Pseudonitzchia Autumn D D D D D 
Nearfield
nuisance algae 
Alexandrium
fundyense 
Any sample D D D D D 
Farfield
shellfish PSP toxin extent D D D D D 
Plume Initial dilution NA D Completed 
Sea Floor 
Nearfield
sediment RPD depth NA D D D D 
Species per sample NA D D D D 
Fisher’s log-series
alpha NA D D D D 
Shannon diversity NA D D D D 
Nearfield
benthic
diversity 
Pielou’s evenness NA D D D D 
Nearfield
species
composition 
Percent opportunists NA D D D D 
Fish and Shellfish 
Total PCBs NA D D D NA 
Mercury NA D D D NA 
Chlordane NA D D D NA 
Dieldrin NA D D D NA 
Nearfield
flounder tissue 
Total DDTs NA D D D NA 
Nearfield
flounder Liver disease (CHV) NA D D D D 
Total PCBs NA D D D NA 
Mercury NA D D D NA 
Chlordane NA D D D NA 
Dieldrin NA D D D NA 
Nearfield
lobster tissue 
Total DDTs NA D D D NA 
Total PCBs NA D D D NA 
Lead NA D D D NA 
Mercury NA D D D NA 
Chlordane NA C C D NA 
Dieldrin NA D D D NA 
Total DDTs NA D D D NA 
Nearfield
mussel tissue 
Total PAHs NA C C C NA

2004 OUTFALL MONITORING OVERVIEW 1 
1. Introduction 
Background 
For 20 years, the Massachusetts Water Resources Authority (MWRA) has
worked to end long-standing violations of the Clean Water Act and to
minimize the effects of wastewater discharge on the marine environment.
Before MWRA was created in 1985, 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 the southern
Quincy Bay. MWRA ended discharge of municipal sludge into northern
and southern 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 involves removal of solids through settlement and disinfection.)
Batteries of secondary treatment (which includes bacterial decomposition
as well as settlement and 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. 
Better dilution was achieved in 2000, by diverting the effluent discharge
from Boston Harbor to a new outfall and diffuser system, located 9.5 miles
offshore in Massachusetts Bay (Figure 1-1).

2004 OUTFALL MONITORING OVERVIEW 2 
Figure 1-1. Map of Massachusetts and Cape Cod bays 
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 diffuser ensures that effluent
will not reach beaches or shellfish beds within a tidal cycle, even if
currents are shoreward.

2004 OUTFALL MONITORING OVERVIEW 3 
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. One aspect of the project, moving the effluent outfall from
the harbor to Massachusetts Bay, raised 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). 
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. (After expiration, MWRA
operates under the conditions of the permit until a new permit 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.

2004 OUTFALL MONITORING OVERVIEW 4 
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. 
Table 1-1. Roster of panel and committee members 
OMSAP as of December 2004 
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) 
Winifred Donnolly, MA Department of Environmental Protection (staff) 
IAAC as of December 2004 
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 2004 
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

2004 OUTFALL MONITORING OVERVIEW 5 
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 plan that eliminated unnecessary work were
proposed during 2003. 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. 
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). 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.

2004 OUTFALL MONITORING OVERVIEW 6 
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. 
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?

2004 OUTFALL MONITORING OVERVIEW 7 
Table 1-3. Summary of the monitoring program 
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 near outfall location 
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

2004 OUTFALL MONITORING OVERVIEW 8 
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. 
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 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.

2004 OUTFALL MONITORING OVERVIEW 9 
Exceeding warning levels could, in some circumstances, indicate a need
for a response to avoid potential adverse environmental effects. If a
threshold is exceeded at a warning level, the response includes early
notification to EPA and MADEP and, if the outfall has contributed to
adverse environmental effects, the quick development of a response plan.
Response plans include a schedule for implementing actions, such as
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
set forth in MWRA’s NPDES permit. Revision 1 to the Contingency Plan
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 associated 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

2004 OUTFALL MONITORING OVERVIEW 10 
results become available, and MWRA must make all reasonable efforts to
report all data within 90 days of each sampling event. 
Reports are posted on MWRA’s web site (www.mwra.com), with copies
placed in repository libraries in Boston and on Cape Cod. OMSAP also
holds public workshops where outfall monitoring results are presented. 
Table 1-5. List of monitoring reports submitted to OMSAP 
Report Description/Objectives 
Outfall Monitoring Plan 
Phase I—Baseline Studies (MWRA
1991) 
Phase II—Discharge Ambient
Monitoring (MWRA 1997a, 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). 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 data that exceeded thresholds,
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 presents monitoring program
results for effluent and field data for 2004. It compares all results to
Contingency Plan thresholds. The overview also includes a section on
data relevant to the Stellwagen Bank National Marine Sanctuary.

2004 OUTFALL MONITORING OVERVIEW 11 
2. Effluent 
Background 
Pollution Prevention and Wastewater Treatment 
Ensuring that the final treated 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 Program (TRAC) 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

2004 OUTFALL MONITORING OVERVIEW 12 
permit limits (Table 2-1). Other questions require the use of effluent data
in conjunction with plume studies (Hunt et al. 2002a, 2002b) and water
column monitoring (see Section 3, Water Column). 
Table 2-1. Monitoring questions related to effluent monitoring 
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

2004 OUTFALL MONITORING OVERVIEW 13 
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 and variability of
constituents of the effluent 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
accurate mass loads of effluent constituents, so that fate, transport, and
risk of contaminants can be assessed.

2004 OUTFALL MONITORING OVERVIEW 14 
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 
Ammonia-nitrogen 24-hr composite 1/month 
Total Kjeldahl nitrogen 24-hr composite 1/month 
Total nitrate 24-hr composite 1/month 
Total nitrite 24-hr composite 1/month 
Cyanide, total Grab 1/month 
Copper, total 24-hr composite 1/month 
Total arsenic 24-hr composite 1/month 
Hexachlorobenzene 24-hr composite 1/month 
Aldrin 24-hr composite 1/month 
Heptachlor epoxide 24-hr composite 1/month 
Total PCBs 24-hr composite 1/month 
Volatile organic
compounds Grab 1/month 
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

2004 OUTFALL MONITORING OVERVIEW 15 
The permit also prohibits discharge of nutrients in amounts that would
cause eutrophication. The permit requires MWRA to test the toxicity of
the effluent as a whole on sensitive organisms and establishes limits based
on the tests. Allowable concentrations of contaminants were based on the
predicted dilution at the outfall, which was verified in the field during
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, ammonia,
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. Methods for
measuring floatables remain 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.
Section 6, Special Studies, reports on virus monitoring in Boston Harbor
and the Charles River.

2004 OUTFALL MONITORING OVERVIEW 16 
Table 2-3. Monitoring plan parameters for effluent 
Parameter Sample Type Frequency 
Total Kjeldahl nitrogen Composite Weekly 
Ammonia 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 of effluent from the Deer Island Treatment Plant in
2004 was slightly lower than in 2003 (Figure 2-1). Approximately 90% of
the flow received secondary treatment. 
MWRA Primary and Secondary Flows 1990-2004
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
Million Gallons per Day 
Primary-treated Flows Secondary-treated Flows 
Figure 2-1. Annual effluent flows, 1990-2004

2004 OUTFALL MONITORING OVERVIEW 17 
Nitrogen and solids discharges decreased slightly in 2004 (Figure 2-2),
reflecting the lower flow. Similarly, metals loads were slightly lower in
2004 than in 2003 (Figure 2-3, top). Overall, toxic compound
concentrations decrease with increased levels of secondary treatment (see
for example, mercury in Figure 2-3, bottom). 
Deer Island Treatment Plant Nitrogen Discharges 1996-2004
0
2000
4000
6000
8000
10000
12000
14000
1996 1997 1998 1999 2000 2001 2002 2003 2004 
*Method change for TKN April 2003 
Metric Tons per Year 
Ammonium Nitrite/Nitrate Other Nitrogen Species* Caution Level 
Solids in MWRA Treatment Plant Discharges 1988-2004
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
Tons per Day 
Deer Island Nut Island Sludge 
Figure 2-2. Annual nitrogen (top) and solids (bottom) discharges

2004 OUTFALL MONITORING OVERVIEW 18 
Metals in MWRA Treatment Plant Discharges 1989-2004
0
200
400
600
800
1000
1200
89 90 91 92 93 94 95 96 97 98 99 00 01 02 03 04
Year
Average pounds per day discharged 
Silver 
Nickel 
Chromium 
Lead 
Copper 
Zinc 
Effluent Mercury Loading vs Percent Secondary
Treatment (2002-2004)
0.00
0.10
0.20
0.30
0.40
0.50
0.60
0 10 20 30 40 50 60 70 80 90 100
Percent Secondary Treatment
Mercury Load (lbs/day) 
Figure 2-3. Top: Annual metals discharges; Bottom: mercury loads as a function of amount of
secondary treatment

2004 OUTFALL MONITORING OVERVIEW 19 
Contingency Plan Thresholds 
The Deer Island Treatment Plant had one permit violation during 2004
(Table 2-4). The permit and Contingency Plan specify that for fecal
coliform bacteria, the daily geometric mean of at least three samples taken
prior to entrance of the effluent into the outfall tunnel may not exceed
14,000 colonies per 100 ml. During an early April storm, the geometric
mean of three samples was 15,233 colonies per 100 ml. Rough weather at
the outfall site precluded a corresponding measurement of ambient
conditions but also promoted increased dilution, minimizing the chances
of any environmental consequence of the threshold exceedance. 
Table 2-4. Contingency Plan threshold values and 2004 results for effluent monitoring 
Parameter Caution Level Warning Level 2004 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) 
One exceedance of daily
geometric mean level. 
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 
Not exceeded 
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

2004 OUTFALL MONITORING OVERVIEW 20 
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. 
Figure 3-1. General circulation within Massachusetts Bay (from Beardsley et al. 1997) 
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 a mean counterclockwise circulation in
Massachusetts Bay and 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

2004 OUTFALL MONITORING OVERVIEW 21 
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). 
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. There are transient gyres in Massachusetts and
Cape Cod bays, which can 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,
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 begin two to three weeks
later. Spring phytoplankton blooms are typically followed by an increase
in zooplankton abundance. These zooplankton populations are food for
many animals, including the endangered right whale. 
Later in the spring, the surface waters warm, and the water column
stratifies. Inputs of freshwater from rivers contribute to the stratification,
with lighter, less saline water remaining at the surface. Stratification
effectively separates the surface and bottom waters, preventing
replenishment of nutrients to the surface and of oxygen to the bottom.
Phytoplankton in the surface waters deplete the available nutrients and
then undergo senescence, sinking 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

2004 OUTFALL MONITORING OVERVIEW 22 
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, 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 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 are of particular
concern: the dinoflagellate Alexandrium fundyense (the A. fundyense/
tamarense species group), the diatom Pseudo-nitzschia multiseries , and
the colonial flagellate Phaeocystis pouchetii . Alexandrium fundyense 
blooms are known in New England as red tides. The associated toxin,
when sufficiently concentrated, can cause paralytic shellfish poisoning
(PSP), which 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. Toxin-forming species occur with and appear identical to non-
toxin forming species when identified under a microscope. Phaeocystis
pouchetii is not toxic, but individual cells can aggregate in gelatinous
colonies that may be aesthetically displeasing, clog nets, or be poor food
for zooplankton. 
Dissolved oxygen concentrations in bottom waters naturally decrease
during the stratified period as part of the natural seasonal pattern.
Discharged nutrients that stimulated large phytoplankton blooms could
lead to even lower levels of dissolved oxygen when the cells sink to the
bottom and decay.

2004 OUTFALL MONITORING OVERVIEW 23 
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?

2004 OUTFALL MONITORING OVERVIEW 24 
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, verified the assumed dilution at the
outfall and confirmed assumptions that bacteria and toxic contaminant
concentrations in the discharged effluent are very low. 
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). Monitoring in 2004
constituted the first year of implementation of revisions to the program,
refocusing monitoring away from localized, short-term effects and
towards determining the potential for long-term effects (MWRA 2004).
Twelve surveys of seven nearfield stations and six surveys of 25 farfield
stations were conducted. Parameters measured are listed in Tables 3-3 and
3-4. 
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

2004 OUTFALL MONITORING OVERVIEW 25 
Figure 3-2. Water column sampling stations and regions

2004 OUTFALL MONITORING OVERVIEW 26 
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 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

2004 OUTFALL MONITORING OVERVIEW 27 
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 the forms most readily used
by phytoplankton. Since 1999, the surveys have also included
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. 
Results 
Physical Conditions 
Over the course of the entire year, runoff to Massachusetts Bay in 2004
was typical of all the years of monitoring, very similar to 2003 and greater
than in the drought years of 1992, 1995, and 2002 (Libby et al. 2005a;
Figure 3-3). The months January through March were dry, followed by a
typically rainy April and higher than average flow in September and
October. 
On average, temperature, salinity, and stratification in the nearfield since
the outfall went on-line are similar to the baseline. Baseline and post-
discharge monitoring has shown that the north-south component of the
wind stress in the region is important in determining water conditions, as
those winds determine the degree of upwelling and downwelling. For
most of 2004, the winds followed a typical pattern of wind stresses,
beginning with downwelling, transitioning to upwelling in the summer,
and returning to downwelling in the late fall. The summer upwelling was
somewhat weaker than usual, and there was an unusually strong period of
downwelling in the fall, causing warm bottom temperatures throughout the
fall (Figure 3-4 top). Salinity and stratification patterns were typical
(Figure 3-4, middle and bottom). Strong northeast winds that occurred
during storms in September and October appeared to cause partial mixing
of the near-bottom waters.

2004 OUTFALL MONITORING OVERVIEW 28 
Figure 3-3. Top: Charles River discharge, 1992-early 2005 (data from a gauge at Waltham and
3-month moving average); Bottom: 2004 Charles River discharge compared to observations
since 1992

2004 OUTFALL MONITORING OVERVIEW 29

25

nN
i=)

Degrees C
a

a
i=)

N wo
T T T
1 1 i

Stratification, kg/m

a
T
L

ie) iL 1 I
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005

2004 OUTFALL MONITORING OVERVIEW 30 
Figure 3-4. Nearfield surface and bottom water temperature, salinity, and stratification (Surface
measurements are the upper line for temperature and the lower line for salinity.) 
Water Quality 
As in every year since the Massachusetts Bay outfall began operation,
water quality measurements in 2004 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. 2005a). For example, while increased concentrations of
ammonia have been observed in the nearfield, decreased concentrations
have been observed in Boston Harbor and along the coast (Figure 3-5,
top). Concentrations of nitrate show almost no change from baseline
conditions (Figure 3-5, bottom). 
Ammonia is the form of nitrogen most readily taken up by phytoplankton,
and localized, elevated concentrations have been observed in the nearfield
during most surveys since the outfall began operation (Figure 3-6). These
elevated levels had been anticipated, because a large portion of the
dissolved inorganic nitrogen in treated effluent is ammonia; in fact,
ammonia has proven to be a good short-term tracer of the effluent plume. 
Conversely, concentrations of ammonia in Boston Harbor dropped
dramatically following effluent diversion to Massachusetts Bay and have
remained low (Figure 3-7). Averaged over the entire year, the increase in
ammonia concentrations in the vicinity of the outfall has been small in
comparison to the large decrease in ammonia concentrations in the harbor.
Ammonia concentrations have also declined at the coastal stations
compared to the years immediately preceding the outfall diversion.
Because of the volume of water available for dilution in the offshore, the
increase in ammonia in the nearfield is smaller than the corresponding
decrease in the harbor. 
Unlike 2001, 2002, and 2003, there were some surveys in 2004 during
which nearfield ammonia concentrations were not elevated over baseline
levels. Reasons for this outcome varied by season. During April 2004, all
available nutrients were being taken up by a large Phaeocystis pouchetii 
bloom. In July, a deep and strong pycnocline constrained nutrients to
deeper waters, causing nutrient depletion in the surface waters and
decreased mean water column values. A third event, in October, was not
as easily explained but may have resulted from current flow and horizontal
advection away from the nearfield.

2004 OUTFALL MONITORING OVERVIEW 31 
-71 -70.9 -70.8 -70.7 -70.6 -70.5 -70.4 -70.3 -70.2 
41.9
42
42.1
42.2
42.3
42.4
42.5
42.6 
-5 -3 -1 1 3 
Ammonium
Winter/Spring 
-71 -70.9 -70.8 -70.7 -70.6 -70.5 -70.4 -70.3 -70.2 
41.9
42
42.1
42.2
42.3
42.4
42.5
42.6 
-5 -3 -1 1 3 
Nitrate
Winter/Spring 
Figure 3-5. Post-diversion winter concentrations of ammonia (top) and nitrate (bottom)
expressed as change from the baseline in micromoles (μM). Both plots are winter/spring data
and reflect the changes from 1992-2000 to 2001-2004.

2004 OUTFALL MONITORING OVERVIEW 32 
0
2
4
6
8
10
12
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
NH4 ( 8 M) 
Baseline Mean+/-1SD 
Post Transfer Mean +/-1SD 
Figure 3-6. Post-transfer nearfield ammonia concentrations compared to baseline 
0
1
2
3
4
5
6
7
8
9
10
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
NH4 ( μ M) 
Boston Harbor Nearfield N. Boundary Cape Cod 
Coastal Offshore Outfall Startup 
Figure 3-7. Annual mean ammonia concentrations in Massachusetts Bay regions 
Unlike ammonia, for most surveys, concentrations of nitrate, another form
of nitrogen readily used by phytoplankton and present in the effluent, have
fallen within the baseline range and showed the same seasonal pattern as
seen in baseline monitoring (Figure 3-8), and there have been no regional
changes (Figure 3-9). Higher nitrate concentrations have been observed
during the early part and at the end of the year. Seasonal stratification has
continued to lead to typical, nutrient depletion in the surface waters, with
no evidence of inputs from the outfall.

2004 OUTFALL MONITORING OVERVIEW 33 
0
2
4
6
8
10
12
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
NO3 ( ℵ M) 
Baseline Mean+/-1SD 
Post Transfer Mean+/-1SD 
Figure 3-8. Post-transfer nearfield nitrate concentrations compared to baseline 
0
2
4
6
8
10
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
NO3 ( μ M) 
Nearfield Boston Harbor N. Boundary Cape Cod 
Coastal Offshore Outfall Startup 
Figure 3-9. Annual mean nitrate concentrations in Massachusetts Bay regions

2004 OUTFALL MONITORING OVERVIEW 34 
Chlorophyll (mg per square meter), a measure of phytoplankton biomass,
has also shown no response to nutrient enrichment of the outfall, even in
the nearfield (Figure 3-10), although the data are marked by large
variability in timing and magnitude of spring and fall peaks. Annual
chlorophyll measurements have shown no response to the outfall in the
nearfield or any region of the farfield. The year 2004 was somewhat
unusual in that no fall phytoplankton bloom was detected by the sampling
program, and SeaWIFS satellite imagery confirmed that no major bloom
occurred during or after sampling had been completed for the year.
Consequently, chlorophyll values remained low in all regions from June
through November (data not shown). The strong downwelling conditions
that were present at the time may have contributed to the lack of a bloom. 
0
2
4
6
8
10
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Chla ( ℵ g L -1 ) 
Baseline Mean+/-1SD 
Post Transfer Mean+/-1SD 
Figure 3-10. Post-transfer nearfield chlorophyll compared to baseline 
Measurements of concentrations (Figure 3-11) and percent saturation (not
shown) of dissolved oxygen in the bottom waters have also 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. In fact, the fall 2004 near-bottom oxygen
concentrations were higher than predicted from temperature and salinity
data, probably due to the partial mixing of the bottom waters during the
September and October storms.

2004 OUTFALL MONITORING OVERVIEW 35 
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+/-1SD 
Post Transfer Mean+/-1SD 
Figure 3-11. Post-transfer nearfield dissolved oxygen concentrations compared to baseline 
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. 2005a; Figure 3-12), and the taxonomic composition of the
phytoplankton community has been relatively consistent. Small
microflagellates and cryptomonads 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. 
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 3-13, top). 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, in 2001,
2002, 2003, and 2004.

2004 OUTFALL MONITORING OVERVIEW 36 
0
2
4
6
8
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
10 6 cells L -1 
Baseline Mean+/-1SD 
Post Transfer Mean+/-1SD 
Figure 3-12. Post-transfer nearfield phytoplankton abundance compared to baseline 
There has also been an earlier onset and longer duration of Phaeocystis 
blooms (Figure 3-13, middle). Prior to 2002, the blooms tended to occur
primarily during late March and April. Since 2002, blooms have started
earlier in March and lasted until early May. The 2004 bloom was the
largest recorded, with a nearfield survey maximum of 8 million cells per
liter. Cells were first detected in mid-March, peaked in April, and
declined in May. 
The broad geographic extent of Phaeocystis blooms argues against an
effect of the outfall. 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. Conceivably, increased
ammonia in the nearfield could enhance the magnitude and duration of the
bloom in the nearfield, but the local nutrient regime cannot explain the
overall increase in frequency of the regional blooms. 
The regional temperature regime may be one factor contributing to the
increased duration of the blooms that has been observed since 2002.
Regression analysis using temperature data from the Boston Buoy
indicates that the 2002, 2003, and 2004 blooms corresponded to years
when temperatures cooler than 14°C persisted into June (Figure 3-13,
bottom). (Data from years prior to 2000 were not included in the analysis
because of insufficient phytoplankton or temperature data.) Temperature
has been suggested as a major factor controlling Phaeocystis blooms
around the world (Schoemann et al. 2005).

2004 OUTFALL MONITORING OVERVIEW 37 
Phaeocystis - Nearfield
0
2
4
6
8
10
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
Abundance (millions of cells L -1 ) Phaeocystis abundance 
Outfall startup 
Phaeocystis Bloom Duration
0
30
60
90
120
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
Year
Days 
Outfall startup 
Phaeocystis Bloom Duration vs. Day of Year 
2000
2001
2002
2003
2004 
R 2 = 0.83
0
30
60
90
120
120 130 140 150 160 170
Day of Year 14 Degrees Celsius First Reached
Days 
Figure 3-13. Top: Abundance of Phaeocystis pouchetii in the nearfield, 1992-2004; Middle:
Duration of blooms by year; Bottom: duration of blooms vs. day of the year that water
temperatures reached 14°C

2004 OUTFALL MONITORING OVERVIEW 38 
In 2004, as in other post-diversion years, there were no detectable
increases in other nuisance species compared to the baseline. The
dinoflagellates Alexandrium spp. and diatoms in the genus Pseudo-
nitzschia were present but in low numbers. (A large Alexandrium bloom
occurred in 2005; that event is described briefly in Section 6, Special
Studies, and will be described in full in the 2005 outfall monitoring
overview.) 
Zooplankton Communities 
The structure of the zooplankton community in 2004 was similar to many
earlier years and continued to show no effects of the outfall (Libby et al. 
2005a). As in prior years, abundance was dominated by copepod nauplii
and copepodites and adults of the small copepod Oithona similis. 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 2001-2004 in comparison to the baseline period (Figure
3-14). Total abundance has been lower during the late spring and early
summer and during the fall. 
0
50,000
100,000
150,000
200,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
10 6 cells L -1 
Baseline Mean+/-1SD 
Post Transfer Mean+/-1SD 
Figure 3-14. Post-transfer nearfield zooplankton abundance compared to baseline 
The low mean nearfield abundance during the late spring and summer
reflects 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

2004 OUTFALL MONITORING OVERVIEW 39 
may be due to normal, large variability, but may also be a response to the
consecutive Phaeocystis pouchetii blooms that have occurred during those
years. 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 of the
monitoring data indicates that there decreased abundance of Oithona but
increased abundance of Calanus finmarchicus with increases in 
Phaeocystis abundance. 
The mean decrease in total nearfield zooplankton abundance during the
fall months appears to 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 a geographic larger area,
beginning in August and persisting to November. Mnemiopsis was
relatively low in abundance in 2004, but the lack of a fall phytoplankton
bloom may have provided less food and contributed to continuing low fall
abundance of zooplankton. 
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. 
Thresholds and baseline values presented in Table 3-5 were recalculated in
2004 to account for the changes in the monitoring program. There were
two exceedances of thresholds in 2004—the spring and summer 
Phaeocystis thresholds. The summer 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. All
other monitoring results were within ranges that met the thresholds.

2004 OUTFALL MONITORING OVERVIEW 40 
Table 3-5. Contingency Plan threshold values for water-column monitoring 
Location/ 
Parameter 
Specific 
Parameter Baseline Caution Level Warning 
Level 
2004 
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 =
7.55 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 =
80.4% 
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 =
7.72 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 =
80.4% 
Bottom water
nearfield 
DO depletion
rate (June-
October) 
0.024 mg/l/d 0.037 mg/l/d 0.049 mg/l/d 0.020
mg/l/d 
Annual 79 mg/m 2 118 mg/m 2 158 mg/m 2 69 mg/m 2 
Winter/spring 62 mgml 2 238 mg/m 2 None 101 mg/m 2 
Summer 51 mg/m 2 93 mg/m 2 None 61 mg/m 2 
Chlorophyll
nearfield 
Autumn 97 mg/m 2 212 mg/m 2 None 44 mg/m 2 
Winter/spring 468,000 cells/l 2,020,000 cells/l None 
2,870,000
cells/l,
caution
exceedance 
Summer 72 cells/l 357 cells/l None 
164,000
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 11 cells/l 
Summer 14,600 cells/l 43,100 cells/l None 3,375 cells/l 
Nuisance
algae
nearfield 
Pseudo-
nitzschia 
Autumn 9,940 cells/l 24,700 cells/l None 660 cells/l 
Nuisance
algae
nearfield 
Alexandrium
fundyense 
Any nearfield
sample 
Baseline
maximum =
163 cells/l 
100 cells/l None 5 cells/l
maximum 
Farfield PSP toxin
extent Not applicable New incidence None 
No toxicity
or shellfish
closures

2004 OUTFALL MONITORING OVERVIEW 41 
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
(USGS 1997, 1998). 
Sediment transport in the region occurs primarily during storms.
Typically, waves during storms with winds from the northeast resuspend
sediments, which are transported by shallow currents from western
Massachusetts Bay toward Cape Cod Bay and by deeper currents to
Stellwagen Basin. 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. An updated review of sediment transport is being completed
by USGS and will be presented in the 2005 outfall monitoring overview. 
Environmental Concerns 
Within Boston Harbor, studies of the sediments have documented
recovery following the cessation of sludge and effluent discharges and
other improvements. 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).

2004 OUTFALL MONITORING OVERVIEW 42 
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 considerable 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).

2004 OUTFALL MONITORING OVERVIEW 43 
Figure 4-1. Locations of nearfield soft-bottom stations sampled in August 2004 (BMBSOFT=soft-
bottom)

2004 OUTFALL MONITORING OVERVIEW 44 
z
z
z
z 
FF09
FF07
FF05
FF04 
70°50'0"W 
70°50'0"W 
70°40'0"W 
70°40'0"W 
70°30'0"W 
70°30'0"W 
70°20'0"W 
70°20'0"W 
41°50'0"N 
41°50'0"N 
42°0'0"N 
42°0'0"N 
42°10'0"N 
42°10'0"N 
42°20'0"N 
42°20'0"N 
Scituate 
Benthic Farfield Stations 
z Farfield Stations 
Outfall Diffuser 
0 2 4 6 1
Kilometers 
Benthic_Stations_Near_Scituate.mxd 
Figure 4-2. Locations of farfield soft-bottom stations sampled in August 2004

2004 OUTFALL MONITORING OVERVIEW 45 
Figure 4-3. Locations of hard-bottom stations monitored in June 2004

2004 OUTFALL MONITORING OVERVIEW 46 
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. One study, a collaborative effort between MWRA and USGS, has
investigated sediment transport and contaminant levels in Boston Harbor,
Massachusetts Bay, and Cape Cod Bay. USGS has periodically sampled
four stations within Boston Harbor since 1977 and has taken sediment
cores three times a year from two stations, one sandy and one muddy, near
the Massachusetts Bay outfall since 1989. USGS also uses a mooring in
the nearfield to collect hydrographic data and samples of suspended matter
in sediment traps. Suspended matter samples are analyzed for metals,
grain size, TOC, and effluent tracers. 
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

2004 OUTFALL MONITORING OVERVIEW 47 
(the degree to which a layer of fine material covers the hard surface), and
biota (taxa identified to species or species groups and counted). 
Several changes to the monitoring design were implemented in 2003 and
2004, as the monitoring program shifted its emphasis from the potential
for short-term, nearfield effects to investigation of long-term effects
(MWRA 2004). To effect these changes, 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 USGS) being included in both groups. The adjusted 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 the next sampling scheduled for 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. 
Since the outfall began operation, sediment grain size and total organic
carbon content at most stations have remained within the range of
variability measured during the baseline period (Maciolek et al. 2005).
Small increases in percentage of clay and total organic carbon have been
detected at some stations, but there has been no indication of any regional
effect. Abundance of the sewage tracer Clostridium perfringens spores

2004 OUTFALL MONITORING OVERVIEW 48 
has been within the baseline range, although increases in abundance in
comparison to the two years immediately prior to the outfall startup could
be measured. These increases were detected at stations located within
approximately two kilometers of the outfall. Abundances of Clostridium
perfringens spores, normalized to sediment grain size, decreased in 2003
and 2004 compared to 2001 and 2002. 
Data from the two stations sampled for toxic contaminants in 2004
remained within the baseline range for most samples. Small increases in
some metals and organic contaminants have been measured in some
samples during 2001 through 2004, but there have been no systematic or
widespread changes compared to the baseline. 
Sediment-Profile Imaging 
Sediment-profile imaging measurements in 2004 showed no changes from
the baseline to the post-baseline period (Figure 4-4). 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. 
Both physical and biological processes appeared to be responsible for
structuring the surface sediments in 2004 (Figure 4-5). The prominence of
biogenic features was similar to what was seen in 2003, but less than what
had been observed during the last years of the baseline period. All but one
station had high densities of small polychaete tubes.

2004 OUTFALL MONITORING OVERVIEW 49 
0.0
1.0
2.0
3.0
4.0
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
Year
RPD (cm) 
Mean RPD Depth +/- 1SD 
Outfall Startup 
Baseline Mean 
Threshold 
Figure 4-4. Apparent color RPD for all data from nearfield stations

2004 OUTFALL MONITORING OVERVIEW 50 
Figure 4-5. Top: Sediment profile image from Station NF23, showing physically structured
sediment surface (“pipe” is part of profiling gear): Bottom: Image from Station NF08, showing
biologically structured surface

2004 OUTFALL MONITORING OVERVIEW 51 
Soft-bottom Communities 
The soft-bottom communities have also shown no response to the outfall
(Maciolek et al. 2005). 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 2004, mean total abundance fell in both the nearfield (Figure 4-6, top)
and the farfield (not shown), primarily because of a major decline in the
abundance of one species, Prionospio steenstrupi (Maciolek et al. 2005).
Changes in species richness and diversity measured as log-series alpha
(Figure 4-6, middle and bottom), appeared to be part of the natural cycles
rather than indicative of any effects of the outfall. Both Shannon diversity
and Pielou’s evenness indices (not shown) were higher in 2004 than in
previous years, and above the baseline means. The changes in these
indices reflect the decrease in abundance of the formerly dominant 
Prionospio steenstrupi while numbers of total species remained fairly
constant.

2004 OUTFALL MONITORING OVERVIEW 52 
Nearfield Abundance
0
1000
2000
3000
4000
5000
6000
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 
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 
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 
Year
Log-Series Alpha 
Mean +/-1SD 
Baseline Mean:13.06 
Outfall Startup 
Figure 4-6. Community parameters in the nearfield, 1992-2004: abundance per sample, species
richness (number species per sample, log-series alpha)

2004 OUTFALL MONITORING OVERVIEW 53 
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. Lush epifaunal growth continues to
thrive, even on the diffuser heads (Figure 4-7). Sediment drape has
increased at some stations north and south of the outfall, with concurrent
declines in coralline algae cover at the same stations. Declines in upright
algae had been detected some stations in 2003, but that trend did not
continue in 2004. 
Figure 4-7. Head of active diffuser #2, with frilly anemones surrounding the discharge port.

2004 OUTFALL MONITORING OVERVIEW 54 
Contingency Plan Thresholds 
The revisions to the monitoring program that were enacted in 2004
required recalculating some Contingency Plan thresholds to account for
splitting the soft-bottom sampling into two subgroups (Table 4-2). None
of those Contingency Plan thresholds for sea-floor monitoring were
exceeded in 2004. No comparisons to thresholds for contaminants
concentrations in sediments were made. 
Table 4-2. No Contingency Plan baseline and threshold values for sea-floor monitoring were
exceeded in 2004 
Location Parameter Caution Level Warning Level 2004 Results 
Sediments,
nearfield RPD depth 1.18 cm None 2.4 cm 
Species per sample <48.41 or >82.00 None 77 
Fisher’s log-series
alpha <9.99 or >16.47 None 14.87 
Shannon diversity <3.37 or >4.14 None 4.07 
Even years, 
Benthic
diversity,
nearfield Pielou’s evenness <0.58 or >0.68 None 0.66 
Species per sample <46.52 or >79.95 None Not applicable 
Fisher’s log-series
alpha <9.95 or >15.17 None Not applicable 
Shannon diversity <3.30 or >3.91 None Not applicable 
Odd years, 
Benthic
diversity,
nearfield Pielou’s evenness <0.56 or >0.66 None Not applicable 
Benthic
opportunists % opportunists >10% >25% 0.23%

2004 OUTFALL MONITORING OVERVIEW 55 
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. Concerns have been expressed that the relocation 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, animals that live on
the bottom, in contact with sediments, and animals that eat bottom-
dwelling organisms are most likely to be affected. Exposure to
contaminated sediments could result in fin erosion, black gill disease, or
other, subtler, abnormalities in flounder, lobster, or other bottom-dwelling
animals. Shellfish that feed by filtering suspended matter from large
volumes of water are also potential bioaccumulators of toxic
contaminants. Consumption of filter-feeding animals by predators could
result in transferring contaminants up the food chain and ultimately to
humans.

2004 OUTFALL MONITORING OVERVIEW 56 
Monitoring Design 
The monitoring program focuses on three indicator species: winter
flounder, lobster, and blue mussel. Winter flounder and lobster are
important resource species in the region. The blue mussel is also a fishery
species and 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.

2004 OUTFALL MONITORING OVERVIEW 57 
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 
Revisions to the monitoring program (MWRA 2004) reduced the
frequency of fish and shellfish monitoring, because the aim is to detect
long-term rather than acute effects. 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. Flounder
and lobster are examined for external lesions. Histology analyses for
flounder will be made every year; chemical analyses for lobsters and
flounder will be completed every third year. Mussels will be deployed
every three years at three locations: outside the mixing zone at the outfall,
in Inner Boston Harbor, and at Deer Island Light.

2004 OUTFALL MONITORING OVERVIEW 58 
Results 
In 2004, only winter flounder were studied. Fifty sexually mature (at least
three years old) winter flounder were taken from each of the five sampling
sites during April. Each of the fish was examined for physical
characteristics. All fish were used for histological and age analyses.
Flounder tissue was also analyzed for mercury content. 
As in previous years, the mild centrotubular hydropic vacuolation (CHV)
was the most common form of vacuolation noted in histological analyses.
Incidence of CHV was low at all sites (Figure 5-1) and below the baseline
mean at the outfall site. 
Hydropic Vacuolation Index (CHV%/Age) for Each Station by Year
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 
*FF041 Data Only
* 
Figure 5-1. Prevalence of centrotubular hydropic vacuolation (CHV) normalized for age
(DIF = Deer Island Flats, OS = Outfall Site, ECCB = Eastern Cape Cod Bay, NB =
Nantasket Beach, and BS = Broad Sound)

2004 OUTFALL MONITORING OVERVIEW 59 
As in 2003, external ulcers were noted on the blind side of many fish
(Figure 5-2). Ulcers had not been specifically included as part of the
physical assessment provided for in the monitoring plan, prompting
additional studies, which were carried out in 2004 and early 2005 (Moore
2005). Studies included a review of additional information from other
investigators, sampling at additional stations, attempts to culture bacteria
that might be responsible for the ulcers, and additional histology. Surveys
were made in late June, October, and December 2004 and early March
2005. 
Figure 5-2. Blind-side flounder ulcers 
Those additional studies found ulcers on flounder throughout
Massachusetts Bay (Figure 5-3). Ulceration appeared to be limited to the
spring, with evidence of healing in June. No specific pathogenic bacteria
were found, and histological examination did not find evidence of a viral
or fungal cause of the ulcers (Moore et al. 2004).

2004 OUTFALL MONITORING OVERVIEW 60 
Figure 5-3. Percent of flounder with ulcers (M=March ’05, J=June ’04, N=October ’04,
D=December ’04) 
An OMSAP focus group met in March 2005 to review data and develop
recommendations for additional studies. The focus group concluded that
the appearance of ulcers was cause for concern and made suggestions for
studies that might help identify a cause. OMSAP recommended that
MWRA continue tracking and reporting on the prevalence of the ulcers. 
Mercury levels in 2004 were within the baseline ranges in flounder fillets
and liver samples (Figure 5-4, top and bottom). Elevated levels of
mercury in fillets from fish taken near the outfall, which had been noted in
2003, were also found in 2004, but at a slightly lower degree of elevation.

2004 OUTFALL MONITORING OVERVIEW 61 
Mercury in Flounder Fillets 1992-2004
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
Year
ug/g dry weight 
DIF 
OS 
ECCB 
NB 
BS 
Outfall Startup 
Mercury in Flounder Livers 1992-2004
0.0
0.2
0.4
0.6
0.8
1.0
1.2
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
Year
ug/g dry weight 
DIF 
OS 
ECCB 
NB 
BS 
Outfall Startup 
Figure 5-4. Mercury in flounder fillets and livers, 1992-2004

2004 OUTFALL MONITORING OVERVIEW 62 
Contingency Plan Thresholds 
Threshold parameters for fish and shellfish include levels of toxic
contaminants in flounder, lobster, and mussels and liver disease in
flounder (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. During 2004, only two thresholds were tested: mercury in
flounder tissue and liver disease in flounder. Both values remained well
below caution and warning thresholds. 
Table 5-3. Contingency Plan baseline, threshold, and 2004 values for fish and shellfish
monitoring 
Parameter 
Type/ 
Location 
Parameter Baseline Caution 
Level 
Warning 
Level 
2004 
Results 
PCB 0.033 ppm 1 ppm wet weight 1.6 ppm wet
weight Not applicable Flounder
tissue
nearfield Mercury 0.074 ppm 0.5 ppm wet
weight 
0.8 ppm wet
weight 0.107 ppm 
Chlordane 242 ppb 484 ppb None Not applicable 
Dieldrin 63.7 ppb 127 ppb None Not applicable 
Flounder
tissue, lipid
normalized,
nearfield DDT 775.9 ppb 1552 ppb None Not applicable 
Flounder 
Nearfield 
Liver disease
(CHV) 24.4% 44.9% None 18% 
PCB 0.015 ppm 1 ppm wet weight 1.6 ppm wet
weight Not applicable 
Lobster tissue
nearfield Mercury 0.148 ppm 0.5 ppm wet
weight 
0.8 ppm wet
weight Not applicable 
Chlordane 75 ppb 150 ppb None Not applicable 
Dieldrin 161 ppb 322 ppb None Not applicable 
Lobster
tissue, lipid
normalized,
nearfield DDT 341.3 ppb 683 ppb None Not applicable 
PCB 0.011 ppm 1 ppm wet weight 1.6 ppm wet
weight Not applicable 
Lead 0.415 ppm 2 ppm wet weight 3 ppm wet
weight Not applicable 
Mussel tissue 
Nearfield 
Mercury 0.019 ppm 0.5 ppm wet
weight 
0.8 ppm wet
weight Not applicable 
Chlordane 102.3 ppb 205 ppb None Not applicable 
Dieldrin 25 ppb 50 ppb None Not applicable 
DDT 241.7 ppb 483 ppb None Not applicable 
Mussel tissue,
lipid
normalized,
nearfield PAH 1080 ppb 2160 ppb None Not applicable

2004 OUTFALL MONITORING OVERVIEW 63 
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 2004, special studies
included nutrient flux at the sediment-water interface, marine mammal
observations, water quality modeling, viruses, and contaminant loading to
Boston Harbor. This section also includes a preliminary description of
activities initiated in response to an Alexandrium bloom or red tide, which
occurred in 2005. 
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 6-1). Comparable studies take place in Boston Harbor. 
Table 6-1. 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?

2004 OUTFALL MONITORING OVERVIEW 64 
In 2004, 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. 2005). Total organic carbon levels
were elevated above the baseline at one nearfield station, but the carbon-
to-nitrogen ratio and chlorophyll measurements suggested a relation to the
large spring Phaeocystis bloom rather than to the outfall. 
Sediment oxygen demand continued to be typical of the years since the
outfall came on line and at the low end of the baseline range. Nutrient
fluxes also continued to be well within and at the low end of the baseline
ranges. 
Studies also continued at the four Boston Harbor stations, where positive
effects of cessation of sludge disposal, improved sewage treatment, and
diversion of the outfall continued. Sediment oxygen demand was lower
than in any year except for 2002, and dissolved organic nitrogen and
phosphate fluxes were lower than at any previous time during the
monitoring period. For most measurements, there has been a 40-60%
decrease in fluxes from the pre- to the post-diversion period. 
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 declined to
levels lower than many estuaries, while the rates in Massachusetts Bay
have remained unchanged. The change is even more dramatic if only the
early part of the pre-diversion period (1993-1995) is considered. During
those years (data not shown), the sediment oxygen demand in Boston
Harbor was approximately the same as that of the Pawtuxent River. The
remarkable improvements in Boston Harbor with corresponding little
change in Massachusetts Bay is one measure of the success of the Boston
Harbor clean-up.

2004 OUTFALL MONITORING OVERVIEW 65 
0 20 40 60 80 100
Pawtuxent River Est, Md
BOSTON HARBOR, MA pre-diversion
Narragansett Bay, RI
South River Est, NC
Buzzards Bay, MA
BOSTON HARBOR, MA post diversion
Eel Pond, MA
Vostok Bay, Russia
Lock Eye, Scotland
New York Bight, NY
MASSACHUSETTS BAY, MA pre-diversion
MASSACHUSETTS BAY, MA post-diversion
Kaneohe Bay, HI
Site
O2 (mmol 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 May-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 2004, observers were included on all nearfield
water quality surveys, three farfield surveys, and two fecal coliform
surveys of the nearfield and near-shore area (Short and Shaub 2005).
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.

2004 OUTFALL MONITORING OVERVIEW 66 
The surveys are not designed to determine possible effects of the outfall
on marine mammals, but do provide some general information. During
the 2004 surveys, 11 individual whales, 14 harbor porpoise, one
unidentified porpoise, and more than 27 Atlantic white-sided dolphins
were directly observed by the trained observers and other members of the
monitoring team. The low number of whale sightings reflected a paucity
of whales in Massachusetts Bay that has been confirmed by the Whale
Center of New England, an organization founded in 1980 to study whales
along the Massachusetts coast. 
During the spring and summer of 2004, there were frequent reports of a
beluga whale along the coast of Maine and Massachusetts, including the
Boston Harbor area. Beluga whales are more typically seen in arctic
waters, where their white coloring provides camouflage with ice flows.
They are also more typically found in large social groups or pods. The
whale was very sociable, frequently interacting with humans, including a
diver on an MWRA survey who was in the water to free a tangled
propeller (Figure 6-2). Sadly, in November 2004, the whale was found
dead in southern Maine; a necropsy found no indication that its death was
related to interactions with humans. 
Figure 6-2. Beluga whale interacts with diver during MWRA survey in April 2004 (Photograph
courtesy of Michael Moore, Woods Hole Oceanographic Institution)

2004 OUTFALL MONITORING OVERVIEW 67 
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
Hydroqual, Inc. (2000) for MWRA. Working now with the University of
Massachusetts Boston, MWRA continues to maintain, enhance, and apply
the models and in 2004 completed updates on each of the models (Jiang
and Zhou 2004a, 2004b, additional reports in preparation). Figure 6-3
presents a comparison of modeled and observed data at one station in
2002. 
The modeled results compare well with observed conditions for many
factors, including seasonal changes in response to heat fluxes, daylight,
freshwater inputs, and boundary forcing. The model was able to
reproduce the strong response of the summer temperature, salinity, and
circulation to upwelling and downwelling winds, which has been reported
by Geyer et al. (1992, 2002) and by Libby et al. (2002, 2004). It also
reproduces the seasonal cycles and spatial patterns of phytoplankton
abundance, nutrients, and dissolved oxygen. It was not as successful at
predicting variations in chlorophyll. For other parameters, modeled
results did not match the actual conditions; for example, the model
underestimates salinity in the nearfield during the summer and fall, and
predicted summer current variations are out of phase with observed
variations. At some stations, the model does not show the same seasonal
variation in primary production as the data. As is usual for this type of
model, the simulations tend to show less variability in space and time than
the observations. The model can not reproduce very short-term events,
especially when these events are not observed in the boundary data. 
In September 2005, MWRA and the modeling team met with OMSAP's
Bays Eutrophication Model Evaluation Group (BEMEG), to present recent
results and discuss future directions for the modeling effort. Among other
findings and recommendations, the BEMEG agreed that, even considering
the model-data comparison issues mentioned above, the model reflects the
current state of the science.

2004 OUTFALL MONITORING OVERVIEW 68 
Figure 6-3. Time series of modeled and observed temperature, salinity, dissolved inorganic
nitrogen, chlorophyll, oxygen, and productivity at station N04 near the outfall in 2002.

2004 OUTFALL MONITORING OVERVIEW 69 
Virus Monitoring in Boston Harbor and
the Charles River 
MWRA’s routine monitoring of water quality in Boston Harbor and the
Charles River includes assessment of indicator bacteria ( E. coli and 
Enterococcus ) to gauge the potential risk to public health from pathogens.
Use of these indicators over the past century has been crucial in the
dramatic reduction of bacterial waterborne illnesses like typhoid fever and
dysentery. Today, however, the most common waterborne diseases are
caused by viruses, not bacteria, and there are scientific questions about
whether bacteria-indicator monitoring adequately predicts the risk from
viruses. 
In 1995, MWRA began the first studies ever conducted of viral pathogens
and viral indicators (also called coliphages) in Boston Harbor and the
Charles River (Ballester et al. 2004). At that time, there was no
information available about levels or prevalence of pathogens in the
Charles River or Boston Harbor. Testing was also done at the Deer Island
Treatment Plant and the Cottage Farm Combined Sewer Overflow (CSO)
Treatment Facility, which discharges to the Charles River. Goals of this
exploratory study were to learn whether human enteric viruses and viral
indicators (coliphages) could be detected in the study area and at what
levels; and to develop correlative data among bacterial sewage indicators,
human disease-causing viruses, coliphages, and environmental parameters
such as antecedent rainfall or CSO discharge. 
During 1995-2003, 138 samples were taken from five locations in Boston
Harbor, and 91 samples were taken from six locations in the lower Charles
River. The study confirmed that pathogenic viruses could be detected in
Boston Harbor and the Charles River—overall about 30% of samples had
detectable virus, which is comparable to what investigators have found in
other parts of the U.S. and the world. The lowest prevalence was at the
beaches. The abundance of pathogens in the harbor and the river was very
low; the highest count was about one virus per 10 liters of water and the
overall average for all samples was less than two virus per 100 liters of
water. Enteroviruses, which are common causes of gastroenteritis, were
the most frequently detected type of virus. Treatment at the CSO
treatment facility and at the Deer Island Treatment Plant both reduced the
number of viruses in wastewater by about 90%. 
Because pathogen presence is highly variable and sporadic in human
populations, it is inherently difficult to predict. Neither coliphages nor
bacterial indicators correlated well with the day-to-day presence of
pathogenic viruses in wastewater or natural waters, but the overall picture
of water quality at each location was reasonably consistent for both
viruses and bacteria.

2004 OUTFALL MONITORING OVERVIEW 70 
Recent Trends in Solids and Nutrient
Loadings to Boston Harbor 
In 2004, MWRA conducted a special study to update information on
freshwater flows and nutrient loading to Boston Harbor (Taylor 2005).
The study focused on the years 1994-2003; earlier studies (Menzie et al. 
1999, Alber and Chan 1994) had synthesized data from the beginning
years of the Boston Harbor Project. The 2004 study specifically focused
on measurements that could influence eutrophication, such as total
suspended solids, particulate organic carbon, total nitrogen, and total
phosphorus. 
The study confirmed reductions in freshwater flow and loadings of the
eutrophication-related contaminants over the 10-year period (Figure 6-4). 
Changes in flow and loadings can be divided into three periods: 
• Period A: the period prior to 1998, when the harbor received
discharges from both Deer Island Treatment Plant in the north and
Nut Island Treatment Plant in the south. Freshwater flows and
loadings of total nitrogen, total phosphorus, total suspended solids,
and particulate organic carbon loadings were elevated, primarily due
to inputs from the wastewater treatment plants. 
• Period B: the two and a half years in which all effluent was
discharged from Deer Island Treatment Plant to the harbor.
Freshwater flows and loadings of nitrogen and phosphorus continued
to be high, but there were decreased loadings of total suspended solids
and particulate organic carbon. These reductions were brought about
almost entirely by inter-island transfer and the upgrades to secondary
treatment. 
• Period C: the years after effluent discharge to the harbor ended.
These years were characterized by lowered freshwater flows to the
harbor, additional decreases in loadings of total suspended solids and
particulate organic carbon, and relatively larger decreases in loadings
of total nitrogen and total phosphorus. The transfer of effluent
discharges from the harbor was largely responsible for the decreases.

2004 OUTFALL MONITORING OVERVIEW 71 
1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
0
1
2
3
4
5 
Period 
C
Period 
B
Period
A 
FLOW
( x10 6 M 3 D -1 ) 
NPS 
RIVERS 
WWTF
1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
0
20
40
60
80
100 
TSS LOADING
( TON D -1 )
1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
0
1000
2000
3000
4000 
POC LOADING
( KMOL D -1 )
1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
0
500
1000
1500
2000
2500 
TN LOADING
( KMOL D -1 )
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
0
20
40
60
80
100
120
140 
TP LOADING
( KMOL D -1 ) 
Figure 6-4. Changes in annual freshwater flow and loading to Boston Harbor, 1994-2003.
TSS=total suspended solids, POC=particulate organic carbon, TN=total nitrogen, TP=total
phosphorus, NPS=nonpoint sources, WWTF=wastewater treatment facility. Nonpoint source
data are from Alber and Chan 1994. Data for September 2000 through 2003 include estimates of
wastewater re-entering the harbor from the bay.

2004 OUTFALL MONITORING OVERVIEW 72 
2005 Alexandrium Bloom 
During May-July 2005, an extensive bloom of Alexandrium fundyense 
occurred along the coast of southern New England (Figure 6-5). MWRA
monitoring detected levels well in excess of the Contingency Plan
threshold of 100 cells per liter in the outfall nearfield and region-wide. 
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 people. In
Massachusetts, the Division of Marine Fisheries tests for PSP toxin in
shellfish and closes beds if the level of toxin is too high. 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 the Bay from 1994 to 2004. 
Alexandrium cell counts during the 2005 bloom were higher than
previously observed. The outbreak eventually closed shellfish beds from
central Maine to Massachusetts, including Nantucket Island and portions
of Martha’s Vineyard, and resulted in the closure of 40,000 km 2 of
offshore federal waters (Figure 6-6). The 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. 
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. Preliminary indications were that a
large spring bloom occurred in the coastal waters of Maine, and this
bloom moved south with stronger-than-usual coastal currents, a result of
high spring runoff from large rivers in Maine. The bloom was transported
into Massachusetts and Cape Cod bays and to waters south of the Cape by
two strong northeast storms in May. 
The causes and effects of the bloom continue to be evaluated, and a more
complete analysis will be presented in the 2005 outfall monitoring
overview. The MWRA outfall is not suspected to be a significant factor in
the size or extent of this bloom. More complete analysis will help
determine whether the outfall may have had a local effect.

2004 OUTFALL MONITORING OVERVIEW 73 
Mass
Bay
Nearfield
Boston
Harbor
Cape
Cod
Bay 
Alexandrium fundyense (cells/L)
surface sam p les sub surface sam p les 
1
10
100
1,000
10,000
100,000 
1
10
100
1,000
10,000
100,000 
1
10
100
1,000
10,000
100,000 
1
10
100
1,000
10,000
100,000
5/1 6/1 7/1 8/1 5/1 6/1 7/1 8/1 
Figure 6-5. Alexandrium cell counts measured during MWRA monitoring surveys in response to
the red tide

2004 OUTFALL MONITORING OVERVIEW 74 
Figure 6-6. Geographic extent of shellfish bed closures in July 2005 (figure courtesy of Don
Anderson, Woods Hole Oceanographic Institution)

2004 OUTFALL MONITORING OVERVIEW 75 
7. Stellwagen Bank 
National Marine Sanctuary 
Background 
The Gerry E. Studds Stellwagen Bank National Marine Sanctuary
comprises 842 square miles located at the boundary between
Massachusetts Bay and the rest of the Gulf of Maine. The Sanctuary’s
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. 
The MWRA 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. The revisions to the water-column portion of the monitoring
program implemented in 2004 did not change the stations sampled within
and in the vicinity of the sanctuary. 
Since 2001, the sanctuary managers, in conjunction with MWRA’s
contractor Battelle, have conducted a supplemental monitoring program,
which added four stations to the August and October MWRA surveys
(Figure 7-1). These sites were selected to provide a more comprehensive
evaluation of water quality across the sanctuary and to increase the
understanding of the potential effects of the relocated outfall. The

2004 OUTFALL MONITORING OVERVIEW 76 
program and results for 2004 are presented described in Libby et al. 
(2005b). 
Figure 7-1. Water column stations, including the additional Stellwagen Bank National Marine
Sanctuary stations sampled in August and October 2001-2004

2004 OUTFALL MONITORING OVERVIEW 77 
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. In 2004, only Stations FF04 and FF05 were sampled, with
Stations FF11 and FF14 to be sampled in 2005. 
Results 
Water Column 
Overall, water quality within the sanctuary was excellent during 2004.
There was no indication of any effect of the MWRA outfall (Libby et al. 
2005a, 2005b). Annual mean nutrient concentrations in the sanctuary
have not changed substantially since the outfall began operation. While
ammonia concentrations have risen in the nearfield, there has been no
comparable annual increase in Stellwagen Bank or Cape Cod Bay (Figure
7-2, top). Nitrate concentrations have shown a long upward trend in all
regions; this trend predates the outfall diversion. Concentrations of nitrate
in the sanctuary have remained the consistently higher than levels at other
monitoring stations (Figure 7-2, bottom). 
The mean annual chlorophyll levels have not changed in response to the
outfall discharge (Figure 7-3). Annual chlorophyll levels were similar in
the nearfield, Cape Cod Bay, and Stellwagen Bank.

2004 OUTFALL MONITORING OVERVIEW 78 
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
Year
NH4 (mM) 
SBNMS 
Nearfield 
Cape Cod Bay 
Outfall Startup 
0
1
2
3
4
5
6
7
8
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
Year
NO3 ( μ M) 
SBNMS 
Nearfield 
Cape Cod 
Outfall Startup 
Figure 7-2. Annual mean ammonia (top) and nitrate (bottom) in the Stellwagen Bank National
Marine Sanctuary and other regions of Massachusetts and Cape Cod bays

2004 OUTFALL MONITORING OVERVIEW 79 
0
20
40
60
80
100
120
140
160
180
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
Year
Chlorophyll (mg m -2 ) 
SBNMS 
Nearfield 
Cape Cod 
Outfall Startup 
Figure 7-3. Annual mean chlorophyll in Stellwagen Bank National Marine Sanctuary and other
regions 
There were no confirmed blooms of harmful or nuisance phytoplankton
species during August-October 2004 (Libby et al. 2005a). The MWRA
monitoring program documented a spring Phaeocystis pouchetii bloom
throughout Massachusetts and Cape Cod bays. This large bloom is
discussed in Section 3, Water Column. 
Concentrations of dissolved oxygen and percent saturation have remained
unchanged in the Stellwagen Basin, as well as in the nearfield (data not
shown). Levels in 2004 were relatively high compared to other years of
baseline and post-discharge-transfer monitoring. 
Sea Floor 
No changes in concentrations of sewage tracers or sewage-related
contaminants were observed in the sediments from stations within the
sanctuary, and there were no changes in community parameters in 2004
(Maciolek et al. 2005). 
The deep-water stations 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 7-4). 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.

2004 OUTFALL MONITORING OVERVIEW 80 
0
1000
2000
3000
4000
5000
6000
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004
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
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
Year
Log Series Alpha 
FF05 
FF04 
FF14 
FF11 
Outfall startup 
Figure 7-4. Benthic community parameters at stations within the boundary region, 1992-2004

2004 OUTFALL MONITORING OVERVIEW 81 
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2004 OUTFALL MONITORING OVERVIEW 87 
List of Acronyms 
BEM Bays Eutrophication Model 
BEMEG Bays Eutrophication Model Evaluation Group 
BOD Biochemical oxygen demand 
BS Broad Sound 
cBOD Carbonaceous biochemical oxygen demand 
CCB Cape Cod Bay 
CHV Centrotubular hydropic vacuolation 
C-NOEC Chronic test, no observable effect concentration 
CSO Combined sewer overflow 
DDT Dichlorodiphenyltrichloroethane 
DO Dissolved oxygen 
ECCB Eastern Cape Cod Bay 
EPA U.S. Environmental Protection Agency 
FDA U.S. Food and Drug Administration 
FF Farfield 
GoMOOS Gulf of Maine Ocean Observation System 
IAAC Inter-agency Advisory Committee 
LC50 50% mortality concentration 
MADEP Massachusetts Department of Environmental Protection 
MGD Million gallons per day 
MWRA Massachusetts Water Resources Authority 
NA Not analyzed 
NB Nantasket Beach 
ND Not detected 
NMFS National Marine Fisheries Service 
NPS Nonpoint source 
NOEC No observable effect concentration 
NPDES National Pollutant Discharge Elimination System 
OMSAP Outfall Monitoring Science Advisory Panel 
OMTF Outfall Monitoring Task Force 
OS Outfall site 
PAH Polycyclic aromatic hydrocarbon 
PC Particulate carbon 
PCB Polychlorinated biphenyl 
ppb Parts per billion 
ppm Parts per million 
PIAC Public Interest Advisory Committee 
RPD Redox potential discontinuity 
PSP Paralytic shellfish poisoning 
SeaWIFS Sea-viewing Wide Field-of-view Sensor 
SBNMS Stellwagen Bank National Marine Sanctuary 
SEIS Supplemental Environmental Impact Statement 
SPI Sediment-profile imaging 
TCR Total chlorine residual 
TOC Total organic carbon

2004 OUTFALL MONITORING OVERVIEW 88 
TRAC Toxic Reduction and Control Program 
TSS Total suspended solids 
USGS U.S. Geological Survey 
WWTF Wastewater treatment facility

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

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