2003 overview

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2003 outfall monitoring overview 
Massachusetts Water Resources Authority 
Environmental Quality Department 
Report ENQUAD 2004-13

Citation: 
Werme C, Hunt CD. 2004. 2003 Outfall monitoring overview. Boston: Massachusetts
Water Resources Authority. Report ENQUAD 2004-13. 97p.

2003 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 ........................................................................................................ 4 
Contingency Plan ............................................................................................................ 7 
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 ....................................................................................... 20 
3. Water Column ............................................................................................................... 21 
Background ................................................................................................................... 21 
Circulation and Water Properties .............................................................................. 21 
Environmental Concerns ........................................................................................... 23 
Monitoring Design ........................................................................................................ 25 
Results ........................................................................................................................... 28 
Physical Conditions .................................................................................................. 28 
Water Quality ............................................................................................................ 29 
Phytoplankton Communities ..................................................................................... 35 
Zooplankton Communities ........................................................................................ 37 
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 Contaminants ............................................................................................ 47 
Sediment-Profile Imaging ......................................................................................... 48 
Soft-bottom Communities ......................................................................................... 49 
Hard-bottom Communities ....................................................................................... 52 
Contingency Plan Thresholds ....................................................................................... 54 
5. Fish and Shellfish .......................................................................................................... 55 
Background ................................................................................................................... 55

2003 OUTFALL MONITORING OVERVIEW II 
Monitoring Design ........................................................................................................ 56 
Winter Flounder ........................................................................................................ 57 
Lobster ...................................................................................................................... 57 
Blue Mussel .............................................................................................................. 57 
Results ........................................................................................................................... 58 
Winter Flounder ........................................................................................................ 58 
Lobster ...................................................................................................................... 60 
Blue Mussel .............................................................................................................. 62 
Contingency Plan Thresholds ....................................................................................... 64 
6. Special Studies .............................................................................................................. 66 
Background ................................................................................................................... 66 
Outfall Inspection .......................................................................................................... 66 
Water Chemistry in Boston Harbor and Massachusetts Bay ........................................ 67 
Nutrient Flux ................................................................................................................. 69 
Marine Mammal Observations ..................................................................................... 70 
PCB Analyses ............................................................................................................... 71 
Flounder Ulcers ............................................................................................................. 72 
7. Stellwagen Bank National Marine Sanctuary ............................................................... 74 
Background ................................................................................................................... 74 
Monitoring Design ........................................................................................................ 74 
Results ........................................................................................................................... 76 
Water Column ........................................................................................................... 76 
Sea Floor ................................................................................................................... 80 
8. Monitoring Plan Revision ............................................................................................. 82 
Effluent ......................................................................................................................... 83 
Water Column ............................................................................................................... 84 
Sea Floor ....................................................................................................................... 89 
Fish and Shellfish .......................................................................................................... 89 
References ......................................................................................................................... 91 
List of Acronyms .............................................................................................................. 96

2003 OUTFALL MONITORING OVERVIEW III 
List of Figures 
Figure 1-1. Map of Massachusetts and Cape Cod bays ...................................................... 2 
Figure 2-1. Annual effluent flow ..................................................................................... 16 
Figure 2-2. Annual nitrogen and solids discharges ........................................................... 17 
Figure 2-3. Top: Annual metals load; Bottom: mercury loads as a function of amount of
secondary treatment. ......................................................................................................... 18 
Figure 2-4. Total chlorine residual, 1997-2004 ................................................................ 19 
Figure 3-1. General circulation within Massachusetts Bay .............................................. 21 
Figure 3-2. Nearfield sampling stations ............................................................................ 26 
Figure 3-3. Farfield geographic regions and sampling stations ........................................ 27 
Figure 3-4. Top: Charles River discharge, 1990-early 2004; Bottom: 2003 discharge
compared to observations from the past 12 years ............................................................. 29 
Figure 3-5. Nearfield surface and bottom water temperature, salinity, and stratification 30 
Figure 3-6. Top: 2003 nearfield ammonia concentrations compared to baseline range and
mean; Bottom: annual mean ammonia concentrations in Massachusetts Bay regions .... 31 
Figure 3-7. Top: 2003 nearfield nitrate concentrations compared to baseline range and
mean; Bottom: annual mean nitrate concentrations in Massachusetts Bay regions ......... 32 
Figure 3-8. Top: 2003 nearfield chlorophyll compared to baseline range and mean;
Bottom: annual mean chlorophyll in Massachusetts Bay regions .................................... 33 
Figure 3-9. 2003 nearfield dissolved oxygen concentrations compared to baseline range
and mean ........................................................................................................................... 34 
Figure 3-10. Observed and modeled average nearfield near-bottom dissolved oxygen
concentrations during September through October .......................................................... 34 
Figure 3-11. Nearfield phytoplankton abundance ............................................................ 35 
Figure 3-12. Top: abundance of Phaeocystis pouchetii in the nearfield, 1992-2003:
Bottom: SeaWiFS chlorophyll a image for March 27, 2003 ............................................ 36 
Figure 3-13. Nearfield zooplankton abundance ................................................................ 37 
Figure 3-14. Monthly abundance of zooplankton species in Massachusetts Bay, 1992-
2003 ................................................................................................................................... 38 
Figure 3-15. Mean monthly winter wind speed vs. monthly winter abundance of Calanus
finmarchicus adults and copepodites at one nearfield station ........................................... 39 
Figure 4-1. Locations of nearfield soft-bottom stations .................................................... 43 
Figure 4-2. Locations of farfield soft-bottom stations ...................................................... 44 
Figure 4-3. Locations of hard-bottom stations .................................................................. 45 
Figure 4-4. Clostridium perfringens spores and percent fine sediments at nearfield
stations .............................................................................................................................. 48 
Figure 4-5. Apparent color RPD for all data from nearfield stations ............................... 49 
Figure 4-6. Community parameters in the nearfield, 1992-2003: abundance per sample,
number species per sample, Shannon diversity, Pielou’s evenness, log-series alpha ....... 51 
Figure 4-7. Top: dense barnacle settlement photographed in 2003; Bottom: abundance of
barnacle larvae in the water column, 1992-2003 .............................................................. 53 
Figure 5-1. Sampling areas for fish and shellfish monitoring .......................................... 56 
Figure 5-2. Prevalence of centrotubular hydropic vacuolation normalized for age ......... 58

2003 OUTFALL MONITORING OVERVIEW IV 
Figure 5-3. PCB concentrations in flounder fillets and livers .......................................... 59 
Figure 5-4. Mercury in flounder fillets, 1992-2003 .......................................................... 60 
Figure 5-5. PCB concentrations in lobster meat and hepatopancreas ............................. 61 
Figure 5-6. Distribution of selected PCB congeners in lobster hepatopancreas samples
from Massachusetts Bay and New Bedford Harbor ......................................................... 62 
Figure 5-7. Selected contaminant concentrations in mussels ........................................... 63 
Figure 6-1. Outfall diffuser #2 .......................................................................................... 66 
Figure 6-2. Dissolved inorganic nitrogen and chlorophyll concentrations before and after
outfall transfer from Boston Harbor to Massachusetts Bay .............................................. 68 
Figure 6-3. Total PCBs in lobster hepatopancreas at Deer Island Flats and the outfall site
with and without PCB 180 ................................................................................................ 71 
Figure 6-4. Blind-side flounder ulcers .............................................................................. 72 
Figure 6-5. Prevalence of ulcers in winter flounder noted in 2002 and 2003 ................... 73 
Figure 7-1. Water column stations, including the additional Stellwagen Bank National
Marine Sanctuary stations sampled in August and October 2001-2003 ........................... 75 
Figure 7-2. Post-discharge survey mean dissolved oxygen concentrations in Stellwagen
Basin compared to, baseline mean and range ................................................................... 77 
Figure 7-3. Near-bottom salinity, temperature, and dissolved oxygen data from the
GoMOOS “A” mooring, and MWRA and Stellwagen Bank monitoring stations ........... 77 
Figure 7-4. Annual mean ammonia and nitrate in the Stellwagen Bank National Marine
Sanctuary and other regions of Massachusetts and Cape Cod bays ................................. 78 
Figure 7-5. Annual mean chlorophyll concentrations in Stellwagen Bank National Marine
Sanctuary and other regions .............................................................................................. 79 
Figure 7-6. Benthic community parameters at stations within the boundary region, 1992-
2003 ................................................................................................................................... 81 
Figure 8-1. Top: Actual and modeled chlorophyll; Bottom: actual and modeled dissolved
oxygen concentrations ...................................................................................................... 85 
Figure 8-2. Top: Survey average chlorophyll plotted by day of year; Bottom: survey
average dissolved oxygen plotted by day of year ............................................................. 86

2003 OUTFALL MONITORING OVERVIEW V 
List of Tables 
Table 1. Summary of monitoring questions and status as of the end of 2003 ................. viii 
Table 2. Summary of contingency plan thresholds and exceedances as of 2003 .............. xi 
Table 1-1. Roster of panel and committee members .......................................................... 4 
Table 1-2. Public concerns and possible environmental responses .................................... 5 
Table 1-3. Summary of the monitoring program ................................................................ 6 
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 ......................................................... 15 
Table 2-4. Contingency plan threshold values and 2003 results for effluent monitoring . 20 
Table 3-1. Monitoring questions related to the water column ......................................... 24 
Table 3-2. Components of water-column monitoring ....................................................... 25 
Table 3-3. Contingency plan threshold values for water-column monitoring .................. 40 
Table 4-1. Monitoring questions related to the sea floor .................................................. 42 
Table 4-2. Components of sea-floor monitoring ............................................................... 43 
Table 4-3. No contingency plan baseline and threshold values for sea-floor monitoring
were exceeded in 2003. ..................................................................................................... 54 
Table 5-1. Monitoring questions related to fish and shellfish .......................................... 55 
Table 5-2. Comparison of contaminant concentrations at the outfall site during the three
years prior to and the three years since outfall operation ................................................. 64 
Table 5-3. Contingency plan baseline, threshold, and 2003 values for fish and shellfish
monitoring ......................................................................................................................... 65 
Table 6-1. Monitoring questions related to nutrient flux .................................................. 69 
Table 8-1. Effluent monitoring parameters ....................................................................... 83 
Table 8-2. Nearfield water column monitoring ................................................................ 87 
Table 8-3. Farfield water column monitoring ................................................................... 88 
Table 8-4. Fish and shellfish analyses .............................................................................. 90

2003 OUTFALL MONITORING OVERVIEW VI 
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2003 OUTFALL MONITORING OVERVIEW VII 
Summary 
During 2003, the third 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, were low. The treatment plant
earned the Association of Metropolitan Sewerage Agencies Gold Peak Performance
Award for facilities that had no permit violations during the year. 
After nine years of baseline monitoring and three 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 baseline
conditions. 
There were two contingency plan exceedances during the year (Table 2). As in 2002,
summer concentrations of the nuisance algal species Phaeocystis pouchetii exceeded the
caution level. As has been the case each year since the outfall began operation,
concentrations of total polycyclic aromatic hydrocarbons (PAHs) exceeded the caution
level for mussels deployed in cages at the outfall. These exceedances have been
reviewed and are not considered to indicate environmental problems caused by outfall
discharge. 
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 2003, MWRA completed a review of the monitoring program and revised the
monitoring plan to focus it on the potential for long-term chronic effects.

2003 OUTFALL MONITORING OVERVIEW VIII 
Table 1. Summary of monitoring questions and status as of the end of 2003 
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. 
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 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.
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
other dissolved components not detected within
tens of meters of outfall and not observed in farfield
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 have been 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 have not changed from background.

2003 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 have 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 has been 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 does not appear to 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 has been detected.
Frequency of Phaeocystis blooms may be
increasing 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 has been 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 can be 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. No other
changes detectable. 
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 has been 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.

2003 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. 
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. 
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 were found on flounder
collected in 2003. No changes in liver disease.

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

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

2003 OUTFALL MONITORING OVERVIEW 1 
1. Introduction 
Background 
Since its creation in 1985, the Massachusetts Water Resources Authority
(MWRA) has worked to end long-standing violations of the Clean Water
Act and to minimize the effects of wastewater discharge on the marine
environment. In 1991, MWRA ended discharge of municipal sludge into
Boston Harbor. Steps to minimize effects of effluent discharge have
included source reduction to prevent pollutants from entering the waste
stream, improved treatment before discharge, and better dilution once the
effluent enters the marine environment. 
Source reduction has included projects to lessen household hazardous
waste disposal and minimize mercury discharges from hospitals and
dentists. An industrial pretreatment/pollution prevention program ensures
that toxic contaminants are removed before they reach the sewer system.
In addition, best management practices are employed at sewer facilities to
mitigate accidental discharge of pollutants. Operator training programs
and process control and maintenance tracking systems are also in place. 
Improved treatment began in 1995, when a new primary treatment plant at
Deer Island was brought on line, and disinfection facilities were
completed. (Primary treatment involves removal of solids through
settlement and disinfection.) The first and second batteries of secondary
treatment (which includes bacterial decomposition as well as settlement
and disinfection) went on line in 1997 and 1998. 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. A final battery of
secondary treatment became operational in 2001. 
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). 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.

2003 OUTFALL MONITORING OVERVIEW 2 
Figure 1-1. Map of Massachusetts and Cape Cod bays 
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 5 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. 
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 questions:

2003 OUTFALL MONITORING OVERVIEW 3 
ƒ Is it safe to eat fish and shellfish? 
ƒ Are natural/living resources protected? 
ƒ Is it safe to swim? 
ƒ Are aesthetics being maintained? 
These concerns were recognized by MWRA and by the joint permit for the
outfall issued by the U.S. Environmental Protection Agency (EPA) and the
Massachusetts Department of Environmental Protection (MADEP). 
Outfall Permit 
The permit issued by EPA and MADEP under the National Pollutant
Discharge Elimination System (NPDES) became effective on August 9,
2000. 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, which encompasses
industrial, commercial, and residential users of the system, 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) developed in response to the
EPA Supplemental Environmental Impact Statement (SEIS, EPA 1988).
The permit requires MWRA to update, maintain, and run the three-
dimensional Bays Eutrophication Model and to measure the dilution at the
discharge. It requires that MWRA implement a contingency plan
(MWRA 1997b, 2001), which identifies relevant environmental quality
parameters and thresholds, which, if exceeded, would require a response. 
EPA and MADEP have established an independent panel of scientists to
review monitoring data and provide advice on key scientific issues related
to the permit. This panel, the Outfall Monitoring Science Advisory Panel
(OMSAP, Table 1-1), conducts peer reviews of monitoring reports,
evaluates the data, and advises EPA and MADEP on scientific
implications. OMSAP also provides advice concerning any proposed
modifications to the monitoring or contingency plans. 
OMSAP may form specialized focus groups when specific technical issues
require expanded depth or breadth of expertise. Two standing sub-
committees also advise OMSAP. The Public Interest Advisory Committee
(PIAC) represents local, non-governmental organizations and
environmental groups and advises OMSAP on values and uses of the
harbor and the bays. The Inter-agency Advisory Committee (IAAC)

2003 OUTFALL MONITORING OVERVIEW 4 
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 2003 
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, MA Department of Environmental Protection 
(OMSAP staff) 
Winifred Donnolly, MA Department of Environmental Protection (staff) 
IAAC as of December 2003 
MA Coastal Zone Management 
Todd Callaghan 
Jan Smith (alternate) 
MA Department of Environmental Protection 
Russell Isaac 
Catherine Coniaris 
MA Division of Marine Fisheries 
Jack Schwartz 
James Fair (alternate) 
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 2003 
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 
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 by MWRA, under the direction of an Outfall

2003 OUTFALL MONITORING OVERVIEW 5 
Monitoring Task Force (OMTF), made up of scientists, regulators, and
environmental advocacy groups (MWRA 1991, 1997a). (The OMTF was
disbanded upon creation of OMSAP in 1998.) 
The outfall ambient monitoring plan expands the general questions of
public concern by translating them into possible “environmental
responses” to the outfall (Table 1-2). To answer those questions, the
monitoring program focuses on critical constituents in 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). 
Table 1-2. Public concerns and possible environmental responses (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?

2003 OUTFALL MONITORING OVERVIEW 6 
Table 1-3. Summary of the monitoring program 
Task Objective Sampling Locations 
And Schedule Analyses 
Effluent 
Monthly Toxicity 
Weekly Nutrients 
Daily Organic material (cBOD) 
Several times monthly Toxic contaminants 
3x/day Bacterial indicators, total
chlorine residual 
Effluent sampling Characterize wastewater
discharge from Deer Island
Treatment Plant 
Daily Solids 
Water Column 
Nearfield surveys Collect water quality data near
outfall location 
17 surveys/year 
21 stations 
Farfield surveys Collect water quality data
throughout Massachusetts and
Cape Cod bays 
6 surveys/year 
26 stations 
Temperature 
Salinity 
Dissolved oxygen 
Nutrients 
Solids 
Chlorophyll 
Water clarity 
Photosynthesis 
Respiration 
Plankton 
Marine mammal observations 
Moorings (GoMOOS
and USGS) 
GoMOOS near Cape Ann and
USGS near outfall provide
continuous oceanographic
data near outfall location 
Continuous monitoring 
GoMOOS at one location 
USGS at two locations 
3 depths 
Currents 
Temperature 
Salinity 
Water clarity 
Chlorophyll 
Remote sensing Provides oceanographic data
on a regional scale through
satellite imagery 
Available daily (cloud-cover
permitting) 
Surface temperature 
Chlorophyll 
Sea Floor 
Soft-bottom studies Evaluate sediment quality and
benthos in Boston Harbor and
Massachusetts Bay 
1 survey/year 
20 nearfield stations 
11 farfield stations 
Sediment chemistry 
Sediment profile imagery 
Community composition 
Hard-bottom studies Characterize marine benthic
communities in rock and
cobble areas 
1 survey/year 
21 stations on 6 transects 
Topography 
Substrate 
Community composition 
Fish and Shellfish 
Winter flounder Determine contaminant body
burden and population health 
1 survey/year 
5 locations 
Tissue contaminant
concentrations 
Physical abnormalities,
including liver histopathology 
American lobster Determine contaminant body
burden 
1 survey/year 
3 locations 
Tissue contaminant
concentrations 
Physical abnormalities 
Blue mussel Evaluate biological condition
and potential contaminant
bioaccumulation 
1 survey/year 
4 locations 
Tissue contaminant
concentrations 
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.

2003 OUTFALL MONITORING OVERVIEW 7 
Baseline monitoring was initially planned to last for a minimum of three
years, as the outfall was originally planned for completion in 1995.
Delays in outfall construction 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 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). The extended period also
meant that the discharge to Massachusetts Bay, when it did begin, had the
benefit of nearly complete implementation of secondary treatment. 
The monitoring plan is a “living document.” That is, every effort is made
to incorporate new scientific information and improved understanding
resulting from the monitoring program into appropriate continued
measurements. MWRA’s NPDES permit allows an annual list of
proposed changes to the monitoring plan. 
Because monitoring had found no unexpected changes to the system after
the outfall began operation, extensive changes to the plan were proposed
during 2003. A new plan (MWRA 2004), which was accepted by
OMSAP and incorporated changes approved by EPA and MADEP, will be
implemented in the 2004 monitoring year. Details of that plan are
presented in Section 8 of this report. 
Contingency Plan 
The MWRA contingency plan (MWRA 1997b, 2001, and available at
www.mwra.com) describes how, if monitoring results indicate a possible
environmental problem, MWRA and the regulatory agencies will respond
to determine the cause of the problem and to specify the corrective actions
that should be taken if the problem appears to be related to the discharge.
The contingency plan identifies the parameters that represent
environmentally significant components of the effluent or the ecosystem
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. 
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
“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

2003 OUTFALL MONITORING OVERVIEW 8 
quality and environmental conditions. The data are examined to
determine whether it is likely that an unacceptable effect resulting from
the outfall has occurred. 
Exceeding warning levels could, in some circumstances, indicate a need
for a response to avoid potential adverse environmental effects. If a
threshold is exceeded at a warning level, the response includes early
notification to EPA and MADEP and, if the outfall has contributed to
adverse environmental effects, the quick development of a response plan.
Response plans include a schedule for implementing actions, such as
making adjustments in plant operations or undertaking an engineering
feasibility study regarding specific potential corrective activities. 
Table 1-4. Contingency plan threshold parameters 
Monitoring 
Area 
Parameter 
pH 
Fecal coliform bacteria 
Residual chlorine 
Total suspended solids 
Biological oxygen demand 
Toxicity 
PCBs 
Petroleum hydrocarbons 
Plant performance 
Effluent 
Total nitrogen load 
Floatables 
Dissolved oxygen concentration and saturation 
Dissolved oxygen depletion rate 
Chlorophyll 
Nuisance and noxious algae 
Water Column 
Effluent dilution 
Benthic community structure 
Sediment oxygen 
Sea Floor 
Sediment toxic metal and organic chemicals 
Mercury, PCBs, and lipid-normalized toxic
compounds in mussels and flounder and lobster
meat 
Lead in mussels 
Fish and Shellfish 
Liver disease in flounder 
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.

2003 OUTFALL MONITORING OVERVIEW 9 
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 contingency plan must be reviewed by regulators and
published in the Environmental Monitor . Data that exceed contingency
plan thresholds, and corrective actions, must also be reported. Data that
exceed thresholds must be reported within five days after the results
become available, and MWRA must make all reasonable efforts to report
all data within 90 days of each sampling event. 
Reports are posted on MWRA’s web site (www.mwra.com), with copies
placed in repository libraries in Boston and on Cape Cod. OMSAP also
holds public workshops where outfall monitoring results are presented.

2003 OUTFALL MONITORING OVERVIEW 10 
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). 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 exceed thresholds, responses,
and corrective activities. 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 2003. It compares all results to
contingency plan thresholds. The overview also includes a section on data
relevant to the Stellwagen Bank National Marine Sanctuary. This year’s
report also contains a section on revisions to the monitoring plan.

2003 OUTFALL MONITORING OVERVIEW 11 
2. Effluent 
Background 
Pollution Prevention and Wastewater Treatment 
Ensuring that the final treated effluent is as clean as possible 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 the cleanest possible effluent through a vigorous
pretreatment program and by maintaining and operating the treatment
plant well. 
The MWRA Toxic Reduction and Control Program sets and enforces
limits on the types and amounts of pollutants that industries can discharge
into the sewer system. The program minimizes the contaminants present
in the effluent and in the sludge (which is removed during treatment). In
addition to regulating industrial discharges, MWRA has implemented
programs to reduce mercury from dental facilities and to educate the
public about proper disposal of hazardous wastes. 
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 compounds, and about 20% of the
nitrogen from the influent. 
To mitigate accidental discharge of pollutants to the system, MWRA has
implemented best management practice plans for the treatment plant, its
headworks facilities, the combined sewer overflow facilities, and the
sludge pelletizing 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 set 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
permit limits (Table 2-1). Other questions require the use of effluent data

2003 OUTFALL MONITORING OVERVIEW 12 
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, and the MWRA
permit also sets limits for chlorine and pH: 
ƒ 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. 
ƒ 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 of marine
organisms. Some toxic contaminants can accumulate in marine

2003 OUTFALL MONITORING OVERVIEW 13 
life, potentially affecting human health through seafood
consumption. 
ƒ 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 sea floor
communities. 
ƒ 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. 
ƒ 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. 
ƒ 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. 
ƒ Sewage effluent is disinfected by addition of a form of chlorine ,
sodium hypochlorite, which is the active ingredient in bleach.
Unfortunately, while sodium hypochlorite is effective in destroying
pathogens, at high enough concentrations, it is also harmful to
marine life. MWRA dechlorinates the effluent with sodium
bisulfite before discharge. 
ƒ Seawater is noted for its buffering capacity, that is, its ability to
neutralize acids and bases. However, state water quality standards
dictate that effluent discharges not change the pH of the ambient
seawater more than 0.5 standard units. Consequently, the outfall
permit sets both upper and lower values for pH of the effluent. 
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, ambient conditions, and the dilution at the outfall. Effluent
monitoring also provides accurate mass loads of effluent constituents, so
that fate, transport, and risk of contaminants can be assessed.

2003 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. 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. 
Table 2-2. Reporting requirements of the outfall permit 
Parameter Sample Type Frequency Limit 
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 chlorine residual Grab 3/day 631 ug/l daily 
456 ug/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

2003 OUTFALL MONITORING OVERVIEW 15 
Most parameters are measured in 24-hour composite samples, and some
must meet daily, weekly, or monthly limits (Table 2-3). Flow is measured
continuously. Nutrient measurements include total Kjeldahl 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. 
Table 2-3. Monitoring plan parameters for effluent 
Parameter Sample Type Frequency 
NUTRIENTS 
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 
LOW-DETECTION-LIMIT ANALYSES 
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 
Beyond the requirements of ordinary discharge monitoring, the MWRA
monitoring plan requires additional nutrient measurements and non-

2003 OUTFALL MONITORING OVERVIEW 16 
standard, low-detection methods to measure toxic contaminants. 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. 
Results 
Average daily flow of effluent from the Deer Island treatment plant in
2003 was greater than in 1999-2002, due to rain in the spring and fall
(Figure 2-1). Approximately 95% of the flow received secondary
treatment. 
MWRA Primary and Secondary Flows 1990-2003
0
50
100
150
200
250
300
350
400
450
90 91 92 93 94 95 96 97 98 99 00 01 02 03
million gallons per day 
Primary-treated Flows Secondary-treated Flows 
Figure 2-1. Annual effluent flow 
Nitrogen loads decreased slightly in 2003 (Figure 2-2, top). For other
parameters, the increased flow meant increased total loads. Solids (Figure
2-2, bottom) loads were at approximately the same levels they had been in
1999, slightly higher than in 2001 and 2002.

2003 OUTFALL MONITORING OVERVIEW 17 
Deer Island Treatment Plant Nitrogen Discharges 1996-2003
0
2000
4000
6000
8000
10000
12000
14000
1996 1997 1998 1999 2000 2001 2002 2003
metric tons per year 
Ammonium Nitrite/Nitrate Other Nitrogen Species Caution Level 
Solids in MWRA Treatment Plant Discharges 1988-2003
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
Tons per day 
Sludge 
Nut Island 
Deer Island 
Figure 2-2. Annual nitrogen and solids discharges

2003 OUTFALL MONITORING OVERVIEW 18 
Similarly, metals loads were slightly higher in 2003 than in 2001 and
2002, reflecting the increased flow (Figure 2-3, top). Overall, toxic
compound concentrations have decreased with increased levels of
secondary treatment (for example, mercury in Figure 2-3, bottom). 
Metals in MWRA Treatment Plant Discharges 1989-2003
0
200
400
600
800
1000
1200
89 90 91 92 93 94 95 96 97 98 99 00 01 02 03
Average pounds per da y 
Silver 
Nickel 
Chromium 
Lead 
Copper 
Zinc 
Effluent Loadin g of Mercur y as a Function of Percent
Secondary Treatment (2001-2003)
0.00
0.10
0.20
0.30
0.40
0.50
0.60
0.70
0 20 40 60 80 100
Percent Secondary (%)
Mercury Loading (lbs/day) 
Figure 2-3. Top: Annual metals load; Bottom: mercury loads as a function of amount of
secondary treatment.

2003 OUTFALL MONITORING OVERVIEW 19 
The total chlorine residual also remained low, as it has since the new
outfall began operation and dechlorination of the disinfected effluent
began (Figure 2-4). 
Daily Average TCR, Deer Island, 1 Jan 1997-26 Aug 2004
0
2000
4000
6000
8000
10000
12000
14000
Jan-97
May-97
Sep-97
Jan-98
May-98
Sep-98
Jan-99
May-99
Sep-99
Jan-00
May-00
Sep-00
Jan-01
May-01
Sep-01
Jan-02
May-02
Sep-02
Jan-03
May-03
Sep-03
Jan-04
May-04
Date
TCR (ug/L) 
TCR 
TCR Daily Permit Limit 
Outfall Startup 
Figure 2-4. Total chlorine residual (TCR), 1997-2004

2003 OUTFALL MONITORING OVERVIEW 20 
Contingency Plan Thresholds 
The Deer Island Treatment Plant had no permit violations during 2003
(Table 2-5), qualifying it for the Association of Metropolitan Sewerage
Agencies Gold Peak Performance Award, an award honoring member
agencies that consistently meet all NPDES permit limits during a calendar
year. 
Table 2-4. Contingency plan threshold values and 2003 results for effluent monitoring 
Parameter Caution Level Warning Level 2003 Results 
pH None <6 or >9 Not exceeded 
Fecal coliform bacteria None 
14,000 fecal coliforms/100
ml (monthly 90 th percentile,
weekly geometric mean,
maximum daily geometric
mean, and minimum of 3
consecutive samples) 
Not exceeded 
Chlorine, residual None 631 ug/l daily, 
456 ug/l monthly Not exceeded 
Total suspended solids None 45 mg/l weekly 
30 mg/l monthly Not exceeded 
cBOD None 40 mg/l weekly, 
25 mg/l monthly Not exceeded 
Toxicity None 
Acute: effluent LC50<50%
for shrimp and fish 
Chronic: effluent NOEC for
fish survival and growth and
sea urchin fertilization
<1.5% effluent 
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

2003 OUTFALL MONITORING OVERVIEW 21 
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 and wind patterns (Figure 3-1). 
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

2003 OUTFALL MONITORING OVERVIEW 22 
to the north of Race Point at the tip of Cape Cod. Whether the coastal
current enters the bays and whether it continues south into Cape Cod Bay
depends on the strength of the current and the direction and speed of the
wind. Because the coastal current is strongest during the spring period of
high runoff, the spring circulation pattern is more consistent than that of
the summer and fall (Geyer et al. 1992). 
During the summer and fall, the freshwater inflow is less, and so the wind
and 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). The flow
is very 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. Often, flow can “reverse,” with flow northward along the
coast. There are transient gyres in Massachusetts Bay and Cape Cod Bay,
which can go 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. In Massachusetts Bay, however, spring
blooms do not occur every year. During the years in which there are
spring blooms, they 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 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, bottom-dwelling animals respire, and bacteria use up oxygen as they
decompose the phytoplankton. 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. Typically, fall blooms end in the early winter,
when declining light levels limit photosynthesis. Plankton die and decay,
replenishing nutrients in the water column.

2003 OUTFALL MONITORING OVERVIEW 23 
In Massachusetts Bay, meteorological and oceanographic conditions
greatly influence the timing, magnitude, and spatial extents of the spring
and fall blooms. 
Environmental Concerns 
Water-column monitoring questions focus on the effects of nutrients,
organic matter, pathogens, and floatable debris from wastewater on the
water quality of Massachusetts Bay (MWRA 1991, Table 3-1). Because
organic material and toxic contaminants are effectively removed by
secondary 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 promote
algal blooms 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 can cause paralytic shellfish poisoning, known as
PSP or red tide. Its toxin, when sufficiently concentrated, can be fatal to
marine mammals, fish, and humans. Some diatoms in the genus Pseudo-
nitzschia may, at high concentrations (more than 1 million cells per liter),
produce sufficient quantities of domoic acid to cause a condition known as
amnesic shellfish poisoning. Toxin-forming species occur with and
appear identical to non-toxin forming species, when identified under a
light microscope. Phaeocystis pouchetii is not toxic, but individual cells
can aggregate in gelatinous colonies that are thought to be poor food for
zooplankton. 
Dissolved oxygen concentrations in bottom waters decrease during the
stratified period as part of the natural seasonal pattern. Discharged
nutrients could feed larger phytoplankton blooms, leading to even lower
levels of dissolved oxygen when the cells sink to the bottom and decay.
Because of the concern that low 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 periods of low oxygen that are typical in bottom waters correlate
with warmer and saltier bottom waters.

2003 OUTFALL MONITORING OVERVIEW 24 
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?

2003 OUTFALL MONITORING OVERVIEW 25 
Due to source reduction and treatment, toxic contaminants discharged in
the MWRA effluent are present at extremely low concentrations.
Therefore, most monitoring for the effects of toxic contaminants is
focused not on the water column, but on the sediments, which are known
to be contaminant sinks, and on fish and shellfish, which could accumulate
organic compounds or metals. 
Monitoring Design 
Water-column monitoring includes assessments of water quality,
phytoplankton, and zooplankton in Massachusetts and Cape Cod bays.
Regular monitoring includes four major components: nearfield surveys,
farfield surveys, continuous recording, and remote sensing (Table 3-2).
Plume-tracking studies, conducted in 2001, confirmed the assumptions
that bacteria and toxic contaminant concentrations 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 (Figure
3-2). Farfield surveys assess differences across the bays and seasonal
changes over a large area (Figure 3-3). Five of the farfield stations mark
the boundary of the monitoring area and are in or near the Stellwagen
Bank National Marine Sanctuary. Two of these stations form 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. During 2003, 17 surveys of the
nearfield and 6 surveys of the farfield were conducted. 
Table 3-2. Components of water-column monitoring 
Task Objective Sampling Locations 
And Schedule Analyses 
Nearfield surveys Collect water quality data near
outfall location 
17 surveys/year 
21 stations 
Farfield surveys Collect water quality data
throughout Massachusetts and
Cape Cod bays 
6 surveys/year 
26 stations 
Temperature 
Salinity 
Dissolved oxygen 
Nutrients 
Solids 
Chlorophyll 
Water clarity 
Photosynthesis 
Respiration 
Plankton 
Marine mammal observations 
Moorings (GoMOOS
and USGS) 
GoMOOS near Cape Ann and
USGS near outfall provide
continuous oceanographic
data near outfall location 
Continuous monitoring 
GoMOOS at one location 
USGS at two locations 
3 depths 
Currents 
Temperature 
Salinity 
Water clarity 
Chlorophyll 
Remote sensing Provides oceanographic data
on a regional scale through
satellite imagery 
Available daily (cloud-cover
permitting) 
Surface temperature 
Chlorophyll

2003 OUTFALL MONITORING OVERVIEW 26 
Figure 3-2. Nearfield sampling stations

2003 OUTFALL MONITORING OVERVIEW 27 
Figure 3-3. Farfield geographic regions and sampling stations

2003 OUTFALL MONITORING OVERVIEW 28 
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. Nutrient measurements include the
major forms of nitrogen, phosphorus and silica. The measurements focus
on the dissolved inorganic forms, which are readily used by
phytoplankton. Since 1999, the surveys have also included observations
and net tows in the outfall area to assess the presence of floatables. 
The continuous recording components of the program, the USGS and Gulf
of Maine Ocean Observing System (GoMOOS) moorings, capture
temporal variations in water quality between nearfield water quality
surveys. Remote sensing by satellite captures spatial variations in water
quality on a regional scale. 
Results 
Physical Conditions 
Drought, which began in the fall of 2001, continued until April 2003, after
which there was a return to more normal freshwater flow conditions
(Figure 3-4). (Libby et al. 2004a). 
Monitoring has shown that the north-south component of the wind stress
in the region is important in determining water conditions, as these winds
determine the degree of upwelling or downwelling. The year followed a
typical pattern of wind stresses, beginning with downwelling, transitioning
to upwelling in the summer, and returning to downwelling in the late fall.
Stronger summer upwelling resulted in particularly cold bottom waters
(Figure 3-5, top). 
Surface salinity was lower in 2003 than in 2002, reflecting the end of the
drought (Figure 3-5, middle). Bottom salinity decreased more slowly.
The pronounced difference in salinity in surface and bottom waters meant
greater than usual summer stratification (Figure 3-5, bottom), which
persisted through November.

2003 OUTFALL MONITORING OVERVIEW 29 
Figure 3-4. Top: Charles River discharge, 1990-early 2004 (data from a gauge at Waltham and
3-month moving average); Bottom: 2003 discharge compared to observations from the past 12
years 
Water Quality 
As in 2001 and 2002, water quality measurements in 2003 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. 2004a). 
Elevated concentrations of ammonia, the form of nitrogen most readily
taken up by phytoplankton, were observed in the nearfield during many
surveys, as they had been since the outfall began operation (Figure 3-6,
top). These elevated levels had been anticipated, because a large portion
of the dissolved inorganic nitrogen in treated effluent is ammonia, and
ammonia has proven to be a good short-term tracer of the effluent plume.
During the same period, concentrations of ammonia in Boston Harbor
have remained low, following a dramatic drop in concentration following
effluent diversion to Massachusetts Bay. Averaged over the entire year,
the increase in ammonia concentrations in the vicinity of the outfall was
small in comparison to the large decrease in ammonia concentrations in
the harbor (Figure 3-6, bottom). Ammonia concentrations have also
declined at the coastal stations compared to the years immediately
preceding the outfall diversion.

2003 OUTFALL MONITORING OVERVIEW 30 
Figure 3-5. Nearfield surface and bottom water temperature, salinity, and stratification (Surface
measurements are the upper line for temperature and the lower line for salinity.)

2003 OUTFALL MONITORING OVERVIEW 31 
0
1
2
3
4
5
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
NH4 ( μ M) 
Baseline Range 
Baseline Mean 
2001 
2002 
2003 
0
2
4
6
8
10
12
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
NH4 ( μ M) 
Boston Harbor Nearfield N. Boundary Cape Cod Coastal Offshore 
Figure 3-6. Top: 2003 nearfield ammonia concentrations compared to baseline range and mean;
Bottom: 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, fell
within the baseline range and showed the same seasonal pattern as seen in
baseline monitoring (Figure 3-7, top). Just as during the baseline period,
higher nitrate concentrations were observed during the early part of the
year. Seasonal stratification led to typical, persistent nutrient depletion in
the surface waters, with no evidence of inputs from the outfall (the figures
show data averaged over the entire water column). Elevated nitrate levels
were observed in the nearfield during the fall, and concentrations of two
other nutrients, silicate and phosphate (data not shown), were also present
in concentrations above the baseline ranges during these months.

2003 OUTFALL MONITORING OVERVIEW 32 
Surprisingly high nutrient concentrations were also observed at farfield
stations, suggesting effects of prolonged stratification and perhaps
transport from offshore waters. Averaged over the entire year, there were
no significant increases in nitrate concentrations (Figure 3-7, bottom).
The typical pattern persisted, with highest concentrations at the northern
boundary, lowest in Cape Cod Bay, and intermediate levels in the
nearfield. 
0
2
4
6
8
10
12
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
NO3 ( μ M) 
Baseline Range 
Baseline Mean 
2001 
2002 
2003 
0
1
2
3
4
5
6
7
8
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
NO3 ( μ M) 
Nearfield Boston Harbor N. Boundary 
Cape Cod Coastal Offshore 
Figure 3-7. Top: 2003 nearfield nitrate concentrations compared to baseline range and mean;
Bottom: annual mean nitrate concentrations in Massachusetts Bay regions 
Chlorophyll (mg per square meter), a measure of phytoplankton biomass,
also continued to show no response to nutrient enrichment of the outfall,
even in the nearfield (Figure 3-8). That is, levels of chlorophyll did not

2003 OUTFALL MONITORING OVERVIEW 33 
increase compared to baseline. The annual and seasonal chlorophyll
measurements showed no response to the outfall in the nearfield or any
region of the farfield. 
0
100
200
300
400
500
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Chlorophyll (mg m -2 ) 
Baseline 
Range 
Baseline Mean 
2000 
2001 
2002 
2003 
0
20
40
60
80
100
120
140
160
180
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
Chlorophyll (mg m -2 ) 
Nearfield Boston Harbor N. Boundary 
Cape Cod Coastal Offshore 
Figure 3-8. Top: 2003 nearfield chlorophyll compared to baseline range and mean; Bottom:
annual mean chlorophyll in Massachusetts Bay regions 
Measurements of concentrations (Figure 3-9) and percent saturation (not
shown) of dissolved oxygen in the bottom waters in 2003 also continued
to show no response to nutrient enrichment or addition of organic matter
from the outfall. 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.
Prolonged stratification in 2003 resulted in continued decline in dissolved
oxygen concentrations until mid-November. Nearfield minimum values

2003 OUTFALL MONITORING OVERVIEW 34 
for 2003 were relatively high considering this prolonged period of
stratification. 
5
6
7
8
9
10
11
12
13
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
DO (mgL -1 ) 
Baseline 
Range 
Baseline Mean 
2001 
2002 
2003 
Figure 3-9. 2003 nearfield dissolved oxygen concentrations compared to baseline range and
mean 
Baseline monitoring identified a relationship between temperature,
salinity, and dissolved oxygen in the nearfield. Data from that period were
used to develop a statistical model (Geyer et al. 2002), which can now be
used to predict nearfield dissolved oxygen minima. Using the temperature
and salinity measurements for 2003, the model predicted that dissolved
oxygen concentrations would be average for 1992-2003 (Figure 3-10).
The agreement between the predicted and observed results indicates that
the relationship between dissolved oxygen and temperature and salinity
has not changed since the outfall began to discharge into Massachusetts
Bay. 
Figure 3-10. Observed and modeled average nearfield near-bottom dissolved oxygen
concentrations during September through October

2003 OUTFALL MONITORING OVERVIEW 35 
Phytoplankton Communities 
Seasonal abundance of phytoplankton in the post-outfall diversion years
has remained at or slightly below the baseline mean for most survey dates
(Figure 3-11; Libby et al. 2004a). Exceptions to this general finding were
an April 2003 Phaeocystis pouchetii bloom, a late summer 2002 diatom
bloom, and later than usual fall blooms in 2001 and 2003. The taxonomic
composition of the phytoplankton community has been relatively
consistent during the pre- and post-diversion years. 
0
1
2
3
4
5
6
7
8
9
10
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
10 6 cells L -1 
Baseline Range 
Baseline Mean 
2001 
2002 
2003 
Figure 3-11. Nearfield phytoplankton abundance 
The most pronounced change in the phytoplankton community has been
the change in the frequency of Phaeocystis pouchetii blooms (Figure 3-12,
top). During the baseline period, there were spring Phaeocystis blooms in
1992, 1994 (only recorded in the farfield), 1997, and 2000. Since the
outfall began operation, the blooms have occurred annually. However,
this increase in frequency does not appear to be related to the outfall. For
example, the 2003 bloom was widespread, occurring at all the
Massachusetts Bay stations sampled by MWRA. Satellite images (Figure
2-12, bottom) suggested that the bloom was most intense in the area off
Cape Ann, which is upstream from the outfall.

2003 OUTFALL MONITORING OVERVIEW 36 
Phaeocystis - Nearfield
0
1
2
3
4
5
6
7
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
10 6 cells L -1 
Figure 3-12. Top: abundance of Phaeocystis pouchetii in the nearfield, 1992-2003: Bottom:
SeaWiFS chlorophyll a image for March 27, 2003 
Other than the Phaeocystis pouchetii bloom, there continued to be no
detectable increases in nuisance species compared to the baseline. The
dinoflagellates Alexandrium spp. and diatoms in the genus Pseudo-
nitzschia were present but in low numbers. Pseudo-nitzschia
pseudodelicatissima , a potentially toxic diatom that is not currently
included in Pseudo-nitzschia threshold calculations, was present and at
times abundant.

2003 OUTFALL MONITORING OVERVIEW 37 
Zooplankton Communities 
Patterns of zooplankton abundance in 2003 were similar to many earlier
years (Figure 3-13; Libby et al. 2004a). As in prior years, abundance was
dominated by copepod nauplii and copepodites and adults of the small
copepod Oithona similis. Ctenophores, which decimated zooplankton
populations in 2000 and 2002, were present but did not have a similar
impact in 2003. 
0
50,000
100,000
150,000
200,000
250,000
300,000
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
animals m -3 
Baseline Range 
Baseline Mean 
2001 
2002 
2003 
Figure 3-13. Nearfield zooplankton abundance 
MWRA’s zooplankton monitoring is particularly comprehensive, in that it
samples and enumerates small species such as Oithona similis . Because
Massachusetts and Cape Cod bays are important as seasonal foraging
grounds for the endangered northern right whale, which feeds on
zooplankton, abundance of larger prey species, such as the more oceanic
copepod Calanus finmarchicus (copepodites and adults) are also of
interest. In the nearfield, abundance of Calanus finmarchicus tends to
peak in April and May, while the more abundant Oithona similis peaks in
mid to late summer (Figure 3-14).

2003 OUTFALL MONITORING OVERVIEW 38 
Monthly Arithmetic Means for Zooplankton
0
10,000
20,000
30,000
40,000
50,000
60,000
70,000
J F M A M J J A S O N D
Month
Abundance 
All other zp 
Oithona similis 
Calanus 
Figure 3-14. Monthly abundance of zooplankton species in Massachusetts Bay, 1992-2003
(individuals per m 3 ) 
Recently, scientists working on the MWRA program analyzed Calanus
finmarchicus abundance data to determine whether there were any
indications of effects of the outfall or whether abundance patterns
reflected long-term, large-scale climatic variation (Turner et al. 
submitted). 
Results of the analyses suggested that large-scale, long-term climate
phenomena may have greater influence on zooplankton populations than
do local perturbations, such as the outfall discharge. There was a
significant negative correlation between annual winter mean abundance of 
Calanus finmarchicus adults and copepodites and the annual boreal North
Atlantic Oscillation (NAO) Index, which is a measure of large-scale
atmospheric factors that affect climate in eastern North America. Data
collected since monitoring began in 1992 show that Calanus finmarchicus 
abundance correlates with higher wind speed (Figure 3-15). Even though
the data are highly variable, the relationship is statistically significant at
one of MWRA’s stations, with wind speed accounting for about 25% of
the variation in abundance. 
The analyses suggest that zooplankton abundance is affected by long-term,
large-scale processes, such as the NAO, and that regional conditions, such
as the winter marine climate, have a greater effect on zooplankton
abundance than local events.

2003 OUTFALL MONITORING OVERVIEW 39 
Station N04 
y = -929.9x + 7297
R2 = 0.25, p = 0.0110
0
2000
4000
6000
8000
10000
4 5 6 7 8
Mean winter wind speed (m s -1 )
Mean winter C. finmarchicus (m -3 ) 
9 
Figure 3-15. Mean monthly winter wind speed vs. monthly winter abundance of Calanus
finmarchicus adults and copepodites at one nearfield station 
Contingency Plan Thresholds 
Threshold parameters for water-column monitoring include minimum
dissolved oxygen concentrations and percent saturation in nearfield and
Stellwagen Bank bottom waters, dissolved oxygen depletion rate in
nearfield bottom waters, chlorophyll levels, abundance of nuisance algal
species, geographic extent of PSP toxin, and initial dilution. 
There was one exceedance of thresholds in 2003—the summer 
Phaeocystis threshold (Table 3-3). This measurement was made at the end
of a typical spring Phaeocystis bloom, and the exceedance was more likely
an artifact of the sampling schedule and the extremely low summer
threshold rather than an indication of an effect of the outfall. The number
of cells was far below levels that have negative environmental effects. All
other monitoring results were within ranges that met the thresholds.

2003 OUTFALL MONITORING OVERVIEW 40 
Table 3-3. Contingency plan threshold values for water-column monitoring 
Location/
Parameter
Specific
Parameter Baseline Caution Level Warning
Level
2003
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 =
6.72 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 =
71.8%
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 =
7.07 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 =
73.2%
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 71 mg/m 2 107 mg/m 2 143 mg/m 2 99 mg/m 2
Winter/spring 81 mgml 2 182 mg/m 2 None 178 mg/m 2
Summer 51 mg/m 2 80 mg/m 2 None 45 mg/m 2
Chlorophyll
nearfield
Autumn 90 mg/m 2 161 mg/m 2 None 87 mg/m 2
Winter/spring 470,000 cells/l 2,020,000 cells/l None 482,000
cells/l
Summer 72 cells/l 334 cells/l None
1700 cells/l,
caution
level
exceedance
Nuisance
algae
nearfield 
Phaeocystis
pouchetii 
Autumn 300 cells/l 2,370 cells/l None 0 cells/l
Winter/spring 6,200 cells/l 21,000 cells/l None 232 cells/l
Summer 13,000 cells/l 38,000 cells/l None 60 cells/l
Nuisance
algae
nearfield 
Pseudo-
nitzschia 
Autumn 9,700 cells/l 37,900 cells/l None 8,900 cells/l
Nuisance
algae
nearfield 
Alexandrium
fundyense 
Any nearfield
sample
Baseline
maximum =
163 cells/l
100 cells/l None 6.6 cells/l
maximum
Farfield PSP toxin
extent Not applicable New incidence None
No toxicity
or shellfish
closures

2003 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 1997a, 1998). 
Sediment transport in the region occurs primarily during storms.
Typically, waves during storms with winds from the northeast resuspend
sediments, which are transported by shallow currents from western
Massachusetts Bay toward Cape Cod Bay and by deeper currents to
Stellwagen Basin. Cape Cod Bay is partially sheltered from large waves
by the arm of Cape Cod, and storm waves are rarely large enough to
resuspend sediments in Stellwagen Basin, which is the deepest feature in
the region. 
Environmental Concerns 
Within Boston Harbor, studies of the sediments have documented
recovery following the cessation of sludge discharge, improvements to
combined sewer overflow (CSO) systems, and improved sewage effluent
treatment. Conversely, relocating the outfall raised concerns about
potential effects on the offshore sea floor. Concern has focused on three
issues: eutrophication and related low levels of dissolved oxygen,
accumulation of toxic contaminants in depositional areas, and smothering
of animals by particulate matter (Table 4-1).

2003 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,
depressed levels of dissolved oxygen could affect bottom communities.
Increasing the amount 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 causes concern about accumulation of toxic contaminants in
Cape Cod Bay and Stellwagen Basin. Similarly, concentrations of
particulate matter are expected to be low, but there remains some
possibility that bottom communities near the outfall could be affected by
deposition. 
Monitoring Design 
Sea floor monitoring includes several components (Table 4-1):
measurements of contaminant concentrations and other chemistry
parameters in sediments, sediment-profile imaging to provide a rapid
assessment of potential effects on 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).

2003 OUTFALL MONITORING OVERVIEW 43 
Table 4-2. Components of sea-floor monitoring 
Task Objective Sampling Locations 
And Schedule Analyses 
Soft-bottom studies Evaluate sediment quality and
benthos in Boston Harbor and
Massachusetts Bay 
1 survey/year 
20 nearfield stations 
11 farfield stations 
Sediment chemistry 
Sediment profile imagery 
Community composition 
Hard-bottom studies Characterize marine benthic
communities in rock and
cobble areas 
1 survey/year 
21 stations on 6 transects 
Topography 
Substrate 
Community composition 
Figure 4-1. Locations of nearfield soft-bottom stations (NF 12 and NF 17 are also sampled by
USGS.)

2003 OUTFALL MONITORING OVERVIEW 44 
Figure 4-2. Locations of farfield soft-bottom stations

2003 OUTFALL MONITORING OVERVIEW 45 
Figure 4-3. Locations of hard-bottom stations

2003 OUTFALL MONITORING OVERVIEW 46 
Through 2002, the core of sediment contaminant monitoring consisted of
annual, mid-August sampling of sediments at 31 stations throughout
Massachusetts and Cape Cod bays. Replicate field samples were taken at
all farfield and selected nearfield stations. Single samples were taken at
the remaining nearfield stations. Samples were analyzed for PAHs, PCBs,
chlorinated pesticides, metals, grain size, total organic carbon (TOC), 
Clostridium perfringens spores, and linear alkyl benzenes. For 2003, EPA
and MADEP approved a reduced plan for monitoring toxic contaminants,
with analyses completed for only two nearfield stations. 
Annual 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
1997b; Figure 4-1). Since 1992, these stations have also been occupied by
MWRA. 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 in August of each year at
23 nearfield stations 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 benthic infauna also consists of annual surveys conducted
in August. Sampling of 23 nearfield stations provides spatial coverage
and local detail about the fauna in depositional areas located within eight
kilometers of the diffuser. Farfield sampling of eight additional stations in
Massachusetts and Cape Cod bays contributes regional data on soft-
bottom habitats. 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 lab.
Animals are sorted, identified, and counted.

2003 OUTFALL MONITORING OVERVIEW 47 
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 23 stations or waypoints, including diffuser head
#44 of the outfall (which was not opened), and diffuser head #2. These
annual surveys are conducted in June. Photographs are examined for
substrate type (top or flank of the drumlin, with relief defined by presence
of boulders and cobbles), amount of sediment drape (the degree to which
there is a layer of fine material on the hard surface), and biota (taxa
identified to species or species groups and counted). 
Some station changes in the hard-bottom program were made for 2003.
Two stations were discontinued, one because it was relatively devoid of
life and one because it was redundant with another station. Two
additional stations were established, one about two miles southeast of the
outfall and one about ten miles off the coast from Scituate, Massachusetts,
well south of the outfall. The sampling plan as of 2003 therefore included
one active diffuser head, one inactive diffuser head, 13 sites near the
outfall (nine to the north and four to the south), three nearfield reference
sites to the north of the outfall, four nearfield reference sites south of the
outfall, and one farfield reference site, the station off Scituate. 
Results 
Sediment 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 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. 
For 2003, data from the two stations sampled for toxic contaminants were
within the baseline range for almost all samples. Bulk sediments and
sewage-tracer data also fell within the baseline range. For example, 2003
concentrations of the sewage tracer Clostridium perfringens spores were
generally below the baseline mean (Figure 4-4).

2003 OUTFALL MONITORING OVERVIEW 48 
0
5,000
10,000
15,000
20,000
25,000
30,000 
Clostridium (cfu/g dry) B a s e lin e R a n g e 
B a s e lin e M e a n 
2 0 0 1 R e p lic a t e s 
2 0 0 2 R e p lic a t e s 
2 0 0 3 R e p lic a t e s 
B a s e lin e M e a n - F in e s 
B a s e lin e M e a n - T O C 
0
25
50
75
100
NF17
NF04
NF23
NF13
NF19
NF02
FF12
FF10
NF18
NF15
NF20
NF09
NF05
NF10
NF14
NF07
NF22
FF13
NF16
NF21
NF24
NF12
NF08
Fines (%)
0.0
0.5
1.0
1.5
2.0
TOC (%
dw) 
Figure 4-4. Clostridium perfringens spores and percent fine sediments at nearfield stations 
A detailed analysis of post-outfall operation Clostridium perfringens spore
concentrations, sediment grain size, and total organic carbon compared
with data from just the two years preceding outfall start-up rather than the
entire baseline period did suggest that an effluent signal could be detected
at stations near the outfall. This finding was expected. 
Sediment-Profile Imaging 
Sediment-profile imaging measurements in 2003 showed no effects from
the outfall. The mean apparent color RPD depth was statistically the same
as the baseline mean (Figure 4-5). No relationship between RPD depth
and outfall operation has been detected, even at Station NF24, a muddy
station close to the outfall, where negative effects might be most expected.

2003 OUTFALL MONITORING OVERVIEW 49 
0.0
1.0
2.0
3.0
4.0
1990 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 
RPD Threshold 
Figure 4-5. Apparent color RPD for all data from nearfield stations 
Soft-bottom Communities 
The soft-bottom communities have also shown no response to the outfall. 
During the baseline period, multivariate analyses indicated that sediment
grain size was the dominant factor in structuring the benthic communities
(Maciolek et al. 2004). In the nearfield, stations with fine sediments are
dominated by polychaete worms, such as Prionospio steenstrupi , Spio
limicola , Mediomastus californiensis , and Aricidea catherinae . Sandier
stations are 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 differ 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 , predominate at most stations. Prionospio steenstrupi, 
which is dominant at many nearfield stations, is also common at some of
the farfield stations. Another polychaete, Cossura longicirrata , dominates
at a station in Cape Cod Bay.

2003 OUTFALL MONITORING OVERVIEW 50 
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 three years of post-discharge monitoring have detected some
statistical differences in community parameters, such as increased
numbers of some species and increased 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 (Maciolek et al. 
2004). 
The mean density of animals was highest in 2002 and only slightly lower
in 2003 (Figure 4-6). The average number of species increased slightly in
2003 (from 74 to 76 species). One diversity measure, log-series alpha ,
continued an upward trend, while other community parameters, Shannon
diversity and Pielou’s evenness were essentially the same in 2003 as in
2002.

2003 OUTFALL MONITORING OVERVIEW 51 
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 
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 
2.5
3.0
3.5
4.0
4.5
5.0
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 
Year
Shannon Diversity (H') per Sample Mean +/-1SD 
Baseline Mean: 3.68 
Outfall Startup 
0.3
0.4
0.5
0.6
0.7
0.8
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 
Year
Pielou's Evenness (J') 
Mean +/-1SD 
Baseline Mean: 0.62 
Outfall Startup 
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 Startu p 
Figure 4-6. Community parameters in the nearfield, 1992-2003: abundance per sample, number
species per sample, Shannon diversity, Pielou’s evenness, log-series alpha

2003 OUTFALL MONITORING OVERVIEW 52 
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. 
Any changes since the outfall began operation have been modest, and it is
difficult to attribute them to outfall operation. Sediment drape has
increased at three of the nine stations directly to the north of the outfall
and at two of the three stations considered northern nearfield reference
stations. There have been decreases in coralline algae cover at the same
stations. The declines were less pronounced in 2003 than in 2001 and
2002, but coralline algae cover did decline at the third northern nearfield
reference site in 2003. Declines in upright algae were also detected at
northern stations. 
Several trends have been observed that appear to be regional. Abundance
of the green sea urchin Strongylocentrotus droebachiensis appears to
follow a cyclical pattern, declining during 1996-2000, increasing in 2001
and 2002, and declining in 2003. Crabs in the genus Cancer and the
lobster Homarus americanus appear to have increased over time. The cod 
Gadus morhua has also increased in numbers since the mid 1990s, with a
decrease in 2003. 
One unusual phenomenon in 2003 was the dense aggregations of barnacles 
Balanus spp. observed throughout the study area. Massive settlements of
barnacles were found at seven sites north and south of the diffuser and off
Scituate. Less dramatic, but still heavy, settlements were found at four
additional sites, both near the outfall and at great distance. Barnacles were
frequently so crowded that they formed tall, twisted colonies, and
overcrowding had led to mass mortality at many sites, including Diffuser
#44. These large settlements followed a peak in barnacle larvae detected
in 2002 water column monitoring (Figure 4-7).

2003 OUTFALL MONITORING OVERVIEW 53 
Barnacle larvae
0
2,000
4,000
6,000
8,000
10,000
12,000
14,000
16,000
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
Animals m -3 
NEARFIELD HARBOR COASTAL 
Figure 4-7. Top: dense barnacle settlement photographed in 2003; Bottom: abundance of
barnacle larvae in the water column, 1992-2003

2003 OUTFALL MONITORING OVERVIEW 54 
Contingency Plan Thresholds 
No contingency plan threshold parameters for sea-floor monitoring were
exceeded in 2003. Those parameters include contaminant concentrations,
RPD depth, and benthic diversity and species composition in soft-bottom
communities (Table 4-3). 
Table 4-3. No contingency plan baseline and threshold values for sea-floor monitoring were
exceeded in 2003. 
Location Parameter Caution Level Warning Level 2003 Results 
Sediments,
nearfield RPD depth 1.18 cm None 2.14 cm 
Species per sample <47.74 or >79.95 None 76.5 
Fisher’s log-series
alpha <10.05 or >15.63 None 14.63 
Shannon diversity <3.30 or >4.02 None 3.61 
Benthic
diversity,
nearfield 
Pielou’s evenness <0.56 or >0.67 None 0.58 
Species
composition,
nearfield 
Percent opportunists 10% 25% 0.53%

2003 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.

2003 OUTFALL MONITORING OVERVIEW 56 
Monitoring Design 
The monitoring program focuses on three indicator species: winter
flounder, lobster, and blue mussel (Figure 5-1). Winter flounder and
lobster are important resource species in the region. The blue mussel is
also a fishery species and a common biomonitoring organism. 
Figure 5-1. Sampling areas for fish and shellfish monitoring

2003 OUTFALL MONITORING OVERVIEW 57 
Winter Flounder 
Like all flatfish, winter flounder live on and eat food from 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 are collected from
five locations—Deer Island Flats, Broad Sound, off Nantasket Beach, the
outfall site, and eastern Cape Cod Bay. Livers are examined to quantify
three types of vacuolation (centrotubular, tubular, and focal, representing
increasing severity), microphage aggregation, biliary duct proliferation,
and neoplasia or tumors. Neoplasia and vacuolation have been associated
with chronic exposure to contaminants. 
Chemical analyses of winter flounder tissues from the five locations are
also made to determine tissue burden and to evaluate whether contaminant
burdens approach human health consumption limits. Chemical analyses of
composite samples of fillets and livers include PCBs, pesticides, mercury,
and lipids. Liver samples are also analyzed for PAHs, lead, silver,
cadmium, chromium, copper, nickel, and zinc. 
Lobster 
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. Lobsters are taken from Deer Island Flats,
the area near the outfall, and eastern Cape Cod Bay to determine specimen
health and tissue contaminant burden. Chemical analyses are performed
on composite samples. Meat (from the tail and claw) and hepatopancreas
are analyzed for lipids, PCBs, pesticides, and mercury. Hepatopancreas
samples are also analyzed for PAHs, lead, silver, cadmium, chromium,
copper, nickel, and zinc. 
Blue Mussel 
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. In 2003, deployment sites included Boston Inner Harbor,
Deer Island Light, the outfall site, the “B” Buoy located just to the south
of the outfall site, and Cape Cod Bay. 
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.

2003 OUTFALL MONITORING OVERVIEW 58 
Results 
Winter Flounder 
Fifty sexually mature (at least three years old) winter flounder were taken
from each of the five sampling sites in April and May 2003 (Lefkovitz et
al. 2004). Each of the fish was examined for physical characteristics. All
fish were used for histological and age analyses. Fifteen fish from each of
three sites were designated for chemical analyses. 
Tumors were absent and incidence of fin erosion was low in fish collected
in 2003. However, external ulcers were noted on many fish, particularly
on fish from Boston Harbor and western Massachusetts Bay. Ulcers had
not been specifically included as part of the physical assessment provided
for in the monitoring plan. Consequently, their presence prompted a
special study (described in Section 6, Special Studies). 
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 5-2) and below the baseline
mean at the outfall site. 
Hydropic Vacuolation Index (HV%/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
Year
Hydropic Vacuolation/ Mean Age DIF 
NB 
BS 
OS 
ECCB 
Figure 5-2. 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)

2003 OUTFALL MONITORING OVERVIEW 59 
Levels of organic contaminants in flounder fillets and livers from fish
caught at the outfall site in 2003 were within the historical baseline range.
In fillets, average levels of organic contaminants (such as PCBs; Figure 5-
3, top) were not significantly different for the three post-discharge years
when compared to the final three years of baseline monitoring, during
which secondary treatment had been implemented. In flounder livers
(Figure 5-3, bottom), mean PCB concentrations were statistically greater
in the post-discharge years compared to the three years immediately
before outfall start-up (2,419 ng/l compared to 1,222 ng/l). However, the
2003 levels of PCBs in flounder livers were within the range for the entire
baseline. 
Total PCB in Flounder Fillets 1992-2003
0
100
200
300
400
500
600
700
800
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
Year
ng/g dry weight 
DIF 
OS 
ECCB 
NB 
BS 
Outfall Startup 
Total PCB in Flounder Livers 1992-2003
0
2,000
4,000
6,000
8,000
10,000
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
Year
ng/g dry weight 
DIF 
OS 
ECCB 
NB 
BS 
Outfall Startup 
Figure 5-3. PCB concentrations in flounder fillets and livers. (DIF = Deer Island Flats, OS =
Outfall Site, ECCB = Eastern Cape Cod Bay, NB = Nantasket Beach, BS = Broad Sound)

2003 OUTFALL MONITORING OVERVIEW 60 
Concentrations of most metals in 2003 fell within the historical range. For
mercury, the 2003 mean level in flounder fillet (Figure 5-4) and livers (not
shown) from the outfall site was relatively high compared to 2001 and
2002; however, mean mercury levels from the three post-outfall-relocation
years (considered together) were not significantly different from the 1998-
2000 years. MWRA is further monitoring mercury levels in flounder to
evaluate whether the high value from 2003 represents a trend or whether it
is a result of variation in sampling and measurement. 
Mercury in Flounder Fillets 1992-2003
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
Year
ug/g dry weight 
DIF 
OS 
ECCB 
NB 
BS 
Outfall Startup 
Figure 5-4. Mercury in flounder fillets, 1992-2003 (DIF = Deer Island Flats, OS = Outfall Site,
ECCB = Eastern Cape Cod Bay, NB = Nantasket Beach, BS = Broad Sound) 
Lobster 
Fifteen lobsters from each of three areas—Deer Island Flats, the outfall
site, and eastern Cape Cod Bay—were purchased from commercial
lobstermen observed to be fishing in the areas (Lefkovitz et al. 2004). The
lobsters were approximately the same size at all sites. Only males were
collected at eastern Cape Cod Bay, mostly males were taken at Deer
Island Flats, and the sex ratio was about even in lobsters from the outfall
site. No gross abnormalities were noted. 
For most compounds, contaminant concentrations in lobster meat and
hepatopancreas were low, and no effects of relocating the outfall were
detected. PCB concentrations showed a different pattern, with an
anomalously high mean concentration in meat and hepatopancreas from
animals collected at the outfall site (Figure 5-5).

2003 OUTFALL MONITORING OVERVIEW 61 
Total PCB in Lobster Meat 1992-2003
0
50
100
150
200
250
300
350
400
450
500
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
Year
ng/g dry weight 
DIF 
OS 
ECCB 
Outfall Startup 
Total PCB in Lobster Hepatopancreas 1992-2003
0
2,000
4,000
6,000
8,000
10,000
12,000
14,000
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
Year
ng/g dry weight 
DIF 
OS 
ECCB 
Outfall Startup 
Figure 5-5. PCB concentrations in lobster meat and hepatopancreas (DIF = Deer Island Flats,
OS = Outfall Site, ECCB = Eastern Cape Cod Bay) 
These findings prompted additional analyses, which showed that the high
values could be attributed to one individual lobster in one of the composite
samples. Confirmatory analyses using gas chromatography/mass
spectrometry (GC/MS) indicated that the pattern of PCB congeners in the
highly contaminated animal was different from the pattern in less
contaminated lobsters (Figure 5-6). The pattern also varied from that seen
in lobsters from New Bedford Harbor, an area that is highly contaminated
with PCBs. The reason for the anomaly is not known.

2003 OUTFALL MONITORING OVERVIEW 62 
Lobster Hepatopancreas 
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
C3-1 C3-2 C3-3 C3-4 C3-5 DIF ECCB NB-III NB-II 
Percent of total PCB 
PCB 206 
PCB 195 
PCB 187 
PCB 153 
PCB 138 
PCB 118 
Individual 2003 Outfall Site Lobster PCB New Bedford Harbor Composites 
Individual OS Lobster with
Anomalous PCB Pattern 
Figure 5-6. Distribution of selected PCB congeners in lobster hepatopancreas samples from
Massachusetts Bay and New Bedford Harbor 
Blue Mussel 
Mussel arrays were recovered after 40 and 60 days (Lefkovitz et al. 2004).
Survival was high, ranging from 92 to 99%. 
Historically, the Boston Inner Harbor and Deer Island sites have shown
the highest concentrations of contaminants, and the Cape Cod Bay and
outfall sites were the lowest. Overall, the inner harbor site still showed the
greatest degree of bioaccumulation (Figure 5-7). 
It has been possible to detect some changes in mussels deployed at the
outfall site (Table 5-2), both because the mussels are placed within the
mixing zone where they are continually exposed to effluent and because
the laboratory measurements used by the program are sensitive and
precise. There have been significant increases in chlordane and PAHs in
mussels deployed at the outfall site and small but statistically significant
increases in mercury, copper, lead, and DDTs. For most constituents, the
increases are only apparent when post-discharge data are compared to data
from the three years prior to outfall start-up, 1998-2000, when secondary
treatment had been implemented but discharge was still to the harbor.

2003 OUTFALL MONITORING OVERVIEW 63 
Total PCB in Mussels 1991-2003
0
100
200
300
400
500
600
700
800
900
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
Year
ng/g dry weight 
Predeployment 
IH 
DIL 
OSM 
CCB 
Outfall Startup 
Total Chlordane in Mussels 1991-2003
0
10
20
30
40
50
60
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
Year
ng/g dry weight 
Predeployment 
IH 
DIL 
OSM 
CCB 
Outfall Startup 
Figure 5-7. Selected contaminant concentrations in mussels. (IH = Inner Harbor, DIL =
Deer Island Light, OSM = Outfall Site, CCB = Cape Cod Bay)

2003 OUTFALL MONITORING OVERVIEW 64 
Table 5-2. Comparison of contaminant concentrations at the outfall site during the three years
prior to and the three years since outfall operation. (Student two-sample T-test, with increases
significant at <0.05; NA=not analyzed; ND=not detected. The comparison of three years before
and after discharge was chosen to examine solely the period in which secondary treatment had
been implemented.) 
Flounder Lobster 
Parameter Fillet Liver Meat Hepatopancreas Mussel 
Cadmium NA No change NA No change NA 
Chromium NA No change NA No change NA 
Copper NA No change NA No change NA 
Lead NA No change NA No change Increased 
Mercury No change No change No change No change Increased 
Nickel NA No change NA No change NA 
Silver NA No change NA No change NA 
Zinc NA No change NA No change NA 
Total DDTs No change No change No change Decreased Increased 
Total PCBs No change Increased No change No change Increased 
Total PAHs NA No change NA No change Increased 
Total chlordanes No change No change Decreased Decreased Increased 
Dieldrin No change No change No change Decreased Increased 
LMW PAHs NA NA NA NA No change 
HMW PAHs NA NA NA NA Increased 
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 2003, as in 2001 and 2002, the caution threshold for PAHs was
exceeded in mussels. The earlier exceedances were reviewed (Hunt et al. 
2002c, OMSAP 2003c) and have been found to be a result of the
placement of the mussels within the plume rather than an unexpected
effect of the discharge.

2003 OUTFALL MONITORING OVERVIEW 65 
Table 5-3. Contingency plan baseline, threshold, and 2003 values for fish and shellfish
monitoring 
Parameter 
Type/ 
Location 
Parameter Baseline Caution 
Level 
Warning 
Level 
2003 
Results 
PCB 0.033 ppm 1 ppm wet weight 1.6 ppm wet
weight 0.030 ppm Flounder
tissue
nearfield Mercury 0.074 ppm 0.5 ppm wet
weight 
0.8 ppm wet
weight 0.105 ppm 
Chlordane 242 ppb 484 ppb None 143 ppb 
Dieldrin 63.7 ppb 127 ppb None 29.2 ppb 
Flounder
tissue, lipid
normalized,
nearfield DDT 775.9 ppb 1552 ppb None 583 ppb 
Flounder 
nearfield 
Liver disease
(CHV) 24.4% 44.9% None 16% 
PCB 0.015 ppm 1 ppm wet weight 1.6 ppm wet
weight 0.029 ppm 
Lobster tissue
nearfield Mercury 0.148 ppm 0.5 ppm wet
weight 
0.8 ppm wet
weight 0.112 ppm 
Chlordane 75 ppb 150 ppb None 77.9 ppb 
Dieldrin 161 ppb 322 ppb None 27.8 ppb 
Lobster
tissue, lipid
normalized,
nearfield DDT 341.3 ppb 683 ppb None 129 ppb 
PCB 0.011 ppm 1 ppm wet weight 1.6 ppm wet
weight 0.0085 ppm 
Lead 0.415 ppm 2 ppm wet weight 3 ppm wet
weight 0.226 ppm 
Mussel tissue 
nearfield 
Mercury 0.019 ppm 0.5 ppm wet
weight 
0.8 ppm wet
weight 0.017 ppm 
Chlordane 102.3 ppb 205 ppb None 191 ppb 
Dieldrin 25 ppb 50 ppb None 21.6 ppb 
DDT 241.7 ppb 483 ppb None 179 ppb 
Mussel tissue,
lipid
normalized,
nearfield PAH 1080 ppb 2160 ppb None 
3690 ppb,
caution level
exceedance

2003 OUTFALL MONITORING OVERVIEW 66 
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 2003, special studies
included a visual inspection of the outfall, an analysis of water chemistry
data from Boston Harbor and Massachusetts Bay, continued study of
nutrient flux at the sediment-water interface, marine mammal
observations, assessment of PCB analyses used in fish and shellfish
monitoring, and a review of available information on flounder ulcers. 
Outfall Inspection 
MWRA conducted a visual inspection of the outfall during June 2003.
The inspection used the same equipment as is used in hard-bottom surveys
to record the condition of each outfall riser and diffuser cap on videotape.
The survey found no damage that might affect proper functioning of the
outfall. All diffuser caps had the same vigorous epifaunal growth as has
been documented during hard-bottom surveys of diffusers #2 and #44,
(such as in Figure 6-1). The growth did not obstruct any of the diffuser
ports that are open and discharging. 
Figure 6-1. Outfall diffuser #2 (photograph taken during 2003 hard-bottom survey)

2003 OUTFALL MONITORING OVERVIEW 67 
Water Chemistry in Boston Harbor and
Massachusetts Bay 
MWRA recently completed an analysis of water chemistry data from
Boston Harbor and Massachusetts Bay to determine the effects of ceasing
effluent discharge in the harbor and transferring it to the bay (Taylor
2004). The analysis used data from the outfall monitoring program and
additional information from a separate harbor monitoring program. It
compared baseline water quality data with information from the first 24
months following relocation of the outfall. 
In Boston Harbor, there were significant improvements in many water
quality parameters during the first 24 months following diversion of the
effluent. Nutrient measurements, including total nitrogen, dissolved
inorganic nitrogen, total phosphorus, dissolved inorganic phosphorus, the
molar ratio of total nitrogen to total phosphorus, and the molar ratio of
dissolved inorganic nitrogen to phosphorus all declined during the period.
Phytoplankton biomass, measured as chlorophyll a, and particulate
organic carbon also declined during the period. These measurements are
all indicative of healthier, less eutrophic conditions. 
During the same period, at the nearfield stations close to the
Massachusetts Bay outfall, there were significant increases in some of the
water quality parameters. Significant increases in total nitrogen, dissolved
organic nitrogen, total phosphorus, the molar ratio of dissolved inorganic
nitrogen to phosphorus, and particulate organic carbon were detected.
Increases in these parameters were not significant when considered over
the whole of Massachusetts Bay. 
For Massachusetts Bay as a whole, significant changes were detected for
three parameters: an increase in the molar ratio of dissolved inorganic
nitrogen to silicate, a decrease in total organic carbon, and an increase in
salinity. These changes are thought to be responses to regional conditions
rather than to the outfall. 
For example, Figure 6-2 shows dissolved inorganic nitrogen (top) and
chlorophyll (bottom) along a transect of stations extending from the New
England Aquarium in Boston’s inner harbor to the outfall and then
southeast to a station located off the tip of Race Point at the edge of Cape
Cod Bay. For both parameters, there were significant decreases in the
harbor following the transfer of the outfall, and for nitrogen, there was a
concurrent increase in concentrations at the outfall site. No significant
changes were detected beyond the nearfield stations. Although dissolved
inorganic nitrogen increased in the nearfield, there was no relative
increase in chlorophyll in the nearfield. There was a dramatic drop in
chlorophyll in the harbor.

2003 OUTFALL MONITORING OVERVIEW 68 
0 10 20 30 40 50 60 70 80 90
2
4
6
8
10
12
14
16
18 
0 10 20 30 40 50 60 70 80 90
0
1
2
3
4
5
6
7
8 
BEFORE 
AFTER 
Cape Cod 
Bay
Massachusetts Bay Nearfield Boston
Harbor 
AVERAGE CHL CONC.
( UG L -1 ) 
Outfall 
Nearfield Massachusetts Bay Boston
Harbor
Cape Cod 
Bay 
AVERAGE DIN CONC.
( UMOL L -1 ) 
BEFORE 
AFTER 
Outfall 
DISTANCE FROM N. E. AQUARIUM (KM) 
Figure 6-2. Dissolved inorganic nitrogen and chlorophyll concentrations before and after outfall
transfer from Boston Harbor to Massachusetts Bay (from Taylor 2004)

2003 OUTFALL MONITORING OVERVIEW 69 
Nutrient Flux 
One concern about the outfall was that diversion of effluent from Boston
Harbor to Massachusetts Bay might increase loads of organic matter to the
nearfield, enhancing benthic respiration and nutrient fluxes between the
sediments and the water column. 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 rates of denitrification, sediment oxygen demand,
and the flux of nutrients in the vicinity of the outfall and to assess the
importance of these processes on nutrient and oxygen levels (Table 6-1). 
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? 
MWRA has been monitoring the sediment-water interface since 1992. In
2003, studies were continued at four sites in the harbor, three sites in the
nearfield, and one site in Stellwagen Basin (Tucker et al. 2004). Since the
outfall came on line, MWRA has detected no changes that could be
attributed to the organic matter enrichment at the nearfield or in
Stellwagen Basin. Rates of benthic respiration and nutrient fluxes have
been well within the baseline ranges. Chlorophyll levels in the sediments
also remained within the baseline range. Small increases in organic matter
content of surface sediments in the nearfield, which had been detected in
2001 and 2002, did not continue in 2003. 
While little or no change has been detected in Massachusetts Bay, positive
changes have been evident in Boston Harbor. Decreases in total organic
carbon have been measured at some stations. Sediment chlorophyll
concentrations decreased at two harbor stations in 2002. At three stations,
sediment oxygen demand and nutrient fluxes were lower than at any
previous time during the monitoring period, and large variability among
harbor stations had essentially vanished.

2003 OUTFALL MONITORING OVERVIEW 70 
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, also occur. 
Since 1995, MWRA has included endangered species observers on
monitoring surveys. In 2003, observers were included on 26 water quality
surveys (Short et al. 2004). 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. 
The surveys are not designed to determine possible effects of the outfall
on marine mammals, but do provide some general information. During
the 2003 surveys, 16 individual whales, 6 harbor porpoise, and more than
100 Atlantic white-sided dolphins were directly observed by the trained
observers and other members of the monitoring team. Thirteen large
baleen whales were sighted, more than twice as many as in 2002, but
fewer than in 1998-2001. Studies by the Whale Center of New England
confirmed an increase in humpback whales in the region compared to
2002, primarily over the southeast portion of Stellwagen Bank.

2003 OUTFALL MONITORING OVERVIEW 71 
PCB Analyses 
Over the years of fish and shellfish monitoring, chemists noted that
concentrations of one PCB congener, PCB 180, were high relative to other
congeners. This finding was particularly noticed in samples with higher
overall concentrations of organic compounds, such as flounder livers and
lobster hepatopancreas. A special study (Lefkovitz et al. 2001) found that
the analytical method used by the program, gas chromatography/electron
capture detection (GC/ECD), could be responsible for the high
concentrations. Using the standard GC/ECD method, a common
environmental compound, bis-2-ethylhexyl phthalate, often coelutes with
PCB 180. 
During 2003, MWRA reviewed monitoring program data to determine the
effects of including or not including PCB 180 data in calculating total
PCB concentrations. The review found that overall, the effects on the data
were not great. Figure 6-3, for example, shows little change to average
total PCB levels over the course of the monitoring program. However, the
difference in some individual samples was high—as high as a 42% change
in total PCBs. As a result of the study, MWRA will exclude PCB 180
from evaluations in its annual fish and shellfish monitoring reports. The
congener will continue to be used in calculations of total PCBs for
threshold testing. 
Total PCB in Lobster Hepatopancreas 1992-2003
(with and without PCB 180)
0
2,000
4,000
6,000
8,000
10,000
12,000
14,000
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
Year
ng/g dry weight 
DIF 
DIF (w/out PCB180) 
OS 
OS (w/out PCB180) 
Outfall Startup 
Figure 6-3. Total PCBs in lobster hepatopancreas at Deer Island Flats (DIF) and the outfall site
(OS) with and without PCB 180

2003 OUTFALL MONITORING OVERVIEW 72 
Flounder Ulcers 
During the 2003 sampling, scientists noted external ulcers on the blind
(bottom) side of a number of flounder (Figure 6-4). This unusual finding
prompted a review of additional information from other investigators,
including the Massachusetts Division of Marine Fisheries (MDMF), EPA
Narragansett Laboratory, and NMFS (Moore 2003, Lefkovitz et al. 2004).
The review found that the highest prevalence of ulcers was found Boston
Harbor and western Massachusetts Bay (Figure 6-5), and indicated that the
ulcers had not been frequently observed prior to 2001. MWRA requested
additional testing of the fish, including microbiological and histological
observations of the ulcers. These tests failed to detect an etiology of the
lesions, although there appeared to be an infectious process involved. 
As a result, studies were planned to expand the regular April 2004
flounder survey to increase the number of stations and to study the
microbiology of the lesions. 
Figure 6-4. Blind-side flounder ulcers

2003 OUTFALL MONITORING OVERVIEW 73 
Figure 6-5. Prevalence of ulcers in winter flounder noted in 2002 and 2003 (Numbers indicate
the percentage of fish with ulcers at each location. Numbers in parentheses indicate number of
fish examined.)

2003 OUTFALL MONITORING OVERVIEW 74 
7. Stellwagen Bank 
National Marine Sanctuary 
Background 
The Gerry E. Studds Stellwagen Bank National Marine Sanctuary
(SBNMS) comprises 842 square miles located at the boundary of
Massachusetts Bay and the rest of the Gulf of Maine. Its 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, that is, they mark the
boundary between Massachusetts Bay and the rest of the Gulf of Maine.
These stations are important to MWRA, not just because of their location
within a marine sanctuary, but also because water column processes
within Massachusetts Bay are largely driven by the regional processes in
the Gulf of Maine. Eight water-column stations located between the
sanctuary and the coast are considered “offshore” stations by the MWRA
program. 
Since 2001, the sanctuary managers, in conjunction with MWRA’s
contractor Battelle, have conducted a 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
program and results for 2003 are presented described in Libby et al. 
2004b.

2003 OUTFALL MONITORING OVERVIEW 75 
Figure 7-1. Water column stations, including the additional Stellwagen Bank National Marine
Sanctuary (SBNMS) stations sampled in August and October 2001-2003

2003 OUTFALL MONITORING OVERVIEW 76 
Two MWRA sea-floor stations are within the sanctuary, one at the
southern boundary and one within Stellwagen Basin (see Figure 4-2). A
third sea-floor station is just north of the sanctuary boundary and a fourth
station 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 circulation pattern that transports diluted effluent
south and southeastward in Massachusetts Bay. These stations are
sampled annually in August. 
Results 
Water Column 
Overall, water quality within the sanctuary was excellent during 2003.
There was no indication of any effect of the MWRA outfall (Libby et al. 
2004a, 2004b). 
Mean concentrations of dissolved oxygen in bottom waters of Stellwagen
Basin during regular MWRA monitoring were within the low end of the
baseline range. The survey minimum concentration measured in
Stellwagen Basin in 2003 was 7.07 mg/l, well above the 6.2 mg/l
contingency plan background measurement (Figure 7-2). The survey
minimum percent saturation was 73.2%, above the 66.3% contingency
plan background. 
In 2003, as in 2002, the water column remained stratified until the late fall,
and dissolved oxygen concentrations continued to decline after the
October survey. Data from the GoMOOS “A” mooring, located in the
northwest corner of the sanctuary, indicated that the minimum
concentration, 6.2 mg/l, was reached on November 10 (Figure 7-3).
Dissolved oxygen probably reached concentrations lower than 6 mg/l
within Stellwagen Basin. 
Elevated concentrations of ammonia were measured at offshore and
boundary stations in October. However, the elevated ammonia
concentrations were not likely to be associated with the outfall. Currents
at the time were not transporting water masses from the outfall to offshore,
and phosphate concentrations did not follow the same pattern of elevated
concentrations.

2003 OUTFALL MONITORING OVERVIEW 77 
5
6
7
8
9
10
11
12
13
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
DO (mg L -1 ) 
Baseline 
Range 
Baseline Mean 
2001 
2002 
2003 
Figure 7-2. Post-discharge survey mean dissolved oxygen concentrations in Stellwagen Basin
compared to baseline mean and range 
Feb03 Mar03 Apr03 May03 Jun03 Jul03 Aug03 Sep03 Oct03 Nov03 Dec03 Jan04 
0 
2 
4 
6 
8 
10 
Temperature ( ° C) GoMOOS Mooring 50M deep
HOM Survey event data 50m
Stellwagen Station SW4 50m 
Feb03 Mar03 Apr03 May03 Jun03 Jul03 Aug03 Sep03 Oct03 Nov03 Dec03 Jan04 
31 
32 
33 
34 
Salinity (ppt) 
GoMOOS Mooring 50M deep
HOM Survey event data 50m
Stellwagen Station SW4 50m 
Feb03 Mar03 Apr03 May03 Jun03 Jul03 Aug03 Sep03 Oct03 Nov03 Dec03 Jan04 
6 
8 
10 
12 
DO mg/L 
GoMOOS Mooring 50M deep
HOM Survey event data 50m
Stellwagen Station SW4 50m 
Figure 7-3. Near-bottom salinity, temperature, and dissolved oxygen data from the GoMOOS
“A” mooring, and MWRA and Stellwagen Bank monitoring stations

2003 OUTFALL MONITORING OVERVIEW 78 
Annual mean nutrient concentrations in the sanctuary have not changed
substantially since the outfall began operation (Figure 7-4). While
ammonia concentrations have risen in the nearfield, there has been no
comparable annual increase in Stellwagen Bank or Cape Cod Bay despite
the elevated levels observed in October 2003. Nitrate concentrations have
remained the same in all regions, with concentrations within the sanctuary
higher than but not significantly different from levels at other monitoring
stations, as they have been in other years. 
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
Year
NH4 ( μ M) 
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
Year
NO3 ( μ M) 
SBNMS 
Nearfield 
Cape Cod 
Outfall Startup 
Figure 7-4. Annual mean ammonia and nitrate in the Stellwagen Bank National Marine
Sanctuary and other regions of Massachusetts and Cape Cod bays

2003 OUTFALL MONITORING OVERVIEW 79 
Similarly, mean annual chlorophyll has not changed in response to the
outfall discharge (Figure 7-5). Annual chlorophyll levels were similar
throughout the region. 
0
20
40
60
80
100
120
140
160
180
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
Year
Chlorophyll (mg m -2 ) 
SBNMS 
Nearfield 
Cape Cod 
Outfall Startup 
Figure 7-5. 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 2003 (Libby et al. 2004a). However, in
October, the potentially toxic species Pseudo-nitzchia pungens was
present throughout Massachusetts Bay and in the sanctuary. Pseudo-
nitzchia delicatissama was also present and in higher numbers. Presence
of these species appeared to be part of a widespread bloom, and they may
have contributed to a marine mammal die-off observed in the Gulf of
Maine and Georges Bank. Presence of these species was not, however,
attributed to the outfall. 
The MWRA monitoring program also documented a spring Phaeocystis
pouchetii bloom throughout Massachusetts and Cape Cod bays. The
bloom was most pronounced in northern Massachusetts Bay, including
stations located within the sanctuary. The 2003 bloom began in February
and lasted until May, beginning earlier and lasting longer than previous
blooms, which have typically occurred during April. MWRA data suggest
that the spring Phaeocystis pouchetii bloom is becoming a more regular
event in the bays (see Section 3, Water Column).

2003 OUTFALL MONITORING OVERVIEW 80 
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 2003
(Maciolek et al. 2004). Concentrations of Clostridium perfringens spores
remained at or below levels measured in the early 1990s. 
All four deep-water stations, both in and outside the sanctuary, continued
to support a distinct infaunal community with recognizable differences
from communities in the nearfield or Cape Cod Bay. Benthic community
parameters at individual stations showed no pattern of change following
start-up of the outfall in 2000 (Figure 7-6). Overall, the numbers of
individual organisms and species per sample have increased, paralleling
results from throughout Massachusetts Bay. No consistent pattern has
been found to relate to outfall operation.

2003 OUTFALL MONITORING OVERVIEW 81 
0
1000
2000
3000
4000
5000
6000
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003
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
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
Year
Log Series Alpha 
FF05 
FF04 
FF14 
FF11 
Outfall startup 
Figure 7-6. Benthic community parameters at stations within the boundary region, 1992-2003

2003 OUTFALL MONITORING OVERVIEW 82 
8. Monitoring Plan Revision 
Much of 2003 was devoted to revising the 1997 monitoring plan. Regular
revisions to the plan were anticipated by the original plan (MWRA 1997a
and available at www.mwra.com) and by the NPDES permit for the
outfall. Two factors suggested that a comprehensive review was
appropriate: 
ƒ The effluent being discharged into Massachusetts Bay is
cleaner than had been anticipated. The original plan had
presumed that the outfall would begin operation before secondary
treatment was implemented. In fact, within about six months of
outfall start-up, all three batteries of secondary treatment were in
operation. The original plan also assumed that concentrations of
toxic contaminants in secondary effluent would be higher than
those that actually occur. 
ƒ Only minimal environmental effects have been detected. After
more than nine years of baseline and two years of post-discharge
monitoring to compare with baseline conditions, only minimal and
expected effects had been detected. 
Therefore, it was time to refocus the program away from localized and
short-term effects to the potential for long-term effects. 
This first revision was developed through a series of OMSAP workshops
held during the spring and summer (MWRA 2003a, b, c; OMSAP 2003a,
b, c). A draft revised plan was submitted to EPA and MADEP and posted
in the Environmental Monitor in November 2003. A final version,
incorporating changes made by EPA and MADEP, was published in
March 2004 (MWRA 2004 and available at www.mwra.com). 
The revised plan continues to be directed towards answering monitoring
questions and is organized by the same environmental measurement areas:
effluent, water column, sea floor, and fish and shellfish. The plan also
continues to include special studies, which focus on emerging issues, may
use novel or non-standard methods, and are designed to be completed in a
definite timeframe.

2003 OUTFALL MONITORING OVERVIEW 83 
Effluent 
The effluent monitoring program continues to focus on NPDES permit
limits and other parameters for which there are contingency plan
thresholds (Table 8-1). 
Table 8-1. Effluent monitoring parameters 
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

2003 OUTFALL MONITORING OVERVIEW 84 
The plan also provides for several special effluent monitoring studies: 
ƒ Detailed characterization of toxic contaminants. 
ƒ Nutrients. 
ƒ Pathogens. 
ƒ Sewage tracers. 
Water Column 
Most of the monitoring questions relating to possible water-column effects
of the outfall have been answered: there are minimal, if any, acute effects
on the environment (OMSAP 2002). Continued monitoring is necessary
to evaluate possible long-term or unexpected effects. 
A review of the monitoring used a statistical model approach to describe
the trends, seasonal cycles, and redundancy in the data. It focused on
chlorophyll and bottom water dissolved oxygen and showed that both
datasets have substantial spatial and temporal redundancy. That is, for
those parameters, the data were similar for adjacent stations or adjacent
surveys (approximately three weeks apart). This finding helped to justify
a reduction in the number of sampling stations and surveys. 
The statistical modeling effort had two additional interesting results: 
(1) The apparent seasonal cycle in chlorophyll was not statistically
significant. As a result, although the statistical model of bottom water
dissolved oxygen had a sinusoidal curve (Figure 8-1, bottom), the model
for chlorophyll did not (Figure 8-1, top). This is due to the substantial
variability in phytoplankton blooms between years which had been noted
during baseline monitoring, but the extent of difference from
oceanographers’ expectations for “typical” cycles was not fully
appreciated until the long-term dataset was subjected to the rigorous
statistical analysis described above. 
(2) There was a significant jump in chlorophyll in year 2000 (Figure 8-1,
top). The modeling approach included a test for a step change in the data
on September 2000, the date of outfall diversion. Although the jump may
appear to be evidence of an outfall effect, further analysis indicated that
the change to higher chlorophyll levels began in late 1998.

2003 OUTFALL MONITORING OVERVIEW 85 
Figure 8-1. Top: Actual and modeled chlorophyll (mg/m 2 ); Bottom: actual and modeled dissolved
oxygen concentrations (mg/l)

2003 OUTFALL MONITORING OVERVIEW 86 
50
100
150
200
250
300
350
400
450
500
30 60 90 120 150 180 210 240 270 300 330 360
Day of year
Areal chlorophyll (ug/m2) 
2
4
6
8
10
12
14
30 60 90 120 150 180 210 240 270 300 330 360
Day of Year
DO (mg/L) 
Figure 8-2. Top: Survey average chlorophyll plotted by day of year; Bottom: survey average
dissolved oxygen plotted by day of year

2003 OUTFALL MONITORING OVERVIEW 87 
The monitoring plan lists several key features that MWRA will continue
to characterize through regular monitoring and special studies: 
ƒ The winter/spring bloom, including peaks in chlorophyll,
production, and phytoplankton biomass in the nearfield. 
ƒ Early spring blooms of the nuisance species Phaeocystis pouchetii 
and resulting effect on zooplankton. 
ƒ Spatial extent of chlorophyll blooms. 
ƒ Late spring occurrence of paralytic shellfish poisoning. 
ƒ Stratification, dissolved oxygen, and nutrient levels at the
beginning of the summer. 
ƒ Summertime levels of chlorophyll and nutrients in the nearfield. 
ƒ Rate of decline of dissolved oxygen concentrations over the
summer and the fall dissolved oxygen minimum. 
ƒ Summer upwelling or mixing events. 
ƒ Fall bloom peaks of chlorophyll, carbon, phytoplankton, and
production in the nearfield. 
ƒ Phytoplankton and zooplankton community structure throughout
the growing season. 
ƒ Exchange between the Gulf of Maine and Massachusetts Bay. 
Beginning in 2004, water-column monitoring will be carried out during
twelve surveys of seven nearfield stations and six surveys of 25 farfield
stations. Parameters included are listed in Tables 8-2 and 8-3. 
Table 8-2. Nearfield water column monitoring 
Parameter Measurement details 
Temperature 
Salinity 
Dissolved oxygen 
Chlorophyll fluorescence 
Transmissometry 
Irradiance 
Depth of sensors 
In-situ sensor measurements 
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

2003 OUTFALL MONITORING OVERVIEW 88 
Table 8-3. Farfield water column monitoring 
Parameter Measurement details 
Temperature 
Salinity 
Dissolved oxygen 
Chlorophyll fluorescence 
Transmissometry 
Irradiance 
Depth of sensors 
In-situ sensor measurements 
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 
Special studies will augment the regular monitoring program: 
ƒ Additional nutrient analyses to support modeling efforts. 
ƒ Additional plankton sampling and analysis to put local blooms into
a regional context. 
ƒ A study of zooplankton in Cape Cod Bay. 
ƒ Additional nutrients and plankton monitoring to examine short-
term variability. 
ƒ Ongoing study of water circulation and particle fate. 
ƒ Continuous measurement of biological parameters. 
ƒ Remote sensing. 
ƒ Modeling. 
ƒ Floatables sampling. 
ƒ Marine mammal observations.

2003 OUTFALL MONITORING OVERVIEW 89 
Sea Floor 
Contaminant concentrations in sediments and sediment traps near the
outfall have not shown rapid increases in sewage tracers since the outfall
began operation (MWRA 2003a, Bothner et al. 2002). Neither have there
been major changes in the soft-bottom infauna or the hard-bottom
communities. Accordingly, the benthic monitoring program will continue
to study soft-bottom chemistry and benthic communities, but will shift in
focus to assessment of long-term effects. 
The core of the monitoring program will be study of 23 nearfield and eight
farfield soft-bottom stations. Two nearfield stations will be sampled
annually, while the remaining stations were randomly split into two
groups, which will be sampled on alternate years. Species composition
and abundance will be measured for all stations sampled. Chemical
constituents, including PAHs, PCBs, pesticides, and metals, and other
sediment characteristics or tracers, such as TOC, sediment grain size, and 
Clostridium perfringens spore counts, will be measured annually at two
stations once every three years at other stations. Sediment-profile images
for measurement of RPD depth and other physical and biological
parameters will be made each year at all 23 nearfield stations. Extensive
sediment contaminant measurements will be made every three years. 
The regular monitoring program will be augmented by special studies: 
ƒ Hard-bottom benthos in the nearfield. 
ƒ Benthic nutrient flux. 
ƒ Sediment transport. 
Fish and Shellfish 
During the first two years after the outfall began operation, there were no
indications that contaminant concentrations increased in the representative
resource species monitored by the program, winter flounder and lobster.
There were measured increases in chlordanes and PAHs in blue mussels
placed within the outfall mixing zone, but the elevated concentrations do
not suggest an environmental risk (Hunt et al. 2002c, OMSAP 2003d).
Ulcers observed on the blind side of flounder from Deer Island and
western Massachusetts Bay are being studied. 
Chemical and histological monitoring of winter flounder and chemical
studies of lobsters and mussels will continue but at a reduced effort and
frequency, aimed at detecting long-term rather than acute effects.

2003 OUTFALL MONITORING OVERVIEW 90 
Flounder and lobster will be sampled from Deer Island Flats, the outfall
site, and eastern Cape Cod Bay. Flounder will also be taken near
Nantasket Beach. Flounder and lobster will be examined for external
lesions. Histology analyses for flounder will be made every year;
chemical analyses 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. Chemical
analyses are listed in Table 8-4. 
Table 8-4. Fish and shellfish analyses 
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 
Special studies will augment the regular monitoring: 
ƒ Enhanced mussel bioaccumulation. 
ƒ Flounder blind side lesions.

2003 OUTFALL MONITORING OVERVIEW 91 
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2003 OUTFALL MONITORING OVERVIEW 96 
List of Acronyms 
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 
DIF Deer Island Flats 
DIL Deer Island Light 
DMF Massachusetts Division of Marine Fisheries 
DO Dissolved oxygen 
ECCB Eastern Cape Cod Bay 
EPA U.S. Environmental Protection Agency 
FDA U.S. Food and Drug Administration 
GC/MS Gas chromatography/mass spectrometry 
GC/ECD Gas chromatography/electron capture detection 
GoMOOS Gulf of Maine Ocean Observation System 
HMW High molecular weight 
IAAC Inter-agency Advisory Committee 
IH Inner Harbor 
LC50 50% mortality concentration 
LMW Low molecular weight 
MADEP Massachusetts Department of Environmental Protection 
MDMF Massachusetts Division of Marine Fisheries 
MGD Million gallons per day 
MWRA Massachusetts Water Resources Authority 
NA Not analyzed 
NAO North Atlantic Oscillation 
NB Nantasket Beach 
ND Not detected 
NMFS National Marine Fisheries Service 
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 
OSM 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

2003 OUTFALL MONITORING OVERVIEW 97 
PSP Paralytic shellfish poisoning 
SBNMS Stellwagen Bank National Marine Sanctuary 
SEIS Supplemental Environmental Impact Statement 
TCR Total chlorine residual 
TOC Total organic carbon 
TSS Total suspended solids 
USGS U.S. Geological Survey

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