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2009 overview

Massachusetts Water Resources Authority · from the MWRA · 87 pages · 8.5 MB
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November 9, 2010
Ms. Ann Lowery
Acting Assistant Commissioner
Bureau of Resource Protection
Department of Environmental Protection
1 Winter Street
Boston, MA 02108
Mr. Stephen Perkins, Director
Office of Ecosystem Protection
U.S. Environmental Protection Agency
Water Technical Unit “SEW”
5 Post Office Square, Suite 100
Boston, MA 02109-3912
Re: Massachusetts Water Resources Authority, Permit Number MA0103284
Report Pursuant to Part I.8. Contingency Plan: Outfall Monitoring Overview
and Part I.20.f Notification to the Stellwagen Bank National Marine Sanctuary
Dear Ms. Lowery and Mr. Perkins:
I am pleased to enclose the report, 2009 Outfall Monitoring Overview Results , in compliance with Part
I.8.a of MWRA’s NPDES Permit which requires, “The results of any monitoring, required by the
contingency plan shall be reported to EPA, MADEP and the public on a yearly basis by November
15…”
MWRA’s ocean outfall began operation September 6, 2000. Therefore, 2009 was the ninth complete
year of ambient monitoring of the discharge. The enclosed report focuses on 2009 results in the context
of the baseline monitoring, and discusses Contingency Plan results for effluent, water column,
sediment, flounder health, and fish and shellfish chemistry. Section 6, Special Studies, describes an
upgrade to the Bays Eutrophication Model, changes in water quality in Boston Harbor, predicting the
severity of red tides, benthic nutrient flux in Boston Harbor and Massachusetts Bay, and marine
mammal observations.
Section 7 of the 2009 Outfall Monitoring Overview reports on monitoring results relative to the
Stellwagen Marine Sanctuary (“SBNMS”). This section, together with any additional data requested by
SBNMS for the year 2009, comprises the report required by the permit in Part I.20.f:
“On or before January 1 st of each year, for the life of this permit, MWRA shall
submit a report to the SBNMS that: (1) includes all monitoring and related data
from the Ambient Monitoring Plan that relates to the SBNMS, and (2)
documents the effects of the Deer Island discharge on Sanctuary resources and
qualities regarding the previous year.”
Overall, the ninth complete year of monitoring continued to show no adverse impacts from the outfall,
and no impacts on SBNMS were detected. The results are consistent with previous years. Region-wide
events such as red tides and Phaeocystis blooms as well as regional variations in water chemistry over
time have been observed; these are attributable to large-scale oceanographic and climatic factors and
not to the discharge.

The report is available online as report number 2010-19 from MWRA’s Technical Reports List at
http://www.mwra.state.ma.us/harbor/enquad/trlist.html
Please let me know if any of MWRA's staff can give you additional assistance regarding this submittal.
Sincerely,
Michael J. Hornbrook
Chief Operating Officer 
Attachment:
Werme C et al. 2010. 2009 Outfall Monitoring Overview Boston: Massachusetts Water Resources
Authority. Report 2010-19. 69p. 
Cc:
Hyannis Library 
Ann-Louise Harries 
MWRA Library 
Rebecca Kenney 
National Marine Fisheries Service 
Chris Mantzaris 
Stellwagen Bank National Marine Sanctuary 
Craig MacDonald 
Environmental Protection Agency, Region I 
Matthew Liebman 
Massachusetts Department of Environmental Protection 
Cathy Vakalopoulos

Cc: Cover letter only, please contact MWRA at (617) 788-4940 if you would like a hard copy. 
Environmental Protection Agency, Region I 
Todd J. Borci
Damien Houlihan 
Outfall Monitoring Science Advisory Panel 
Andrew Solow
Robert Beardsley 
Norb Jaworski
Robert Kenney
Scott Nixon
Judy Pederson
Michael Shiaris
James Shine
Juanita Urban-Rich 
EOEA 
Kathy Baskin 
Inter-Agency Advisory Committee 
Michael Bothner
Todd Callaghan
Tom Fredette
Ben Haskell
Jack Schwartz
Jan Smith 
Public Interest Advisory Committee 
Bruce Berman
Rich Delaney
Ed Bretschneider
Priscilla Brooks
Robert Buchsbaum
Joe Favaloro
Patty Foley
Maggie Geist
Sal Genovese
Vivien Li
Tara Nye 
Cape Cod Commission 
Tom Cambareri

2009 
Outfall Monitoring Overview 
Environmental Quality Department 
Report 2010-19 
Massachusetts Water Resources Authority

Citation: 
Werme C, Rex AC, Hall MP, Keay KE, Leo WS, Mickelson MJ, Hunt CD. 2010. 2009
outfall monitoring overview . Boston: Massachusetts Water Resources Authority. Report
2010-19. 69p.

2009
Outfall Monitoring Overview 
prepared by
Christine Werme
Independent Consultant
Berkeley, CA 94705
and
Andrea C. Rex, Maury P. Hall, Kenneth E. Keay, Wendy S.
Leo, Michael J. Mickelson
Massachusetts Water Resources Authority
Environmental Quality Department
100 First Avenue
Charlestown Navy Yard
Boston, MA 02129
and
Carlton D. Hunt
Battelle
397 Washington Street
Duxbury, MA 02332
November 5, 2010

2009 Outfall Monitoring Panel and Committees 
Outfall Monitoring Science Advisory Panel (OMSAP) 
Andrew Solow (chair), Woods Hole Oceanographic Institution 
Robert Beardsley, Woods Hole Oceanographic Institution 
Norbert Jaworski, retired (Environmental Protection Agency) 
Robert Kenney, University of Rhode Island 
Scott Nixon, University of Rhode Island 
Judy Pederson, Massachusetts Institute of Technology Sea Grant 
Michael Shiaris, University of Massachusetts, Boston 
James Shine, Harvard School of Public Health 
Juanita Urban-Rich, University of Massachusetts, Boston 
Inter-Agency Advisory Committee (IAAC) 
US Geological Survey: Michael Bothner 
Massachusetts Coastal Zone Management: Todd Callaghan, Jan Smith 
US Army Corps of Engineers: Thomas Fredette 
Stellwagen Bank National Marine Sanctuary: Ben Haskell 
US Environmental Protection Agency: Matthew Liebman 
Massachusetts Division of Marine Fisheries: Jack Schwartz 
Massachusetts Department of Environmental Protection: Catherine
Vakalopoulos 
Public Interest Advisory Committee (PIAC) 
Save the Harbor/Save the Bay: Patty Foley (chair), Bruce Berman 
MWRA Wastewater Advisory Committee: Edward Bretschneider 
Conservation Law Foundation: Priscilla Brooks 
Massachusetts Audubon Society: Robert Buchsbaum 
MWRA Advisory Board: Joseph Favaloro 
Association to Preserve Cape Cod: Maggie Geist, Tara Nye 
Safer Waters in Massachusetts: Sal Genovese 
The Boston Harbor Association: Vivian Li

2009 OUTFALL MONITORING OVERVIEW I 
Table of Contents 
Summary ............................................................................................................................ vi 
1. Introduction ..................................................................................................................... 1 
2. Effluent ........................................................................................................................... 2 
2009 Characterization ..................................................................................................... 2 
Contingency Plan Thresholds ......................................................................................... 7 
3. Water Column ................................................................................................................. 8 
Physical Conditions ...................................................................................................... 10 
Water Quality ................................................................................................................ 14 
Phytoplankton Communities......................................................................................... 18 
Zooplankton Communities ........................................................................................... 21 
Contingency Plan Thresholds ....................................................................................... 22 
4. Sea Floor ....................................................................................................................... 24 
Sediment Characteristics and Tracers ........................................................................... 27 
Sediment-Profile Imaging ............................................................................................. 29 
Soft-bottom Communities............................................................................................. 30 
Hard-bottom Communities ........................................................................................... 32 
Contingency Plan Thresholds ....................................................................................... 33 
5. Fish and Shellfish.......................................................................................................... 35 
Flounder Health ............................................................................................................ 36 
Fish and Shellfish Chemistry ........................................................................................ 39 
Contingency Plan Thresholds ....................................................................................... 42 
6. Special Studies .............................................................................................................. 43 
Boston Harbor Water Column Monitoring ................................................................... 45 
Predicting Red Tides ..................................................................................................... 46 
Marine Mammal Observations ..................................................................................... 48 
Benthic Flux .................................................................................................................. 50 
7. Stellwagen Bank N ational Marine Sanctuary ............................................................... 55 
Water Column ............................................................................................................... 55 
Sea Floor ....................................................................................................................... 60 
8. Monitoring Questions and Answers.............................................................................. 63 
References ......................................................................................................................... 67 
List of Acronyms .............................................................................................................. 69

2009 OUTFALL MONITORING OVERVIEW II
List of Figures 
Figure 2-1. MWRA primary and secondary effluent flows ................................................ 2 
Figure 2-2. Solids in MWRA treatment plant discharges ................................................... 3 
Figure 2-3. Biochemical oxygen demand in MWRA discharge ......................................... 3 
Figure 2-4. Deer Island Treatment Plant nitrogen discharges ............................................ 4 
Figure 2-5. Metals in MWRA treatment plant discharges .................................................. 5 
Figure 2-6. Mercury in Deer Island Treatment Plant discharges ........................................ 6 
Figure 3-1. MWRA Bay Water Quality Monitoring stations and regional groupings ....... 8 
Figure 3-2. MWRA plankton stations................................................................................. 9 
Figure 3-3. Flows of the Merrimack and Charles rivers reached record levels during the
summer of 2009 ................................................................................................................ 10 
Figure 3-4. Merrimack River and Charles River discharges to the ocean ........................ 11 
Figure 3-5. Monthly average wind stress at the Boston Buoy .......................................... 12 
Figure 3-6. Wind stress, water temperature, and air temperature at GoMOOS Buoy A in
March–June 2009 .............................................................................................................. 12 
Figure 3-7. Nearfield surface and bottom water temperature ........................................... 13 
Figure 3-8. Nearfield surface and bottom water salinity .................................................. 13 
Figure 3-9. Changes in seasonal ammonium concentrations from the baseline to the post-
diversion period ................................................................................................................ 14 
Figure 3-10. Annual mean ammonium concentrations. .................................................... 15 
Figure 3-11. Changes in seasonal nitrate concentrations from the baseline to the post-
diversion period ................................................................................................................ 15 
Figure 3-12. Changes in phytoplankton biomass, measured as areal chlorophyll, from the
baseline to the post-diversion period ................................................................................ 16 
Figure 3-13. Survey-mean dissolved oxygen levels and percent saturation in nearfield and
Stellwagen Basin bottom waters ....................................................................................... 17 
Figure 3-14. A simple model predicting nearfield dissolved oxygen minima from
temperature and salinity variations in the boundary areas matches observations most
years .................................................................................................................................. 17 
Figure 3-15. Nearfield abundance of total phytoplankton compared to baseline range and
mean and post-diversion mean.......................................................................................... 18 
Figure 3-16. Abundance of Phaeocystis pouchetii since 1992 ......................................... 19 
Figure 3-17. Nearfield abundance of Alexandrium fundyense since 1992 ....................... 20 
Figure 3-18. Abundance of Pseudo-nitzschia spp. since 1992 ......................................... 20 
Figure 3-19. Abundance of total zooplankton since 1992 ................................................ 21 
Figure 4-1. Locations of nearfield soft-bottom stations for chemical parameters,
sediment-profile imaging, and community parameters .................................................... 24 
Figure 4-2. Locations of farfield soft-bottom stations for chemical and community
parameters ......................................................................................................................... 25 
Figure 4-3. Locations of hard-bottom stations .................................................................. 26

2009 OUTFALL MONITORING OVERVIEW III 
Figure 4-4. Clostridium perfringens spores normalized to percent fine fraction in the
sediments compared to the late baseline range and post-diversion mean ......................... 28 
Figure 4-5. Regional trends in PCB concentrations during the baseline and post-diversion
periods ............................................................................................................................... 28 
Figure 4-6. Annual apparent color RPD for data from nearfield stations ......................... 30 
Figure 4-7. Annual community parameters in the nearfield ............................................. 31 
Figure 4-8. Screen captures of the four algal species observed during the 2009 hard-
bottom survey.................................................................................................................... 33 
Figure 5-1. Fish and shellfish monitoring sites................................................................. 35 
Figure 5-2. Annual catch per unit effort ........................................................................... 36 
Figure 5-3. Annual percent females in winter flounder samples ...................................... 37 
Figure 5-4. Annual prevalence of centrotubular hydropic vacuolation corrected for age 38 
Figure 5-5. Stained section of a winter flounder liver showing protozoan parasites in a
bile duct............................................................................................................................. 39 
Figure 5-6. Chlordane levels in flounder fillets, 1994–2009 ............................................ 40 
Figure 5-7. PCB levels in flounder livers, 1994–2009 ..................................................... 40 
Figure 5-8. High molecular weight PAH levels in mussels deployed at and near the
outfall site and at Deer Island Light .................................................................................. 41 
Figure 6-1. The BEM was initially based on a structured grid, but has been replaced by an
unstructured grid, finite volume model ............................................................................. 44 
Figure 6-2. Monthly chlorophyll concentrations since 1995, showing decreases,
particularly since the outfall relocation to Massachusetts Bay ......................................... 45 
Figure 6-3. Top: Annual abundance of Alexandrium cysts in Maine seed beds. Bottom:
Annual modeled concentrations of Alexandrium cells ..................................................... 46 
Figure 6-4. Abundance of Alexandrium cells in 2009 ...................................................... 47 
Figure 6-5. Approximate locations of whale sightings during 2009 nearfield and farfield
water quality surveys ........................................................................................................ 49 
Figure 6-6. Benthic flux stations in Massachusetts Bay and Boston Harbor.................... 50 
Figure 6-7. Sediment oxygen demand in surface sediments in 2009 ............................... 51 
Figure 6-8. Dissolved inorganic nitrogen flux in surface sediments in 2009 ................... 52 
Figure 6-9. Sediment oxygen demand in surface sediments from Boston Harbor ........... 53 
Figure 6-10. Bottom photographs showing heavy colonization of Leptocheirus pinguis in
2008 and subsequent decline in 2009 ............................................................................... 53 
Figure 6-11. Pre-diversion and post-diversion nitrogen budgets for Boston Harbor 
........................................................................................................................................... 54 
Figure 7-1. Water column stations, including those in and near the Stellwagen Bank
National Marine Sanctuary ............................................................................................... 56 
Figure 7-2. 2009 bottom water dissolved oxygen concentrations in Stellwagen Basin
compared to baseline range, baseline mean, and post-diversion mean............................. 57 
Figure 7-3. Annual mean total nitrogen at the Stellwagen Bank National Marine
Sanctuary, the outfall nearfield, and Cape Cod Bay ......................................................... 58

2009 OUTFALL MONITORING OVERVIEW IV 
Figure 7-4. Annual mean ammonium at the Stellwagen Bank National Marine Sanctuary,
the outfall nearfield, and Cape Cod Bay ........................................................................... 58 
Figure 7-5. Annual mean nitrate at the Stellwagen Bank National Marine Sanctuary, the
outfall nearfield, and Cape Cod Bay ................................................................................. 59 
Figure 7-6. Annual chlorophyll at the Stellwagen Bank National Marine Sanctuary
(SBNMS), the outfall nearfield, and Cape Cod Bay......................................................... 60 
Figure 7-7. Farfield benthic stations ................................................................................. 61 
Figure 7-8. Community parameters at stations in or near the Stellwagen Bank National
Marine Sanctuary .............................................................................................................. 62

2009 OUTFALL MONITORING OVERVIEW V 
List of Tables 
Table 1. Contingency Plan thresholds and exceedances as of 2009 ................................. vii 
Table 2-1. Projected and actual mean annual contaminant loads ....................................... 6 
Table 2-2. Contingency Plan threshold values and 2009 results for effluent monitoring .. 7 
Table 3-1. Contingency Plan threshold values and 2009 results for water-column
monitoring ......................................................................................................................... 23 
Table 4-1. Contingency Plan threshold values and 2009 results for sea-floor monitoring34 
Table 5-1. Contingency Plan threshold values and 2009 results for fish and shellfish
monitoring ......................................................................................................................... 42 
Table 8-1. Answers to the monitoring questions at the end of 2009 ................................ 64

2009 OUTFALL MONITORING OVERVIEW VI 
Summary 
Each year, the Massachusetts Water Resources Authority (MWRA) prepares this report,
an overview of environmental monitoring related to the Massachusetts Bay municipal
effluent outfall. It presents information relevant to the MWRA Contingency Plan,
including threshold exceedances, responses, and corrective actions. The overview also
includes sections on special studies and on the Stellwagen Bank National Marine
Sanctuary. Special studies in 2009 included updating the Massachusetts Bay
hydrodynamic model and ongoing studies of water quality in Boston Harbor, red tides,
marine mammals, and nutrient fluxes at the sediment-water interface. 
This year’s outfall monitoring overview marks eight years of baseline monitoring and
more than nine years since discharge was diverted from the shallower, more confined,
waters of Boston Harbor to the deeper waters of Massachusetts Bay. Results continue to
confirm the predictions that the outfall would have only limited and localized effects on
the Massachusetts Bay ecosystem, while greatly benefiting Boston Harbor. 
Throughout 2009, monitoring results were consistent with previous years, with no
unanticipated effects associated with the outfall. There were no exceedances of
Contingency Plan thresholds for effluent, sea floor, or fish and shellfish. There was one
exceedance of a water-column threshold, when concentrations of the red tide
phytoplankton species Alexandrium fundyense exceeded the caution level (Table 1). The
2009 Alexandrium bloom followed the historically typical pattern for red tides in the
region, beginning off the coast of Maine and moving southward along the coast with
winds from the northeast. The pattern suggests no effect of the outfall on the timing or
magnitude of the bloom. Occurrence of Alexandrium blooms since 2005 suggests that
the region has entered a period of regular blooms, similar to conditions during the 1970s.
As in other years, no effects of the outfall on the Stellwagen Bank National Marine
Sanctuary were detected. No effects on the water column or sea floor in or near the
sanctuary had been anticipated, and none have been measured.

2009 OUTFALL MONITORING OVERVIEW VII 
Table 1. Contingency Plan thresholds and exceedances as of 2009 . (NA = not applicable,  = no
exceedance, C = caution level exceedance, W = warning level exceedance) 
Effluent 
Location/ 
Parameter
Type 
Parameter 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 
pH W          
Fecal coliform
bacteria,
monthly 
          
Fecal coliform
bacteria,
weekly 
          
Fecal coliform
bacteria, daily  W   W      
Fecal coliform
bacteria, 
3 consecutive
days 
          
Chlorine
residual, daily W          
Chlorine
residual,
monthly 
          
Total
suspended
solids, weekly 
  W        
Total
suspended
solids, 
Monthly 
  W        
cBOD, weekly           
cBOD, monthly           
Acute toxicity,
mysid shrimp           
Acute toxicity,
fish           
Chronic
toxicity, fish  W     W    
Chronic
toxicity, sea
urchin 
 W    W     
PCBs           
Plant
performance           
Flow NA          
Total nitrogen
load NA          
Floatables NA NA NA NA NA NA NA NA NA NA 
Oil and grease          

2009 OUTFALL MONITORING OVERVIEW VIII 
Table 1, continued. Contingency Plan thresholds and exceedances as of 2009. (NA = not applicable,  
= no exceedance, C = caution level exceedance, W = warning level exceedance) 
Water Column 
Location/ 
Parameter
Type 
Parameter 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 
Nearfield 
bottom water 
Dissolved
oxygen
concentration 
C          
Dissolved
oxygen
saturation 
C          
Stellwagen
Basin 
bottom water 
Dissolved
oxygen
concentration 
          
Dissolved
oxygen
saturation 
          
Nearfield 
bottom water 
Dissolved
oxygen
depletion rate
(June – 
October) 
NA          
Nearfield
chlorophyll 
Annual NA          
Winter/spring NA          
Summer NA      C    
Autumn C          
Nearfield
nuisance algae 
Phaeocystis
pouchetii 
Winter/spring NA    C   C   
Summer NA  C C C C C    
Autumn           
Nearfield
nuisance algae 
Pseudonitzschia 
Winter/spring NA          
Summer NA          
Autumn           
Nearfield
nuisance algae 
Alexandrium 
Any sample      C C  C C 
Farfield shellfish PSP toxin
extent           
Plume Initial dilution NA  Complete

2009 OUTFALL MONITORING OVERVIEW IX 
Table 1, continued. Contingency Plan thresholds and exceedances as of 2009. (NA = not applicable,  = no
exceedance, C = caution level exceedance, W = warning level exceedance) 
Sea Floor 
Location/ 
Parameter
Type 
Parameter 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 
Nearfield
sediment 
contaminants 
Acenaphthene NA   NA NA  NA NA  NA 
Acenaphylene NA   NA NA  NA NA  NA 
Anthracene NA   NA NA  NA NA  NA 
Benzo(a)anthracene NA   NA NA  NA NA  NA 
Benzo(a)pyrene NA   NA NA  NA NA  NA 
Cadmium NA   NA NA  NA NA  NA 
Chromium NA   NA NA  NA NA  NA 
Chrysene NA   NA NA  NA NA  NA 
Copper NA   NA NA  NA NA  NA 
Dibenzo(a,h)anthracene NA   NA NA  NA NA  NA 
Fluoranthene NA   NA NA  NA NA  NA 
Fluorene NA   NA NA  NA NA  NA 
Lead NA   NA NA  NA NA  NA 
Mercury NA   NA NA  NA NA  NA 
Naphthalene NA   NA NA  NA NA  NA 
Nickel NA   NA NA  NA NA  NA 
p,p’-DDE NA   NA NA  NA NA  NA 
Phenanthrene NA   NA NA  NA NA  NA 
Pyrene NA   NA NA  NA NA  NA 
Silver NA   NA NA  NA NA  NA 
Total DDTs NA   NA NA  NA NA  NA 
Total HMW PAH NA   NA NA  NA NA  NA 
Total LMW PAH NA   NA NA  NA NA  NA 
Total PAHs NA   NA NA  NA NA  NA 
Total PCBs NA   NA NA  NA NA  NA 
Zinc NA   NA NA  NA NA  NA 
Nearfield
sediment RPD depth NA          
Nearfield
benthic
diversity 
Species per sample NA          
Fisher’s log-series
alpha NA          
Shannon diversity NA          
Pielou’s evenness NA          
Nearfield
species
composition 
Percent opportunists NA         

2009 OUTFALL MONITORING OVERVIEW X 
Table 1, continued. Contingency Plan thresholds and exceedances as of 2009. (NA = not applicable,  
= no exceedance, C = caution level exceedance, W = warning level exceedance) 
Fish and Shellfish 
Location/ 
Parameter
Type 
Parameter 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 
Nearfield
flounder tissue 
Total PCBs NA    NA NA  NA NA  
Mercury NA     NA  NA NA  
Chlordane NA    NA NA  NA NA  
Dieldrin NA    NA NA  NA NA  
Total DDTs NA    NA NA  NA NA  
Nearfield
flounder 
Liver disease
(CHV) NA          
Nearfield
lobster tissue 
Total PCBs NA    NA NA  NA NA  
Mercury NA    NA NA  NA NA  
Chlordane NA    NA NA  NA NA  
Dieldrin NA    NA NA  NA NA  
Total DDTs NA    NA NA  NA NA  
Nearfield
mussel tissue 
Total PCBs NA    NA NA  NA NA  
Lead NA    NA NA  NA NA  
Mercury NA    NA NA  NA NA  
Chlordane NA C C  NA NA  NA NA  
Dieldrin NA    NA NA  NA NA  
Total DDTs NA    NA NA  NA NA  
Total PAHs NA C C C NA NA  NA NA 

2009 OUTFALL MONITORING OVERVIEW 1 
1. Introduction 
For more than two decades, the Massachusetts Water Resources Authority
(MWRA) has worked to minimize the effects of wastewater discharge on
the marine environment. One important part of that mission has been a
diversion of the municipal wastewater discharge from Boston Harbor to
the deeper, less confined waters of Massachusetts Bay. A monitoring
program assesses compliance with the National Pollutant Discharge
Elimination System (NPDES) permit to discharge effluent from the Deer
Island Treatment Plant (DITP) into Massachusetts Bay, assures that there
are no unanticipated environmental effects of the discharge, and provides
information for management of the outfall. 
Results from most of the baseline-monitoring years and each post-
diversion year have been documented in annual reports such as this one,
the Outfall Monitoring Overview . Background information for these
overviews and a complete description of the monitoring program can be
found in Werme and Hunt (2008). That document, the monitoring plans
(MWRA 1991, 1997a, 2004), the Contingency Plan (MWRA 1997b,
2001), area-specific technical reports, and past outfall monitoring
overviews are available on the technical report list at MWRA’s website, 
www.mwra.com/harbor/enquad/trlist.html . 
Overviews for 1994 through 1999 included only baseline information.
After the Massachusetts Bay outfall became operational in September
2000, reports have included post-diversion data relevant to the outfall
permit, including Contingency Plan threshold exceedances, responses, and
corrective actions. This year’s overview presents monitoring results for
effluent, water column, sea floor, and fish and shellfish. It also includes
sections on special studies and the Stellwagen Bank National Marine
Sanctuary. 
Eight years of baseline monitoring and nine years of post-diversion
monitoring have confirmed the predictions that the outfall would have
only limited and localized effects on the Massachusetts Bay ecosystem,
while the benefits to Boston Harbor have been dramatic.

2009 OUTFALL MONITORING OVERVIEW 2 
2. Effluent 
2009 Characterization 
Throughout 2009, DITP continued to operate as designed, and
contaminant loads remained low. It was a relatively wet year in the
Boston area, although there was less rainfall than in 2008, and flows from
the treatment plant were correspondingly lower. Almost all the flow
received both primary and secondary treatment (Figure 2-1). 
Figure 2-1. MWRA primary and secondary effluent flows. Almost all the flow from the
treatment plant received primary and secondary treatment. (Primary-only flows are blended with
secondary flows, and the blended flows meet permit limits.) 
Contaminant loads in the effluent remained low. Solids discharges
reached a record low (Figure 2-2). Biochemical oxygen demand (BOD),
regulated as carbonaceous BOD, decreased slightly in 2009 in comparison
to 2008 (Figure 2-3), remaining well below levels that might be expected
to affect ambient waters at the discharge site. 
MWRA Primary and Secondary Flows 1990-2009
0
50
100
150
200
250
300
350
400
450
90 91 92 93 94 95 96 97 98 99 00 01 02 03 04 05 06 07 08 09
million gallons per day
Primary and Secondary Treated Flows
Primary-only (Blended) Treated Flows

2009 OUTFALL MONITORING OVERVIEW 3 
Figure 2-2. Solids in MWRA treatment plant discharges . Solids discharges reached a record
low in 2009. 
Figure 2-3. Biochemical oxygen demand in MWRA discharge. MWRA’s permit limits
carbonaceous BOD, which remained low in 2009. Nitrogenous BOD is the result of
microbiological breakdown that occurs as a result of secondary treatment. 
0
20
40
60
80
100
120
140
160
180
90 91 92 93 94 95 96 97 98 99 00 01 02 03 04 05 06 07 08 09
Tons per day
Solids in MWRA Treatment Plant Discharges 1990-2009
Sludge
Nut Island
Deer Island
Year 
0
10
20
30
40
1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009
Tons per day
Year
Biochemical Oxygen Demand in MWRA Discharge
1999-2009
Carbonaceous BOD Nitrogenous BOD

2009 OUTFALL MONITORING OVERVIEW 4 
Nitrogenous BOD (also shown in Figure 2-3), which is a result of the
biological processes in secondary treatment and not a permit limit or
Contingency Plan parameter, remained higher than historic levels, as it has
since the full implementation of secondary treatment. This increase has
not proved deleterious to the dissolved oxygen levels in the environment
(see Section 3, Water Column). 
Total nitrogen loads were slightly higher in 2009 than in 2008, and the
proportion of the load made up of ammonium increased, as it has each
year since 2005 (Figure 2-4). About 10% of the ammonium in the sewage
influent is removed by secondary treatment, but the biological treatment
process converts some nitrate, nitrite, and other forms of nitrogen to
ammonium. MWRA continually evaluates nitrogen-removal technologies,
so that nitrogen removal could be implemented at DITP if the need arose
(Bigornia-Vitale 2010). However, nitrogen loads have remained below
the Contingency Plan threshold, and nitrogen removal has not been
implemented. 
Figure 2-4. Deer Island Treatment Plant nitrogen discharges. Discharges of ammonium
remained relatively high, a result of the secondary treatment process. (TKN = total Kjeldahl
nitrogen, a measure of total nitrogen in the effluent) 
0
2,000
4,000
6,000
8,000
10,000
12,000
14,000
1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009
Metric Tons per Year
*Method change for TKN April 2003
Deer Island Treatment Plant Nitrogen Discharges 1996-2009
Caution Level Other Nitrogen Species* Nitrite/Nitrate Ammonium

2009 OUTFALL MONITORING OVERVIEW 5 
Among the metals, only copper and zinc remain in notable, though
reduced, quantities, with other metals present in only trace amounts
(Figure 2-5). In fact, except for copper, the metals meet receiving water
quality criteria in the effluent. Mercury levels were especially low in 2009
(Figure 2-6). Extremely sensitive methods are used in mercury analysis
but mercury is now only rarely detected in effluent samples, the
consequence of efforts on the part of MWRA and the New England states
to reduce mercury use, handle workplace spills, and discourage disposal
practices that introduce mercury into the sewer system. 
Figure 2-5. Metals in MWRA treatment plant discharges . Total metals discharges remained
low in 2009. 
0
100
200
300
400
500
600
700
91 92 93 94 95 96 97 98 99 00 01 02 03 04 05 06 07 08 09
Average pounds per day discharged
Year
Metals in MWRA Treatment Plant Discharges 199 1 -2009
Silver
Nickel
Chromium
Lead
Copper
Zinc

2009 OUTFALL MONITORING OVERVIEW 6 
Figure 2-6. Mercury in Deer Island Treatment Plant discharges. 
Loads of organic contaminants also continued to be low in 2009. Metals
and organic contaminant data from August 2005 through December 2009
(Delaney 2010) show that the contaminant levels in DITP effluent are
substantially lower than had been predicted in the U.S. Environmental
Protection Agency (EPA) Supplemental Environmental Impact Statement
(SEIS, EPA 1988), which was prepared during planning and permitting of
the Massachusetts Bay outfall (Table 2-1). For example, annual loadings
of polychlorinated biphenyls (PCBs) were only 0.53 kg/year, compared to
the SEIS estimate of 50 kg/year. In 2009, PCBs were never detected in
DITP effluent as Aroclor mixtures, the only PCB measures limited in the
NPDES permit. 
Table 2-1. Projected and actual mean annual contaminant loads. 
Parameter Projected Load 
kg/year 
Actual Load 
kg/year 
Cadmium 697 29 
Chromium 3,517 481 
Copper 11,945 3,253 
Lead 4,961 674 
Mercury 216 5.1 
Nickel 8,926 1,150 
Silver 299 67 
Total PCB 50 0.52 
4-4’ DDT 28 0.31 
0.00
0.02
0.04
0.06
0.08
0.10
0.12
0.14
0.16
99 00 01 02 03 04 05 06 07 08 09
Average pounds
discharged per day
Year
Mercury in DITP Discharges 1999-2009

2009 OUTFALL MONITORING OVERVIEW 7 
Contingency Plan Thresholds 
As in 2007 and 2008, DITP had no permit violations and no exceedances
of the Contingency Plan thresholds in 2009 (Table 2-2). Of thousands of
measurements, there have been only eleven effluent Contingency Plan
exceedances since the permit went into effect and no exceedances of
overall plant performance, total nitrogen load, or oil and grease.
Floatables, for which there are no caution or warning levels, are present at
extremely low levels, measured in parts per billion. 
Table 2-2. Contingency Plan threshold values and 2009 results for effluent monitoring.
( cBOD=carbonaceous biological oxygen demand, NOEC=no observable effect concentration, LC50=50%
mortality concentration, MGD=million gallons per day; NA=not applicable) 
Parameter Caution Level Warning Level 2009 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 μg/L daily, 
456 μg/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 MGD for annual
average of dry days Not exceeded 
Total nitrogen load 12,500 mtons/year 14,000 mtons/year Not exceeded 
Floatables NA 
Oil and grease None 15 mg/L weekly Not exceeded

2009 OUTFALL MONITORING OVERVIEW 8
3. Water Column 
The monitoring program measures water quality and studies
phytoplankton and zooplankton at stations in Boston Harbor,
Massachusetts Bay, and Cape Cod Bay (Figures 3-1, 3-2). 
 
 







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





 

















 
F33
F32
F19
F18
F17
F16
F15
F14
F12
F10
F07
F05
N20
N10
N07
N01
F29
F28
F03
F23
F22
F13
F06
N18
N16
N04
F31
F30
F27
F26
F25
F24
F02
F01 
70°15'W
70°15'W
70°30'W
70°30'W
70°45'W
70°45'W
71°0'W
71°0'W
42°30'N
42°30'N
42°15'N
42°15'N
42°0'N
42°0'N
41°45'N
41°45'N 
 
 














 

















 
F33
F32
F19
F18
F17
F16
F15
F14
F12
F10
F07
F05
N20
N10
N07
N01
F29
F28
F03
F23
F22
F13
F06
N18
N16
N04
F31
F30
F27
F26
F25
F24
F02
F01 
70°15'W
70°15'W
70°30'W
70°30'W
70°45'W
70°45'W
71°0'W
71°0'W
42°30'N
42°30'N
42°15'N
42°15'N
42°0'N
42°0'N
41°45'N
41°45'N 
Cape Cod Bay
Boston
Harbor Massachusetts Bay 
0 10 20 30 40 50 5
Kilometers 
boundary region
northern
boundary
region
offshore
region
coastal region
nearfield region 
 MWRA stations (BWQM) 
  GoMOOS Buoy A 
  NOAA Buoy 44013
MWRA outfall diffuser
Regions
Stellwagen Bank Sanctuary
High : 0
Low : -125 
Figure 3-1. MWRA Bay Water Quality Monitoring (BWQM) stations and regional groupings. 
“Farfield” stations include all stations in Boston Harbor; the coastal, offshore, and northern boundary
regions; and Cape Cod Bay. Also shown are the MWRA outfall; two instrumented buoys, one operated by
the Gulf of Maine Ocean Observing System (GoMOOS) and the other by the National Oceanic and
Atmospheric Administration (NOAA) National Data Buoy Center (NDBC); and the Stellwagen Bank
National Marine Sanctuary.

2009 OUTFALL MONITORING OVERVIEW 9 
The Massachusetts Bay stations located within seven kilometers of the
outfall diffusers are called nearfield stations. Those beyond are grouped
into regions, which together are called farfield stations. Twelve surveys of
seven nearfield stations and six surveys of 27 farfield stations were
completed in 2009. Sampling was augmented by instrumented buoys and
remote sensing. A separate Boston Harbor program contributed additional
data. 
 
 


 
 
 
 
 
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 
 
 
 
 
 
 
 
  
F33
F32
F23
F22
F13
F06
N18
N16
N04
F31
F30
F27
F26
F25
F24
F02
F01 
70°15'W
70°15'W
70°30'W
70°30'W
70°45'W
70°45'W
71°0'W
71°0'W
42°30'N
42°3 0'N
42°1 5'N
42°15'N
42°0'N
42°0 'N
41°45'N
41°4 5'N 
 
 


 
 
 
 
 
 
 
 
 
 
 
 
 
 
  
F33
F32
F23
F22
F13
F06
N18
N16
N04
F31
F30
F27
F26
F25
F24
F02
F01 
70°15'W
70°15'W
70°30'W
70°30'W
70°45'W
70°45'W
71°0'W
71°0'W
42°30'N
42°3 0'N
42°1 5'N
42°15'N
42°0'N
42°0 'N
41°45'N
41°4 5'N 
Cape Cod Bay
Boston
Harbor Massachusetts Bay 
0 10 20 30 40 50 5
Kilometers 
northern
boundary
region
offshore
region
coastal region
nearfield region 
  Phytoplankton and zooplankton station 
 Zooplankton-only station 
  GoMOOS Buoy A 
  NOAA Buoy 44013
MWRA outfall diffuser
Regions
High : 0
Low : -125 
Figure 3-2. MWRA plankton stations. The stations are a subset of those included in water quality
monitoring. Regional groupings, the instrumented buoys, and the MWRA outfall are also shown.

2009 OUTFALL MONITORING OVERVIEW 10 
Physical Conditions 
Baseline and post-diversion monitoring have found that the water column
in the vicinity of the outfall and throughout Massachusetts and Cape Cod
bays is heavily influenced by river inflows, weather, and other physical
factors. Information about physical conditions has proven to be key to
interpreting the annual monitoring data. 
Although the annual precipitation in the Boston area was lower in 2009
than in 2008, relatively wet conditions continued, particularly during the
summer and fall (Libby et al. 2010). The wet summer resulted in record
summer maximum flows from the Merrimack and Charles rivers (Figures
3-3 and 3-4). (Flow from the Merrimack River tends to reflect regional
conditions and affects the salinity of bottom waters. Flow from the
Charles River reflects local conditions and may influence surface salinity.) 
Figure 3-3. Flows of the Merrimack (top) and Charles (bottom) rivers reached record levels during
the summer of 2009 . Flows from the Charles River were also high during the stormy fall. The average
July–September flows in both rivers were the greatest measured by the monitoring program, translating to
the 98 th percentile, record highs. Flows during 2008, shown for contrast, reached record highs during
January–March. 
28 th
58 th
percentile
98 th 58 th
28 th 58 th
percentile 98 th
83 rd
record-max*
record-max*

2009 OUTFALL MONITORING OVERVIEW 11 
Figure 3-4. Merrimack River (top) and Charles River (bottom) discharges to the ocean. Note
the lack of a spring freshet (a rise in water flow due to snow melt) during 2009. (Data are from
gauges at Lowell and Waltham, Massachusetts; smooth lines are 3-month moving averages; note
the differences in scale for the rivers.) 
The wind-forcing conditions in 2009 also reflected the rainy summer, with
downwelling conditions, which are marked by winds pushing water
toward the coast, dominating in June (Figure 3-5). In most years, spring is
a transitional period between winter downwelling and spring upwelling
conditions. In 2009, upwelling occurred during May and July, but, but
over the course of the year, downwelling conditions predominated, as they
have in recent years. Wave heights were also greatest in June, with late
June average wave heights reaching levels that might be expected to
resuspend sediments in Boston Harbor. An early May storm from the
northeast was not large but may have been sufficient to bring the 
Alexandrium fundyense red tide phytoplankton species into the bay
(Figure 3-6).

2009 OUTFALL MONITORING OVERVIEW 12 
Figure 3-5. Monthly average wind stress at the Boston Buoy. Positive values indicate winds
from the south or southwest, which result in upwelling-favorable wind stress; negative values
indicate winds from the north or northeast, which favor downwelling. Downwelling conditions in
June 2009 were consistent with poor weather conditions. Data from 2007 and 2008 are shown for
comparison. 
Figure 3-6. Wind stress, water temperature, and air temperature at GoMOOS Buoy A in
March–June 2009. The wind stress figure shows a weak storm with winds from the northeast in
early May (circled), which may have been sufficient to bring Alexandrium fundyense into
Massachusetts Bay. The vertical dashed lines indicate the timing of water column surveys.

2009 OUTFALL MONITORING OVERVIEW 13 
Surface water temperatures were warmer than average, particularly during
the summer, in response to the downwelling conditions, which prevented
cooler waters from being brought to the surface (Figure 3-7). Similar to
2008, bottom waters were cooler than average during the spring but were
relatively warm during the fall. 
Figure 3-7. Nearfield surface and bottom water temperature. Surface measurements are the
upper line. Summer surface temperatures were warm, a result of the downwelling conditions. 
Salinity was affected by the continued wet conditions compared to other
summers (Figure 3-8). Surface salinity was particularly low during the
rainy summer but did not reach the extreme late summer to fall lows of
2005–2008. 
Figure 3-8. Nearfield surface and bottom water salinity. Surface measurements are the lower
line. Surface salinity has been low in 2005–2009, reflecting a period of wet years.

2009 OUTFALL MONITORING OVERVIEW 14 
Water Quality 
Water quality measurements for 2009, including measurements of
nutrients, dissolved oxygen, and phytoplankton biomass (measured as
chlorophyll), followed typical annual cycles and continued to confirm
predictions that there would be detectable local effects of the discharge for
certain parameters and no detectable adverse effects for other parameters
or for any measurements outside the immediate vicinity of the discharge
(Libby et al. 2010). Similar measurements in Boston Harbor continued to
show improvements. 
Ammonium is the major component of total inorganic nitrogen in the
effluent, and a variety of dilution models had suggested that, following the
diversion, increased concentrations of ammonium would be detectable in
the nearfield. As anticipated, there have been increases in ammonium at
the stations closest to the discharge compared to baseline conditions and
relative to regional background conditions (Figure 3-9). At the same time,
much greater decreases in ammonium concentrations have been measured
in Boston Harbor and in the coastal area. 
Figure 3-9. Changes in seasonal ammonium concentrations (μM) from the baseline to the post-
diversion period. There have been localized increases in ammonium concentrations near the outfall with
concurrent decreases in ammonium concentrations in Boston Harbor. 
The increased ammonium concentrations in the nearfield have become
less apparent in 2005–2009 (Figure 3-10). Ammonium concentrations
have also decreased in the coastal and northern boundary regions,
suggesting that the change is region-wide and not related to the outfall. 
-5 -3 -1 -0.5 0 0.5 1 3 
∆ μ M NH4

2009 OUTFALL MONITORING OVERVIEW 15 
Figure 3-10. Annual mean ammonium concentrations ( μ M). Data represent all depths and all
stations sampled within each region. Vertical line shows the diversion of the discharge from
Boston Harbor to Massachusetts Bay. Error bars represent ±1 standard deviation.
Increases in winter/spring and fall nitrate levels have occurred since the
outfall diversion (Figure 3-11). These changes are also region-wide, with
no indication of an effect of the outfall. In Boston Harbor, levels have
declined in response to the outfall diversion (Tian et al. 2009). 
Figure 3-11. Changes in seasonal nitrate concentrations (μM) from the baseline to the post-
diversion period. Changes across Massachusetts Bay have not been attributed to the outfall. 
0
4
8
12
16
NH4 ( μ M)
Boston Harbor Coastal Nearfield N. Boundary Cape Cod Bay 
Δ μ M NO3 
- 7 1 - 7 0 . 9 - 7 0 . 8 - 7 0 . 7 - 7 0 . 6 -7 0 . 5 - 7 0. 4 - 7 0. 3 -7 0. 2
4 1 . 9
4 2
4 2 . 1
4 2 . 2
4 2 . 3
4 2 . 4
4 2 . 5
4 2 . 6
- 7 1 - 7 0 . 9 - 7 0 . 8 - 7 0 . 7 - 7 0 . 6 -7 0. 5 - 7 0. 4 - 7 0. 3 -7 0. 2
4 1 . 9
4 2
4 2 . 1
4 2 . 2
4 2 . 3
4 2 . 4
4 2 . 5
4 2 . 6
- 7 1 - 7 0 . 9 - 7 0. 8 - 70 . 7 - 7 0 . 6 - 7 0 . 5 - 7 0 . 4 - 7 0 . 3 - 7 0 . 2
4 1 . 9
4 2
4 2 . 1
4 2 . 2
4 2 . 3
4 2 . 4
4 2 . 5
4 2 . 6
- 7 1 - 7 0 . 9 - 7 0. 8 - 70 . 7 - 7 0 . 6 - 7 0 . 5 - 7 0 . 4 - 7 0 . 3 - 7 0 . 2
4 1 . 9
4 2
4 2 . 1
4 2 . 2
4 2 . 3
4 2 . 4
4 2 . 5
4 2 . 6
-7 1 - 7 0 . 9 -7 0 . 8 - 7 0 . 7 - 7 0 . 6 -7 0 . 5 - 7 0 . 4 - 7 0. 3 - 70 . 2
4 1 . 9
4 2
4 2 . 1
4 2 . 2
4 2 . 3
4 2 . 4
4 2 . 5
4 2 . 6
-7 1 - 7 0 . 9 -7 0 . 8 - 7 0 . 7 - 7 0 . 6 -7 0 . 5 - 7 0. 4 - 7 0. 3 - 70 . 2
41 . 9
4 2
42 . 1
42 . 2
42 . 3
42 . 4
42 . 5
42 . 6
-1 -0.5 0 0.5 1 
Winter/Spring Summer Fall

2009 OUTFALL MONITORING OVERVIEW 16 
Similarly, there have been region-wide changes in chlorophyll (Figure 3-
12) and particulate organic carbon (not shown). Phaeocystis blooms have
caused winter/spring concentrations of chlorophyll to increase throughout
Massachusetts Bay, while summer concentrations of chlorophyll have
remained close to what they were during the baseline period. Fall
concentrations have declined, particularly at the offshore and northern
boundary stations. These changes have occurred across broad regional
areas. Changes due to the outfall relocation are local and not adverse. 
Figure 3-12. Changes in phytoplankton biomass, measured as areal chlorophyll, from the
baseline to the post-diversion period. The changes reflect an increase in the Phaeocystis blooms
in the spring and relative lack of fall blooms. These changes have occurred across the broad region
and are not attributed to the relocated discharge.
The possibility that the outfall would cause lower dissolved oxygen levels
in bottom waters was one important public concern prior to the diversion.
However, measurements of concentrations and percent saturation of
dissolved oxygen in bottom waters have shown no response to the outfall
(Figure 3-13). There has been no change in levels or the seasonal pattern
in any year. Summer and fall bottom water dissolved oxygen levels were
somewhat lower in 2009 than in 2008, a result of a lack of the
downwelling conditions in 2009. 
-71 -70.9 -70.8 -70.7 -70.6 -70.5 -70.4 -70.3 -70.2
41.9
42
42.1
42.2
42.3
42.4
42.5
42.6
-71 -70.9 -70.8 -70.7 -70.6 -70.5 -70.4 -70.3 -70.2
41.9
42
42.1
42.2
42.3
42.4
42.5
42.6
-71 -70.9 -70.8 -70.7 -70.6 -70.5 -70.4 -70.3 -70.2
41.9
42
42.1
42.2
42.3
42.4
42.5
42.6
-71 -70.9 -70.8 -70.7 -70.6 -70.5 -70.4 -70.3 -70.2
41.9
42
42.1
42.2
42.3
42.4
42.5
42.6
-71 -70.9 -70.8 -70.7 -70.6 -70.5 -70.4 -70.3 -70.2
41.9
42
42.1
42.2
42.3
42.4
42.5
42.6
-71 -70.9 -70.8 -70.7 -70.6 -70.5 -70.4 -70.3 -70.2
41.9
42
42.1
42.2
42.3
42.4
42.5
42.6 
Winter/Spring Summer Fall
-50 -30 -10 10 30 50

2009 OUTFALL MONITORING OVERVIEW 17 
Figure 3-13. Survey-mean dissolved oxygen levels (top graphs) and percent saturation (bottom
graphs) in nearfield and Stellwagen Basin bottom waters. There has been no change between the
baseline period and the post-diversion years. Data for Stellwagen Basin collected from stations F12, F17,
F19, and F22. Error bars represent ± one standard error. 
The data from the baseline and post-diversion years have shown that
temperature and salinity, rather than effluent inputs, control bottom water
dissolved oxygen in the nearfield (Figure 3-14). The observed minimum
dissolved oxygen levels in 2009 matched those that were predicted solely
from temperature and salinity data. 
Figure 3-14. A simple model predicting nearfield dissolved oxygen (DO) minima from temperature
and salinity variations in the boundary areas matches observations most years. 
Baseline Mean Post-Diversion Mean 2009 Mean
6
7
8
9
10
11
12
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
DO (mg L -1 )
Nearfield
70
80
90
100
110
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
DO (% saturation) Nearfield
70
80
90
100
110
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
DO (% saturation) Stellwagen Basin
6
7
8
9
10
11
12
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
DO (mg L -1 )
Stellwagen Basin

2009 OUTFALL MONITORING OVERVIEW 18 
Phytoplankton Communities 
Nearfield abundance of total phytoplankton was within the baseline range
throughout 2009 (Figure 3-15), but the regional changes in phytoplankton
biomass, measured as chlorophyll concentrations (see Figure 3-13, above)
reflect some of the long-term patterns in the phytoplankton populations
(Libby et al. 2010). For example, there has been a general decrease in the
abundance of diatoms. Except in September, diatoms were rare in the
nearfield and throughout the wider region. 
Figure 3-15. Nearfield abundance of total phytoplankton compared to baseline
range and mean and post-diversion mean. 
The general region-wide increase in phytoplankton biomass during the
winter/spring can be attributed to annual blooms of the colonial species 
Phaeocystis pouchetii , which have occurred each year since 2000 (Figure
3-16). Phaeocystis is not toxic but is considered a nuisance species,
because at high densities it forms gelatinous aggregates that may provide
insufficient nutrition for zooplankton egg production (Turner et al. 2002).
The timing and geographical extents of the blooms have not suggested any
effect of the outfall. Rather, it appears that physical processes, such as
water temperature, are the most important factors affecting the timing and
duration of Phaeocystis blooms. 
0
2
4
6
8
10
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
10 6 cells L -1 
Baseline Range
Baseline Mean
2009
Post Mean

2009 OUTFALL MONITORING OVERVIEW 19 
Figure 3-16. Abundance of Phaeocystis pouchetii since 1992. 
Another general change has been an increase in the frequency of 
Alexandrium fundyense red tide blooms (Figure 3-17), which produce a
toxin that causes paralytic shellfish poisoning (PSP). The 2009 
Alexandrium bloom occurred in April and May, with a maximum
abundance of 150 cells per liter at Station N18, located to the south of the
outfall, during the May survey. This abundance triggered a series of
rapid-response surveys, which showed that the bloom had ended by early
June. A small number of cells were detected in November. Frequency of
red tides with PSP toxicity has increased throughout the Gulf of Maine
since 2006, suggesting that the broad region is entering a period of
frequent toxic blooms, similar to conditions during 1970s. More
information about red tides and efforts to predict them is presented in
Section 6, Special Studies. 
A third nuisance species group Pseudo-nitzschia has been rare during the
post-diversion years (Figure 3-18). The 2009 peak of 12,000 cells/L
occurred at the boundary stations in October. 
0
3
6
9
12
10 6 Cells L -1
Boston Harbor Coastal Nearfield Offshore N. Boundary Cape Cod 
Phaeocystis pouchetti

2009 OUTFALL MONITORING OVERVIEW 20 
Figure 3-17. Nearfield abundance of Alexandrium fundyense since 1992. 
Figure 3-18. Abundance of Pseudo-nitzschia spp. since 1992. 
1
10
100
1,000
10,000
100,000
92 93 94 95 96 97 98 99 00 01 02 03 04 05 06 07 08 09
Abundance (cells L-1) 
0.00
0.05
0.10
0.15
0.20
0.25
0.30
10 6 Cells L -1
Boston Harbor Coastal Nearfield Offshore N. Boundary Cape Cod

2009 OUTFALL MONITORING OVERVIEW 21 
Zooplankton Communities 
The total abundance of zooplankton in the nearfield and other regions in
2009 was similar to that of many earlier years (Figure 3-19). As is typical,
abundance was relatively low during the winter and peaked in the summer.
The dominant species group continued to be copepods, and the dominant
copepod continued to be the small species Oithona similis . A trend in 
Oithona similis abundance continued upward after a decline in 2004–
2005. Abundance of the large copepod Calanus finmarchicus was also
high, with the second highest nearfield abundance of the monitoring
program, 14,000 animals per cubic meter, measured in samples from the
May 2009 survey. Other taxa, including barnacle nauplii, bivalve and
gastropod veligers, and polychaete larvae occurred sporadically. The
fluctuations in zooplankton occurrence and abundance appear to be related
to large-scale climatic conditions. 
Figure 3-19. Abundance of total zooplankton since 1992. 
0
50
100
150
200
250
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009
Animals (thousands m -3 )
Boston Harbor
Coastal
Nearfield
Offshore
N. Boundary
Cape Cod

2009 OUTFALL MONITORING OVERVIEW 22 
Contingency Plan Thresholds 
Water quality parameters were within normal ranges throughout 2009. 
There was one exceedance of a nuisance algae threshold, the caution
threshold for Alexandrium fundyense (Table 3-1). This exceedance had
been anticipated, based on information on overwintering Alexandrium 
cysts in the sediments off the coast of Maine (see Section 6, Special
Studies) and spring measurements of Alexandrium cells in coastal waters
of Maine and New Hampshire. As in other years when that level has been
exceeded, MWRA, in cooperation with the Woods Hole Oceanographic
Institution (WHOI) and the Massachusetts Division of Marine Fisheries,
implemented its rapid-response Alexandrium survey plan (Libby 2006),
which provides for assessment of rapidly developing and potentially large
blooms. Results from those surveys indicated that the bloom proceeded in
a pattern that was consistent with historic progressions and that the outfall
discharge did not affect its intensity, timing, or duration.

2009 OUTFALL MONITORING OVERVIEW 23 
Table 3-1. Contingency Plan threshold values and 2009 results for water-column monitoring. 
(DO=dissolved oxygen) 
Location/ 
Parameter 
Specific
Parameter Baseline Caution Level Warning
Level 
2009 
Results 
Bottom water
nearfield 
Dissolved
oxygen
concentration 
Background 5 th
percentile 
5.75 mg/L 
Lower than 6.5
mg/L for any
survey (June-
October) unless
background
conditions are
lower 
Lower than 6.0
mg/L for any
survey (June-
October) unless
background
conditions are
lower 
Lowest survey
mean = 7.23 mg/L 
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 = 77.5% 
Bottom water
Stellwagen
Basin 
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 = 6.79 
mg/L 
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 = 71.8% 
Bottom water
nearfield 
DO depletion
rate (June-
October) 
0.024 mg/L/d 0.037 mg/L/d 0.049 mg/L/d 0.010 mg/L/d 
Chlorophyll
nearfield 
Annual 79 mg/m 2 118 mg/m 2 158 mg/m 2 52 mg/m 2 
Winter/spring 62 mgml 2 238 mg/m 2 None 63 mg/m 2 
Summer 51 mg/m 2 93 mg/m 2 None 43 mg/m 2 
Autumn 97 mg/m 2 212 mg/m 2 None 49 mg/m 2 
Nuisance
algae
nearfield 
Phaeocystis
pouchetii 
Winter/spring 468,000 cells/L 2,020,000 cells/L None 402,000 cells/L 
Summer 72 cells/L 357 cells/L None Absent 
Autumn 317 cells/L 2,540 cells/L None Absent 
Nuisance
algae
nearfield 
Pseudo-
nitzschia 
Winter/spring 6,200 cells/L 21,000 cells/L None Absent 
Summer 14,600 cells/L 43,100 cells/L None Absent 
Autumn 9,940 cells/L 24,700 cells/L None 1,460 cells/L 
Nuisance
algae
nearfield 
Alexandrium
fundyense 
Any nearfield
sample 
Baseline
maximum =
163 cells/L 
100 cells/L None 
150 cells/L,
caution level
exceedance 
Farfield PSP toxin
extent Not applicable New incidence None No new incidence

2009 OUTFALL MONITORING OVERVIEW 24 
4. Sea Floor 
Sea-floor monitoring in 2009 was conducted at soft-bottom stations in the
nearfield (Figure 4-1) and farfield (Figure 4-2) and through a video and
photographic survey of rocky habitats in the vicinity of the outfall and at
reference locations to the north and south (Figure 4-3). 
Figure 4-1. Locations of nearfield soft-bottom stations for chemical parameters, sediment-
profile imaging (SPI), and community parameters. SPI sampling is performed on all stations
every year.

2009 OUTFALL MONITORING OVERVIEW 25 
Figure 4-2. Locations of farfield soft-bottom stations for chemical and community
parameters. 
The soft-bottom studies included measurements of sediment grain-size
distribution, total organic carbon, the sewage-bacteria tracer Clostridium
perfringens spores, chemical contaminants, and community parameters at
stations labeled as “sampled in odd years” or “sampled every year.”
Sediment-profile imaging measurements were made at all nearfield
Massachusetts Bay stations shown on Figure 4-1, including those denoted
as being sampled in even years.

2009 OUTFALL MONITORING OVERVIEW 26 
Figure 4-3. Locations of hard-bottom stations. Video and still photographs are collected at 17
stations distributed among six transects and at six additional waypoints, including one active
diffuser and one diffuser that has not been opened.

2009 OUTFALL MONITORING OVERVIEW 27 
Sediment Characteristics and Tracers 
Grain-size distributions at the 16 stations sampled in 2009 remained
within the historic ranges of the monitoring program, ranging from coarse
to fine sediments (Maciolek et al. 2010). Total organic carbon
concentrations were relatively low at most stations, especially in the
nearfield. There has been no increase in mean concentrations of total
organic carbon at stations located near the outfall since the outfall
diversion. Rather, there has been a slight decrease in the nearfield and at
stations located between the nearfield and Boston Harbor.
As in other post-diversion years (except 2006), it was possible to detect
elevated levels of Clostridium perfringens spores in some sediments
collected within two kilometers of the outfall. The signal was especially
apparent when comparing the data to those from late baseline years, 1999–
2000 (Figure 4-4). These findings were consistent with predictions that it
would be possible to detect sewage tracers such as Clostridium spores in
the immediate vicinity of the outfall. There has been a decline in spore
counts from stations located in the transition area, located between Boston
Harbor and the outfall, where the single station sampled in 2009 had a
spore count at the bottom of the baseline range.
There has been no indication of accumulation of toxic compounds in the
region surrounding the relocated outfall. Concentrations of chemical
contaminants in the sediments were measured at two stations in 2009
(NF12 and NF17) and were generally at the low ends of the ranges
measured throughout the monitoring program. Concentrations of PCBs
(Figure 4-5) and chlorinated pesticides (not shown) have decreased at both
nearfield and farfield stations, probably reflecting the slow declines in
those contaminants since they were banned in the 1970s and 1980s. There
have also been small decreases in silver, cadmium, and mercury
concentrations. No similar region-wide declines in polycyclic aromatic
hydrocarbons (PAHs) have been observed.
Concentrations of aluminum have increased in the nearfield and at
transition stations since the outfall diversion, but possible reasons for the
increase have not been determined. Aluminum in sediments is more
typically the result of natural processes than anthropological activities.

2009 OUTFALL MONITORING OVERVIEW 28 
Figure 4-4. Clostridium perfringens spores normalized to percent fine fraction in the
sediments compared to the late baseline range and post-diversion mean. Transition area”
denotes stations located between Boston Harbor and the outfall; “Farfield” denotes stations
offshore from the outfall. 
Figure 4-5. Regional trends in PCB concentrations during the baseline and post-
diversion periods. Values are mean ± standard error. The horizontal line represents the
effects range-low (ER-L), the lower tenth percentile of concentrations of PCBs in
sediments that have been determined to be toxic in a broad range of studies. ER-Ls are
not thresholds but are useful for comparisons across regions or time. 
0
50
100
150
200
250
300
FF12
FF10
FF13
NF24
NF17
NF19
NF23
NF14
NF13
NF18
NF15
NF12
NF16
NF07
NF10
NF21
NF20
NF04
NF09
NF22
NF08
NF05
NF02
FF11
FF01A
FF14
FF09
FF04
FF05
FF06
FF07
Transition
Area
Nearf ield (<2 km from outfall) Nearf ield (>2 km from outfall) Farf ield 
Concentration (cfu/g dry/% fines)
Station by Sample Area 
Clostridium perfringens 
(normalized to percent fines) Baseline Range (1999-2000)
Post-diversion Station Mean
2009 Station Mean
Baseline Mean 
0
5
10
15
20
25
Mean(Total PCB (ng/kg dry))
Baseline
Post-diversion
Baseline
Post-diversion
Baseline
Post-diversion
Baseline
Post-diversion
Farfield
Nearfield (<2 km)
Nearfield (>2 km)
Transition
ER-L

2009 OUTFALL MONITORING OVERVIEW 29 
In Boston Harbor, where monitoring has also been conducted since 1991,
data continued to show a decline in concentrations of total organic carbon
at some stations, including those closest to the former harbor outfall near
DITP. The large harbor-wide decline in concentrations of Clostridium
perfringens spores also continued in 2009. 
Sediment-Profile Imaging 
Sediment-profile imaging measurements were made at 23 nearfield
stations in 2009 and continued to show no adverse effects of the outfall
(Maciolek et al. 2010). The number of animals and burrows recorded in
each image has been lower during 2005–2009 since a high in 2004,
continuing to suggest that physical rather than biological processes have
been the primary forces structuring the sediments in recent years. In 2009,
Hurricane Bill passed offshore two days prior to sampling, and storm-
related waves and bottom currents may have destroyed surficial biogenic
structures, such as feeding mounds and pits. Storms and storm-induced
sediment transport and deposition remain the primary stresses on the sea-
floor communities in Massachusetts Bay. 
Concerns that an increase in the amount of organic matter deposited on the
sea floor would result in a shallower apparent redox potential discontinuity
(RPD) at stations near the Massachusetts Bay outfall have not been
realized (Figure 4-6). The mean RPD was shallower in 2009 than in
2006–2008, but remained deeper than the baseline mean. No other
measure, including the organism sediment index (OSI) and accumulation
of fine sediments and organic material, have suggested any adverse effects
of the outfall diversion. 
At Boston Harbor stations, where a separate monitoring program is
conducted, the RPD, successional stage, and OSI remained about the same
in 2009 as in 2008, and the incidence of biogenic features decreased. The
sediment-profile images recorded fewer burrowing amphipods 
Leptocheirus pinguis than in 2008, when there had been a large increase
(see Figure 6-10 in Section 6, Special Studies). For the second year,
eelgrass was detected near Deer Island Flats. Since 1993, there has been
an increase in the number of animals and burrows per image and a
functional shift, with animals that burrow deeper into the sediments
becoming more prevalent.

2009 OUTFALL MONITORING OVERVIEW 30 
Figure 4-6. Annual apparent color RPD for data from nearfield stations. The average
RPD depth in 2009 remained deeper than the baseline mean, continuing to indicate that
there has been no adverse effect from the discharge. Data are mean +1 standard error. 
Soft-bottom Communities 
The soft-bottom communities continued to show no response to the
outfall. Rather, post-diversion monitoring has continued to confirm the
baseline finding that sediment grain size is the most important influence
on the benthic infaunal communities (Maciolek et al. 2010). 
Twenty samples from 12 nearfield stations taken in 2009 yielded more
than 45,000 animals. Species composition remained consistent with
earlier years. Average density of the spionid polychaete Prionospio
steenstrupi , which has been the numerically dominant species in recent
years, was about the same as in 2007, the last year in which the same set
of stations was sampled. The tunicate Molgula sp. was especially
abundant at one station, NF17. 
The number of species per sample, total abundance of animals per sample,
and other community parameters all remained within the baseline ranges
(Figure 4-7). 
0.0
1.0
2.0
3.0
4.0
5.0
RPD (cm)
Year
Mean RPD Depth +/- 1SD
Outfall Startup
Baseline Mean
Threshold

2009 OUTFALL MONITORING OVERVIEW 31 
Figure 4-7. Annual community parameters in the nearfield. 
30
40
50
60
70
80
90
100
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 
Species per Sample
Year
Nearfield Species Richness
Mean +/-1SD; circle and triangles are years with reduced station numbers
Outfall Startup
Baseline 
0
1,000
2,000
3,000
4,000
5,000
6,000
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009
Total Abundance per Sample
Year
Nearfield Abundance
Mean +/-1SD; circle and triangles are years with reduced station numbers
Baseline Mean: 2242
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 2005 2006 2007 2008 2009
Log-Series Alpha
Year
Nearfield Log Series Alpha
Mean +/-1SD; circle and triangles are years with reduced station numbers
Baseline Mean:13.06
Outfall Startup

2009 OUTFALL MONITORING OVERVIEW 32 
The mean values for most community parameters were higher than those
measured in 2007 and similar to or higher than the baseline means. The
diversity measures were influenced by the abundance of tunicates at
Station N17. Over the course of monitoring, some community parameters
have fluctuated in sine wave-like patterns. These patterns appear to be
driven by annual fluctuations in several dominant species, particularly
polychaete worms that inhabit fine-grained sediments. The results have
held constant through both even and odd years, when separate sets of
stations are sampled. 
The farfield stations are more geographically widespread, with mostly
finer sediments, and polychaetes dominate at most stations. The species
compositions at those stations have always differed from those at nearfield
stations. There were no unusual findings in the twelve samples from four
farfield stations in 2009. Dominant species in 2009 were generally similar
to those found in earlier years. Mean total abundance of animals was
lower than the baseline mean but similar to what had been found in the
early 1990s. The decline in total numbers could largely be attributed to a
decline in the regionally abundant polychaete Prionospio steenstrupi . 
Hard-bottom Communities 
The rocky habitats in the vicinity of the outfall and at reference locations
continued to support robust communities of algae, invertebrates, and fish
(Maciolek et al. 2010). Baseline and post-diversion monitoring has shown
that the hard-bottom communities in the region are spatially diverse but
temporally stable. While there have been some shifts in species
composition and abundance, those changes have been modest. Lush
epifaunal growth, particularly sea anemones, has thrived on the diffuser
heads. 
Of the fifty taxa recorded during the 2009 survey, there were 37
invertebrate species, nine fishes, and four algal species (Figure 4-8).
Some modest changes have been noted over time, including decreases in
the number of upright algae at some stations. There have also been
increases in the amount of “sediment drape,” a visual assessment of the
detritus deposited on hard surfaces, with a concurrent decrease in coralline
algae at some stations, including northern reference sites. Some changes
at the northern stations may be attributed to disturbance of the sea floor by
anchors. Sightings of cod and lobster have increased greatly since the
baseline period, but these increases may be the result of quieter sampling
equipment.

2009 OUTFALL MONITORING OVERVIEW 33 
Figure 4-8. Screen captures of the four algal species observed during the 2009 hard-bottom
survey. ( a) coralline algae encrusting rock surfaces at waypoint T1-3; (b) dulse Palmaria palmata 
on a boulder at southern reference site T8-1; (c) red filamentous algae Ptilota serrata at northern
reference site T9-1; (d) shotgun kelp Agarum cribrosum on a boulder at northern reference site
T7-1. 
Contingency Plan Thresholds 
No Contingency Plan thresholds for sea-floor monitoring were exceeded
in 2009 (Table 4-1). There have been no threshold exceedances for any
sea-floor parameter during the course of the monitoring program. RPD
depth continued to be deeper than the baseline mean, and the soft-bottom
community parameters were within normal ranges. The percent of the
soft-bottom community composed of opportunistic species remained low,
about two orders of magnitude below the warning threshold.

2009 OUTFALL MONITORING OVERVIEW 34 
Table 4-1. Contingency Plan threshold values and 2009 results for sea-floor monitoring. 
Location/
Parameter
Type 
Parameter Caution Level Warning Level 2009 Results 
Nearfield RPD depth 1.18 cm None 2.74 cm 
Odd years, 
benthic
diversity,
nearfield 
Species per sample <46.52 or >79.95 None 71.9 
Fisher’s log-series
alpha <9.95 or >15.17 None 14.8 
Shannon diversity <3.30 or >3.91 None 3.84 
Pielou’s evenness <0.56 or >0.66 None 0.622 
Benthic
opportunists % opportunists >10% >25% 0.275 %

2009 OUTFALL MONITORING OVERVIEW 35 
5. Fish and Shellfish 
Each year MWRA monitors the health of winter flounder in Boston
Harbor, Massachusetts Bay, and Cape Cod Bay. Every three years,
including 2009, monitoring also includes chemical analyses of flounder
fillets and liver, lobster meat and hepatopancreas, and blue mussel tissue. 
Flounder and lobster were sampled from Deer Island Flats, near the outfall
site, and Cape Cod Bay (Figure 5-1). Flounder were also taken near
Nantasket Beach. Mussels were collected from a reference site at Stover’s
Point, Maine and deployed in cages at two outfall site locations (the edge
of the mixing zone and one kilometer south of the diffuser line), at Deer
Island Light, and in the Inner Harbor for 60 days. 
Figure 5-1. Fish and shellfish monitoring sites.

2009 OUTFALL MONITORING OVERVIEW 36 
Flounder Health 
Fifty sexually mature winter flounder were taken from each of the four
sampling sites during April and May 2009 for assessment of external
condition and examination of liver histology (Moore et al. 2009, Hall et al.
2010). Catch per unit effort was greater than in 2006–2008 for all sites
except Nantasket Beach (Figure 5-2). In Cape Cod Bay, the catch per unit
effort was the highest measured over the course of the monitoring
program. 
Figure 5-2. Annual catch per unit effort. (DIF = Deer Island Flats, ECCB = Eastern Cape Cod
Bay, NB = Nantasket Beach, OS = Outfall Site) 
Average ages, lengths, and weights of the winter flounder collected in
2009 were within the historic ranges. The catches continued to be
dominated by females, as they have been throughout most of the
monitoring program (Figure 5-3). 
0
0.5
1
1.5
2
2.5
3
3.5
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009
CPUE (fish/min)
DIF ECCB NB OS 
Outfall Startup

2009 OUTFALL MONITORING OVERVIEW 37 
Figure 5-3. Annual percent females in winter flounder samples. (DIF = Deer Island Flats,
ECCB = Eastern Cape Cod Bay, NB = Nantasket Beach, OS = Outfall Site) 
Prevalence of fin erosion, a condition that can be indicative of elevated
concentrations of ammonium and other pollutants, was within the historic
range of the monitoring program and lower than had been observed in the
late 1970s and early 1980s. Blind-side ulcers were present in low
numbers on fish from Deer Island Flats and Nantasket Beach. Ulcers were
first detected in 2003, when they were found on 36% of the fish collected
near the outfall. That year proved to be the peak for the infection, and in
2009, no fish taken from near the outfall had ulcers. The cause of the
ulcers has not been determined. 
No neoplasms were observed in any fish from any site. Incidence of
neoplasia has been rare throughout the area since routine monitoring
started in 1991, although levels were as high as 12% in flounder taken
from Boston Harbor for other monitoring programs during the 1980s.
Neoplasia has never been observed in fish taken from the outfall site. 
The incidence of centrotubular hydropic vacuolation (CHV), a mild
condition associated with exposure to contaminants, remained lower than
the baseline observations (Figure 5-4). Incidence of CHV at Deer Island
Flats was slightly greater in 2009 than in 2008 but less than baseline
levels. Average severity of CHV also remained lower than baseline
levels. 
0
10
20
30
40
50
60
70
80
90
100
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 
Percent Females 
DIF ECCB NB OS 
Outfall Startup

2009 OUTFALL MONITORING OVERVIEW 38 
Figure 5-4. Annual prevalence of centrotubular hydropic vacuolation (CHV), corrected for
age. (DIF = Deer Island Flats, ECCB = Eastern Cape Cod Bay, NB = Nantasket Beach, OS =
Outfall Site) 
Levels of one marker of substandard liver health, biliary proliferation,
were elevated in 2009, particularly in fish from Cape Cod Bay. Three fish
from Cape Cod Bay had single-celled parasites in bile duct cells (Figure 5-
5), and it is possible that the elevated levels of biliary proliferation are
associated with this parasite. 
0
2
4
6
8
10
12
14
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009
Percent CHV /Mean Age
DIF ECCB NB OS 
Outfall Startup

2009 OUTFALL MONITORING OVERVIEW 39 
Figure 5-5. Stained section of a winter flounder liver showing protozoan parasites in a bile
duct. (Arrows indicate the parasites.) 
Fish and Shellfish Chemistry 
Samples for chemical analyses of winter flounder tissues were taken from
the same collections as were used to assess health (Hall et al. 2010).
Three replicates of winter flounder fillets and livers, each composed of
tissue from five fish, were analyzed for PCBs, pesticides, and mercury.
Liver samples were also analyzed for selected metals. Similarly, three
replicates of lobster meat and hepatopancreas were composed of tissues
from seven lobsters and were analyzed for PCBs, pesticides, and mercury.
Hepatopancreas samples were also analyzed for metals. Mussel tissues
were analyzed for PCBs, pesticides, PAHs, mercury, and lead. 
Before-After Control-Impact (BACI) analyses of flounder chemistry data
have detected no changes related to the outfall diversion. There have been
slow declines in contaminant levels of products that have been banned,
such as PCBs, DDTs, and chlordanes. For example, total chlordane levels
have decreased in flounder fillets, particularly in those from Deer Island
Flats (Figure 5-6), and levels of total PCBs in flounder livers have
declined at all sites (Figure 5-7). These declines may reflect region-wide
conditions as the ecosystem slowly cleanses itself, or they may result from
changes in fish distribution. The winter flounder in the more recent
collections may have spent more time in more northern or deeper waters,
which may also be expected to be cleaner.

2009 OUTFALL MONITORING OVERVIEW 40 
Figure 5-6. Chlordane levels in flounder fillets, 1994–2009. (DIF=Deer Island Flats,
ECCB=Eastern Cape Cod Bay, NB=Nantasket Beach, OS=Outfall Site) 
Figure 5-7. PCB levels in flounder livers, 1994–2009. (DIF=Deer Island Flats, ECCB=Eastern
Cape Cod Bay, NB=Nantasket Beach, OS=Outfall Site) 
0.0
2.0
4.0
6.0
8.0
10.0
12.0
14.0
16.0
18.0
20.0
1994 1996 1998 2000 2002 2004 2006 2008 2010 
Year
ng/g dry weight total chlordane 
DIF
ECCB
NB
OS 
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
10000
1994 1996 1998 2000 2002 2004 2006 2008 2010 
Year
ng/g dryweight PCB 
DIF
ECCB
NB
OS

2009 OUTFALL MONITORING OVERVIEW 41 
Chemistry data for lobster meat and hepatopancreas are quite variable,
sometimes the result of one of the seven lobsters making up a replicate
having widely different concentrations than the others. The reason for
such anomalies is not known. 
A 2007 BACI analysis of mussel data, using Cape Cod Bay as a control,
shows that there has been a decrease in concentrations of high molecular
weight PAHs in mussels deployed at Deer Island Light and an increase in
levels deployed at the edge of the outfall mixing zone, particularly in the
years immediately after the diversion (Figure 5-8, Kane-Driscoll et al.
2008). These higher levels were still well below those that are harmful to
mussels or humans. The lower levels in 2006 and 2009 are the result of
the cleaner effluent that has been achieved since 2005. 
Figure 5-8. High molecular weight PAH levels in mussels deployed at and near the outfall
site and at Deer Island Light. (DIL=Deer Island Light, OS=Outfall Site, LNB=Outfall Site B
Buoy) 
0
300
600
900
1200
1500
1800
1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 
Year
ng/g dry weight 
DIL
OS
LNB

2009 OUTFALL MONITORING OVERVIEW 42 
Contingency Plan Thresholds 
There were no exceedances of threshold parameters for fish and shellfish
in 2009 (Table 5-1). Incidence of CHV, the most common indicator of
liver disease in the winter flounder of the region, was 15% in fish taken
from the vicinity of the outfall site, lower than the baseline average (the
threshold) of 24.4%. 
Table 5-1. Contingency Plan threshold values and 2009 results for fish and shellfish monitoring. 
Parameter
Type/ 
Location 
Parameter Baseline Caution
Level 
Warning
Level 
2009
Results 
Flounder 
nearfield 
Liver disease
(CHV) 24.4% 44.9% None 15% 
Flounder
tissue
nearfield 
PCB 0.033 ppm 1 ppm wet weight 1.6 ppm wet
weight 0.028 ppm 
Mercury 0.074 ppm 0.5 ppm wet
weight 
0.8 ppm wet
weight 0.09 ppm 
Flounder
tissue, lipid
normalized,
nearfield 
Chlordane 242 ppb 484 ppb None 74 ppb 
Dieldrin 63.7 ppb 127 ppb None 0 ppb 
DDT 775.9 ppb 1552 ppb None 255 ppb 
Lobster tissue
nearfield 
PCB 0.015 ppm 1 ppm wet weight 1.6 ppm wet
weight 0.022 ppm 
Mercury 0.148 ppm 0.5 ppm wet
weight 
0.8 ppm wet
weight 0.09 ppm 
Lobster
tissue, lipid
normalized,
nearfield 
Chlordane 75 ppb 150 ppb None 12 ppb 
Dieldrin 161 ppb 322 ppb None 13 ppb 
DDT 341.3 ppb 683 ppb None 63 ppb 
Mussel tissue 
nearfield 
PCB 0.011 ppm 1 ppm wet weight 1.6 ppm wet
weight 0.003 ppm 
Lead 0.415 ppm 2 ppm wet weight 3 ppm wet
weight 0.11 ppm 
Mercury 0.019 ppm 0.5 ppm wet
weight 
0.8 ppm wet
weight 0.01 ppm 
Mussel tissue,
lipid
normalized,
nearfield 
Chlordane 102.3 ppb 205 ppb None 62 ppb 
Dieldrin 25 ppb 50 ppb None 0 ppb 
DDT 241.7 ppb 483 ppb None 87 ppb 
PAH 1080 ppb 2160 ppb None 1820 ppb

2009 OUTFALL MONITORING OVERVIEW 43 
6. Special Studies 
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 2009, MWRA continued
several special studies. This section updates information on modeling in
Massachusetts Bay, water quality monitoring in Boston Harbor, tracking
and predicting red tides, marine mammal observations, and nutrient flux at
the sediment-water interface. 
Model Upgrade 
For many years, MWRA has used the numerical Bays Eutrophication
Model (BEM) to simulate and predict the physical and biological
conditions in Massachusetts Bay. BEM was developed as a combination
of the hydrodynamic model ECOMsi (Signell et al. 1996) and the water
quality model RCA (HydroQual 2000). 
In December 2008, OMSAP agreed to MWRA’s recommendation that,
subject to testing and evaluation, the hydrodynamic part of BEM be
upgraded to the Finite Volume Coastal Ocean Model (FVCOM). FVCOM
has several advantages, including being nested within a larger-scale
version, which provides suitable outer boundary conditions for
Massachusetts Bay (Figure 6-1). Each change in the model configuration
was tested to ensure that the results were consistent with past model
results (Chen et al. 2009, Chen et al. 2010).

2009 OUTFALL MONITORING OVERVIEW 44 
Figure 6-1. The BEM was initially based on a structured grid (left), but has been replaced by an
unstructured grid, finite volume model (right) , which provides a more accurate fit to the irregular
geometry of the coast. 
The BEM reproduces the observed seasonal cycles of physical, water
quality, and biological variables, including the spring and fall
phytoplankton blooms. Using the model, the effects of the MWRA outfall
can be isolated by comparing model runs with and without the outfall
nutrients included. These sensitivity analyses indicate that the MWRA
outfall has very little effect on Massachusetts Bay ecosystem function.
Consistent with field observations before and after outfall relocation,
effects of the discharge are limited to small, localized increases in
dissolved inorganic nitrogen concentrations in the bottom layer (Tian et al.
2009, Chen et al. 2010). Water quality in Massachusetts Bay appears
from the modeling studies to be sensitive to the strength and direction of
the wind, the timing of upwelling and storm events, and the availability of
light and nutrients. 
Another sensitivity analysis was conducted (Chen et al. 2010) to
determine whether proposed changes to MWRA’s monitoring program
would compromise the model simulations by reducing the amount of data
available to construct boundary conditions. There are only small
differences in model predictions when the model input data set has fewer
nearfield surveys and fewer farfield stations.

2009 OUTFALL MONITORING OVERVIEW 45 
Boston Harbor Water Column Monitoring 
Water quality monitoring in Boston Harbor continues to demonstrate
improvements in response to decreased loadings of nutrients, total
suspended solids, and organic material (Taylor et al. 2010). Nitrogen
concentrations, weighted across four regions of the harbor, have declined
substantially. Chlorophyll concentrations, measured as chlorophyll-a and
phaeophytin, have also declined, particularly in response to the outfall
diversion (Figure 6-2). Levels of total suspended solids increased in 2009,
although the organic component decreased. 
Figure 6-2. Monthly chlorophyll concentrations since 1995, showing decreases, particularly
since the outfall relocation to Massachusetts Bay . II=January 1992–April 1998, the period after
biosolids discharge to the harbor and ended, upgrades to primary treatment were completed, and
secondary treatment was implement. III=April 1998–September 2000, the period beginning with
the onset of the inter-island diversion, bringing all sewage influent to DITP. IV=September 2000–
December 2009, the period beginning with the diversion of effluent discharge from Boston Harbor
to Massachusetts Bay. 1°=upgrade of primary treatment plant, 2°=implementation of secondary
treatment, I-I=ending of discharge to the southern harbor with construction of the inter-island
tunnel, OFF=ending of effluent discharge to the harbor with the commissioning of the new outfall. 
The data suggest that Boston Harbor may be shifting from a system that
was regulated by the rate that water was flushed from the system to one
that is regulated by the remaining nutrient inputs. 
94 95 96 97 98 99 00 01 02 03 04 05 06 07 08 09
0
5
10
15
20 OFF I-I 2 o
CHLOROPHYLL-A
MONTHLY AVERAGE CHL-A CONC.
( μ g l -1 ) 
CHL-A
PHAEOPHYTIN 
1 o
IV III II

2009 OUTFALL MONITORING OVERVIEW 46 
Predicting Red Tides 
Since 2005, MWRA has conducted targeted research aimed at
understanding and predicting blooms of the red tide dinoflagellate 
Alexandrium fundyense . The studies have been conducted in coordination
with the WHOI Gulf of Maine Toxicity (GOMTOX) program, a
cooperative observation and modeling effort focused on the Gulf of Maine
and the adjacent southern New England coastal region. The GOMTOX
studies have identified the abundance of cysts in seed beds off the coast of
Maine, coupled with a population-dynamics model, as the best predictor of
the magnitude of blooms in the following year. 
In 2009, these studies predicted a moderate red tide in Massachusetts Bay.
Data from fall 2008 surveys of the seed beds (Figure 6-3, top) were used
in a model simulating weather and oceanographic conditions of past years
to predict cell abundance for 2009 (Figure 6-3, bottom). Those
predictions were realized, with shellfish beds being closed to fishing in
May. The bloom ended in early June. 
Figure 6-3. Top: Annual abundance of Alexandrium cysts in Maine seed beds. Bottom:
Annual modeled concentrations of Alexandrium cells. Values for 2009 were predicted from
2008 cyst abundance and weather forcing conditions from 2004–2008.

2009 OUTFALL MONITORING OVERVIEW 47 
There was a much larger and more sustained red tide in Maine, where
persistent winds from the east and northeast resulted in a resurgence in
toxicity in late June and early July. The fall cyst count was high, and the
cyst seed bed extended farther south than had been previously measured
(Figure 6-4). 
Figure 6-4. Abundance of Alexandrium cells in 2009, showing the new extent of cysts into the
south.

2009 OUTFALL MONITORING OVERVIEW 48 
The research and modeling continues to suggest that the western Gulf of
Maine has entered an era of frequent and high-intensity red tides. Prior to
1972, it appears that Alexandrium cysts were abundant in the Bay of
Fundy but not in the western Gulf of Maine. From 1972, when a large red
tide occurred, through the early 1990s, cysts began to accumulate in the
western Gulf of Maine, but abundance then waned. During the early years
of the MWRA monitoring program, there were few cysts in the western
Gulf of Maine, and PSP toxicity resulting from blooms was rare. Since
the mid 2000s, cysts have again become abundant in the Gulf of Maine,
and significant red tides have occurred. 
The timing and geographic progression of the blooms has not been
associated with any stimulating effect from the nutrients in the
Massachusetts Bay discharge. Additional field and modeling studies are
continuing. 
Marine Mammal Observations 
Several species of endangered or threatened whales and turtles visit
Massachusetts and Cape Cod bays, including right, humpback, finback,
sei, and, rarely, blue whales. Also seen are the protected, but not
endangered, minke whale, harbor porpoise, gray seal, harbor seal, and
several species of dolphins. 
Since 1995, MWRA has included endangered species observers on
monitoring surveys. In 2009, observers were included on all nearfield and
farfield water quality surveys (Wu 2010). Besides providing observational
data, the presence of trained marine mammal observers addresses a
request by the National Marine Fisheries Service that MWRA take active
steps to minimize the chances of a collision of one of its survey vessels
with a right whale. 
During the 2009 surveys, the trained observers and other members of the
monitoring team counted 38–39 individual whales, 6–7 Atlantic white-
sided dolphin, two unidentified dolphins, and nine harbor porpoises
(Figure 6-5). Observers also noted 153 pinniped sightings, including 130
harbor seals and one grey seal. The whales included one right whale, ten
humpback whales, and ten minke whales. The 17–18 unidentified species
included 11–12 baleen whales. Whale sightings were concentrated in the
Stellwagen Bank National Marine Sanctuary. Six whales were counted in
the nearfield. 
In an independent study, the Provincetown Center for Coastal Studies
found that in 2009 right whales were resident in Cape Cod Bay and
adjacent waters for 92 days during the winter and spring (Leeney et al.

2009 OUTFALL MONITORING OVERVIEW 49 
2009). That project made 354 sightings and counted 196 individual right
whales. They matched 187 unique individual whales to photographs of
known right whales, comprising 49% of the total known population. Of
the 192 individually identified whales that had visited Cape Cod Bay in
2008, 61% were sighted in 2009. Of 29 right whale calves known to have
been born in 2009, five were seen with their mothers. Surface-feeding
behaviors were observed in March and April. 
Figure 6-5. Approximate locations of whale sightings during 2009 nearfield and
farfield water quality surveys. 
! (
! (
! ( 2
! ( D
2
! ( Y ! (
! ( ! (
! (
2
# *
# * # *
# *
# *
! (
2
2
! (
2
! ( D
! ( D
# *
2
! ( D
# *
2 1
2
1
2
1 1
2
1
1 1
2
2
1
1
1
1
1
1
1 1
2
1
1
1
1
1
2
1
2
1
70°0'0"W
70°0'0"W
70°30'0"W
70°30'0"W
71°0'0"W
71°0'0"W
42°30'0"N
42°30'0"N
42°0'0"N
42°0'0"N 
¯ 
0 5 10 15 2.5 Kilometers 
2009 Whale Sightings 
# * Humpback Whale 
2 Minke Whale 
Y North Atlantic Right Whale 
! ( Unidentified Baleen Whale 
! ( D Unidentified Whale 
Stellwagen Bank National Marine Sanctuary
Depth (m) 
0 - 40 m
40 - 70 m
70+ m

2009 OUTFALL MONITORING OVERVIEW 50 
Benthic Flux 
One concern about the outfall diversion was that increased loads of
organic matter might enhance benthic respiration and increase fluxes of
nutrients between the sediments and the water column. The resulting
higher rates of benthic respiration or sediment oxygen demand might lead
in turn to lower levels of oxygen in both the sediments and the water
column. In response to these concerns, MWRA has conducted studies of
the sediment-water interface in Massachusetts Bay and in Boston Harbor
since 1993 (Figure 6-6). 
Figure 6-6. Benthic flux stations in Massachusetts Bay and Boston Harbor.

2009 OUTFALL MONITORING OVERVIEW 51 
The Massachusetts Bay studies have shown no significant changes from
baseline conditions (Tucker et al. 2010). There has been little or no
indication of increased deposition of organic matter to the sea floor and no
change in the oxidation of the bottom waters or sediments. There have
been no increases in sediment oxygen demand and no changes in nutrient
fluxes at the Massachusetts Bay stations (Figures 6-7, 6-8). In fact, the
overall average nearfield sediment oxygen demand is slightly lower in the
post-diversion period. In 2009, the rate of oxygen consumption by the
sediments in the nearfield was among the lowest in the monitoring
program, possibly because there had been two successive years of
relatively little phytoplankton deposition. Dissolved inorganic nitrogen
fluxes have also declined and were particularly low in 2008 and 2009.
The decline appears to be in the ammonium component of the
measurement. Average ammonium flux was 0.6 mmol per m 2 per day
during the baseline period and has averaged only 0.2 mmol per m 2 per day
during the post-diversion period. 
Figure 6-7. Sediment oxygen demand in surface sediments in 2009 , compared with
baseline (1994–2000) and other post-diversion (2001–2008) years. (NF=nearfield,
FF=farfield) 
0
5
10
15
20
25
30
mmol O2 m -2 d -1
MB01
MB02
MB03
MB05
NF Mean
FF Mean
1994 - 2000 2001 - 2008 2009

2009 OUTFALL MONITORING OVERVIEW 52 
Figure 6-8. Dissolved inorganic nitrogen flux in surface sediments in 2009 , compared
with baseline (1994–2000) and other post-diversion (2001–2008) years. (NF=nearfield,
FF=farfield)
Meanwhile, there have been decreases in fluxes at the four stations in
Boston Harbor, reflecting improvements to the benthic environment
during those same time periods that are considered important in the
evaluation of nutrient loading (see above section on Boston Harbor Water
Quality Monitoring). In 2007 and 2008, there were some increases in the
processes, with subsequent declines in 2009.
For example, during the first stages of the Boston Harbor Project,
sediment oxygen demand measurements at some stations were among the
highest reported in the literature. Sediment oxygen demand began to
decrease during the baseline period, as sewage biosolids were no longer
discharged into the harbor. Declines continued during 2001–2006,
increased in 2007 and 2008, and then declined in 2009 (Figure 6-9). The
increases in 2007 and 2008 coincided with increased colonization by an
amphipod Leptocheirus pinguis , which then declined in abundance in
2009 (Figure 6-10). Similar episodes are likely as the harbor continues to
recover. 
-0.2
0.0
0.2
0.4
0.6
0.8
1.0
1.2
1.4
1.6
1.8
mmol N m -2 d -1
MB01
MB02
MB03
MB05
NF Mean
FF Mean
1994 - 2000 2001 - 2008 2009

2009 OUTFALL MONITORING OVERVIEW 53 
Figure 6-9. Sediment oxygen demand in surface sediments from Boston Harbor in 2009,
compared to baseline (1995–2000), early post-diversion (2001–2006), 2007, and 2008. Sediment
oxygen demand had already begun to fall during the baseline period. 
Figure 6-10. Bottom photographs showing heavy colonization of Leptocheirus pinguis in 2008 (left)
and subsequent decline in 2009 (right). Photographs taken during sediment profile imaging surveys. 
0
20
40
60
80
100
120
140
160
180
200
mmol O2 m -2 d -1
BH02
BH03
BH08A
QB01
Mean
1995-2000 2001-2006 2007 2008 2009

2009 OUTFALL MONITORING OVERVIEW 54 
The total nitrogen budget for Boston Harbor has changed considerably
between the pre-diversion and post-diversion periods (Figure 6-11).
During the early years of monitoring, 1991–1994, Kelly (1997) found that
about 14% of the total nitrogen load to the harbor was lost to
denitrification, and 2% was lost to burial, leaving the bulk of the nitrogen
to be lost through export to Massachusetts Bay. During the post-diversion
years, total loads have decreased to about 14% of the earlier estimate.
Denitrification now removes about 60% of the loads, and losses through
export have been greatly reduced. 
Figure 6-11. Pre-diversion and post-diversion nitrogen budgets for Boston Harbor. ( Values
expressed in mmol nitrogen per m 2 per day.) 
2% 17%
14% 61%
84%
22%
0
5
10
15
20
25
flux
mmol N m-2 d-1
export 19.41 0.72
denitrification 3.25 2.01
burial 0.55 0.55
Pre- Diversion Post- Diversion

2009 OUTFALL MONITORING OVERVIEW 55 
7. Stellwagen Bank 
National Marine Sanctuary 
The Gerry E. Studds Stellwagen Bank National Marine Sanctuary protects
842 square miles of open water at the boundary between Massachusetts
Bay and the rest of the Gulf of Maine. It includes a part of Stellwagen
Basin, which is the deepest part of Massachusetts Bay and a long-term
sediment sink. Stellwagen Bank rises to the east of Stellwagen Basin and
provides a rich habitat for marine life. 
The management plan for the sanctuary (U.S. Department of Commerce
2010) focuses on issues including alteration of ecosystems by cables,
pipelines, and fishing gear; introduction of pollutants from sea- and shore-
based sources; and disturbance of marine mammals by ship vessels,
aircraft, noise, and fishing gear. The NPDES permit to discharge effluent
into Massachusetts Bay requires an annual report on possible effects of the
discharge on the sanctuary. This section of the outfall monitoring
overview meets that requirement. 
Water Column 
The MWRA outfall is located about nine miles from the sanctuary border,
a greater distance than any effects of the discharge have been recorded.
Other wastewater treatment plants discharge to the north and south of the
sanctuary, and the area receives pollutant inputs from aerial deposition,
discharges from commercial and private vessels, dredged material disposal
at the Massachusetts Bay Disposal Site, and other sources. However, the
overall water quality in the sanctuary remains good. The 2009 MWRA
water-quality monitoring measurements at the stations in and near the
sanctuary (Figure 7-1) continued to find that dissolved oxygen, nutrient
concentrations, and plankton abundances and community measures were
within the expected ranges for this region of Massachusetts Bay. 
Concentrations of dissolved oxygen and percent saturation have remained
unchanged in Stellwagen Basin, as they have in the nearfield (Figure 7-2;
see also Figure 3-13 in Section 3, Water Column). Potential decreases in
dissolved oxygen concentrations or percent saturation had been a concern
before the outfall diversion, but those concerns have not been realized.
The 2009 bottom water oxygen concentrations were in the middle of the
baseline range.

2009 OUTFALL MONITORING OVERVIEW 56 
 
 














 

















 
F33
F32
F19
F18
F17
F16
F15
F14
F12
F10
F07
F05
N20
N10
N07
N01
F29
F28
F03
F23
F22
F13
F06
N18
N16
N04
F31
F30
F27
F26
F25
F24
F02
F01 
70°15'W
70°15'W
70°30'W
70°30'W
70°45'W
70°45'W
71°0'W
71°0'W
42°30'N
42°30'N
42°15'N
42°1 5'N
42°0'N
42°0 'N
41°4 5'N
41°45'N 
 
 














 

















 
F33
F32
F19
F18
F17
F16
F15
F14
F12
F10
F07
F05
N20
N10
N07
N01
F29
F28
F03
F23
F22
F13
F06
N18
N16
N04
F31
F30
F27
F26
F25
F24
F02
F01 
70°15'W
70°15'W
70°30'W
70°30'W
70°45'W
70°45'W
71°0'W
71°0'W
42°30'N
42°30'N
42°15'N
42°1 5'N
42°0'N
42°0 'N
41°4 5'N
41°45'N 
Cape Cod Bay
Boston
Harbor Massachusetts Bay 
0 10 20 30 40 50 5
Kilometers 
boundary region
northern
boundary
region
offshore
region
coastal region
nearfield region 
 MWRA stations (BWQM) 
  GoMOOS Buoy A 
  NOAA Buoy 44013
MWRA outfall diffuser
Regions
Stellwagen Bank Sanctuary
High : 0
Low : -125 
Figure 7-1. Water column stations, including those in and near the Stellwagen Bank National
Marine Sanctuary (F27, F28, F12) .

2009 OUTFALL MONITORING OVERVIEW 57 
Figure 7-2. 2009 bottom water dissolved oxygen (DO) concentrations in Stellwagen Basin
compared to baseline range, baseline mean, and post-diversion mean. There has been no
change in patterns of dissolved oxygen concentrations (or saturation) since the outfall diversion. 
Annual mean concentrations of nutrients in water samples have varied
somewhat over the years, but the changes have not been substantial, and
no changes at stations in and near the sanctuary have been attributed to the
outfall diversion. Similar patterns have been observed in and near the
sanctuary, in the nearfield, and in Cape Cod Bay. Annual mean
concentrations of total nitrogen have varied across the study area from
year to year, but the pattern is similar among areas (Figure 7-3). Although
ammonium levels (Figure 7-4) rose in the nearfield when the outfall first
went on line, ammonium concentrations in and near the sanctuary were
not similarly affected. Background ammonium levels vary from year to
year; the nearfield ammonium levels are elevated above background by
about 1μM. 
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
2009
Post Mean

2009 OUTFALL MONITORING OVERVIEW 58 
Figure 7-3. Annual mean total nitrogen (TN) at the Stellwagen Bank National Marine
Sanctuary (SBNMS), the outfall nearfield, and Cape Cod Bay. Concentrations have varied by
year but have been similar across regions. Vertical line indicates when outfall came on-line. 
Figure 7-4. Annual mean ammonium at the Stellwagen Bank National Marine Sanctuary
(SBNMS), the outfall nearfield, and Cape Cod Bay. Vertical line indicates when outfall came
on-line. 
0
5
10
15
20
25
30
TN ( μ M)
YEAR
SBNMS Nearfield Cape Cod 
0.0
0.5
1.0
1.5
2.0
2.5
3.0
NH4 ( μ M)
YEAR
SBNMS Nearfield Cape Cod

2009 OUTFALL MONITORING OVERVIEW 59 
Nitrate concentrations (Figure 7-5) continue to be quite variable across all
regions. Concentrations of nitrate, as well as silicate and phosphate (not
shown), have been consistently higher at stations in and near the sanctuary
than at stations in the nearfield or Cape Cod Bay. These higher levels are
associated with deeper offshore waters. It is these nutrient-rich bottom
waters that feed plankton and small fishes and make Stellwagen Bank a
thriving habitat for commercial fishes and whales. There has been a long-
term, slight, upward trend in nitrate levels across the regions. 
Figure 7-5. Annual mean nitrate at the Stellwagen Bank National Marine Sanctuary
(SBNMS), the outfall nearfield, and Cape Cod Bay. Nitrate concentrations are variable, but
there have been no changes that can be attributed to the outfall. Vertical line indicates when outfall
came on-line. 
The annual mean areal chlorophyll levels have varied at the sanctuary
stations, the nearfield, and in Cape Cod Bay throughout the monitoring
program, but post-diversion levels are not significantly different from the
baseline (Figure 7-6). Chlorophyll levels do not correlate with nitrogen
and have not changed in response to changes in nutrient inputs. 
0.0
1.0
2.0
3.0
4.0
5.0
6.0
7.0
8.0
9.0
NO3 ( μ M)
YEAR
SBNMS Nearfield Cape Cod

2009 OUTFALL MONITORING OVERVIEW 60 
Figure 7-6. Annual chlorophyll at the Stellwagen Bank National Marine Sanctuary
(SBNMS), the outfall nearfield, and Cape Cod Bay. Over the course of monitoring, annual
chlorophyll levels have varied, but similar patterns have been seen in samples from every region.
Vertical line indicates when outfall came on-line. 
Sea Floor 
No changes in bottom community parameters have been measured within
or near the sanctuary since the outfall diversion. Stations FF11 and FF14
were sampled in 2009 (Figure 7-7, Maciolek et al. 2010). 
Those deep-water stations continued to support a distinct infaunal
community, with recognizable differences from communities in the
nearfield and Cape Cod Bay. Benthic community parameters at individual
stations showed no pattern of change following the outfall diversion in
2000. The total number of individual organisms per sample has varied
widely, but remained within the baseline range for stations in or near the
sanctuary in 2009. The numbers of species per sample and the diversity of
organisms within the samples were also within the baseline ranges (Figure
7-8). A general increase in number of species, which began during the
baseline period and peaked in 2003, is considered to be a result of normal
cycling. No patterns that relate to the outfall diversion have been found. 
0
20
40
60
80
100
120
140
160
180
Chlorophyll (mg m-2)
YEAR
SBNMS Nearfield Cape Cod

2009 OUTFALL MONITORING OVERVIEW 61 
Figure 7-7. Farfield benthic stations. Stations FF04, FF05, FF11, and FF14 are in or near the
Stellwagen Bank National Marine Sanctuary. FF11 and FF14 were sampled in 2009.

2009 OUTFALL MONITORING OVERVIEW 62 
Figure 7-8. Community parameters at stations in or near the Stellwagen Bank National
Marine Sanctuary. Top: species richness or number of species per sample; Bottom: Log-series
alpha, a measure of diversity. 
0
10
20
30
40
50
60
70
80
90
100
Total Species per Sample
Year
FF05
FF04
FF14
FF11
Outfall startup 
0
5
10
15
20
25
Log Series Alpha
Year
FF05
FF04
FF14
FF11
Outfall startup

2009 OUTFALL MONITORING OVERVIEW 63 
8. Monitoring Questions 
and Answers 
The monitoring program is based on a series of questions that focused on
plausible unanticipated consequences of the diverted effluent discharge on
the Massachusetts Bay and Cape Cod Bay ecosystems. Those questions
have now been answered (Table 8-1). 
Monitoring has confirmed that any effects of the discharge are small and
localized. Compliance with effluent permit limits has proven to be the key
to ensuring that there are no unanticipated effects. Out of the tens of
thousands of measurements that have been made since the Massachusetts
Bay outfall began to discharge, there have been only eleven violations of
permit limits for effluent (Contingency Plan thresholds exceedances). The
exceedances have included failures of four toxicity tests, none of which
were attributed to toxic constituents of the effluent; an exceedance of the
total suspended solids limits after an industrial discharge caused a
disruption of the secondary treatment process; and exceedances of fecal
coliform limits during storms. 
Water-column monitoring has confirmed that it is possible to detect
sewage tracers at stations in the immediate vicinity of the outfall, but there
have been no unexpected changes resulting from the relocated discharge.
Late summer and fall levels of dissolved oxygen in bottom waters have
not been affected by the outfall. Incidence of nuisance algal blooms has
increased for some species, but those changes have been regional and not
attributed to any nutrient stimulation from the discharge. 
Similarly, there have been no unanticipated changes on the sea floor.
Elevated concentrations of the sewage tracer Clostridium perfringens 
spores are detected at stations within the immediate vicinity of the outfall,
but there are no elevated concentrations of toxic contaminants. The soft-
and hard-bottom communities of Massachusetts and Cape Cod bays
remain healthy. 
There have been no effects on fish or shellfish. Some contaminant levels
have been elevated in mussels deployed in the immediate vicinity of the
outfall, within the mixing zone. There have been no increases in
contaminant levels or disease in the flounder and lobsters included in the
monitoring program or in mussels deployed outside the immediate mixing
zone.

2009 OUTFALL MONITORING OVERVIEW 64 
Table 8-1. Answers to the monitoring questions at the end of 2009. 
Monitoring Question Answer 
Do effluent pathogens exceed the permit
limits? 
No. Secondary treatment and disinfection
effectively remove pathogens. In thousands
of tests, daily fecal coliform limits have been
exceeded twice, both times during storms. 
Does acute or chronic toxicity of effluent
exceed the permit limit? 
No. In more than 500 tests, there have been
four exceedances of permit limits. 
Do effluent contaminant concentrations
exceed permit limits? 
No. Discharges of priority pollutants are 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? 
No. Discharges of solids and BOD have
decreased by 80% compared to the old
treatment plant. In more than 500 tests, there
have been three exceedances of suspended
solids limits, which occurred during an upset
of the secondary treatment process by an
industrial discharge. 
What are the concentrations of
contaminants in the influent and effluent and
their associated variability? 
There has been great success in reducing
contaminants in the influent and a high
degree of removal of contaminants by the
treatment system, with consistently low
concentrations since secondary treatment
was implemented. 
Do levels of contaminants in water outside
the mixing zone exceed water quality
standards? 
No. Water quality standards are not
exceeded. The projected degree of mixing
was confirmed by plume studies conducted in
2001. Ongoing effluent monitoring assures
that standards are not violated. 
Are pathogens transported to shellfish beds
at levels that might affect shellfish consumer
health? 
No. Dilution is sufficient for pathogens to
reach background concentrations before
reaching shellfish beds. Dilution rates were
confirmed by plume studies conducted in
2001. 
Are pathogens transported to beaches at
levels that might affect swimmer health? 
No. Dilution is sufficient for pathogens to
reach background concentrations before
reaching beaches. Dilution rates were
confirmed by plume studies conducted in
2001. 
Has the clarity and/or color of the water
around the outfall changed? 
No. Although clarity and color have not
changed, there are occasional observations
of tiny bits of grease, similar to samples
collected at the treatment plant. 
Has the amount of floatable debris around
the outfall changed? 
Floatable debris of concern is rare in the
effluent. Signs of effluent can occasionally be
detected in the field. 
Are the model estimates of short-term (less
than one day) effluent dilution and transport
accurate? 
Yes. Model estimates were 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 and influenced by tides and
local wind. Bottom currents around the outfall
can flow in any direction with no mean flow
direction.

2009 OUTFALL MONITORING OVERVIEW 65 
Monitoring Question Answer 
What is the farfield fate of dissolved,
conservative, or long-lived effluent
constituents? 
There have been no detectable changes in
the farfield. Changes in salinity and dissolved
components of the effluent are not detected
within tens of meters of outfall and not
observed in farfield water or sediments. 
Have nutrient concentrations changed in the
water near the outfall; have they changed at
farfield stations in Massachusetts Bay or
Cape Cod Bay, and, if so, are they
correlated with changes in the nearfield? 
Changes have been consistent with model
predictions. The effluent signature is
observed in the vicinity of the outfall but is
quickly diluted. 
Do the concentrations (or percent
saturation) of dissolved oxygen in the water
column meet the state water quality
standards? 
Yes. Conditions are unchanged from the
baseline. 
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? 
No. Conditions have not changed from the
baseline. 
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. 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? 
Productivity patterns in Boston Harbor may be
changing, as the area transitions from
eutrophic conditions to a more typical coastal
regime. There has been no concurrent
increase in productivity in Massachusetts
Bay. 
Has the abundance of nuisance or noxious
phytoplankton changed in the vicinity of the
outfall? 
The frequency of Phaeocystis blooms has
increased, but the phenomenon is regional in
nature. Alexandrium blooms, which have
occurred since 2005, are regional and have
not been attributed to the outfall. 
Has the species composition of
phytoplankton or zooplankton changed in
the vicinity of the outfall or at selected
farfield stations in Massachusetts Bay or
Cape Cod Bay? If so, can these changes
be correlated with effluent of ambient water
nutrient concentrations, or can farfield
changes be correlated with nearfield
changes? 
The increase in frequency of Phaeocystis 
blooms is the most marked change in the
phytoplankton community, and the region
appears to be entering a period of frequent
red tides. Those changes have not been
attributed to the outfall. There have been no
marked changes in the zooplankton
community. 
What is the level of sewage contamination
and its spatial distribution in Massachusetts
and Cape Cod bays sediments before
discharge through the new outfall? 
The effects of historic inputs from Boston
Harbor and other sources can be detected,
particularly in coastal stations.

2009 OUTFALL MONITORING OVERVIEW 66 
Monitoring Question Answer 
Has the level of sewage contamination or its
spatial distribution in Massachusetts and
Cape Cod bays sediments changed after
discharge through the new outfall? 
An effluent signal can be detected only in 
Clostridium perfringens spores, the most
sensitive sewage tracer, and is only
detectable within a few kilometers of the
outfall. 
Has the concentration of contaminants in
sediments changed? 
There has been no general increase in
contaminants. An effluent signal can be
detected as Clostridium perfringens spores
within 2 km of the diffuser. 
Has the soft-bottom community changed? Changes have occurred but are the result of
natural variation. The changes are not
significant and are not attributed to the outfall. 
Have the sediments become more anoxic;
that is, has the thickness of the sediment
oxic layer decreased? 
No. The sediment RPD has been deeper
during post-diversion years rather than
shallower; that is, the sediments are more
rather than less oxic. 
Are any benthic community changes
correlated with changes in levels of toxic
contaminants (or sewage tracers) in
sediments? 
There have been no changes detected, even
within 2 km of the outfall. 
Has the hard-bottom community changed? There have been no changes that can be
attributed to the outfall. There have been
decreases in coralline algae at some stations,
but the geographic pattern does not suggest
an outfall effect. 
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? 
These conditions were described by baseline
monitoring. 
Have the rates of these processes
changed? 
Conditions have improved in Boston Harbor
and have not changed in Massachusetts Bay. 
Has the level of contaminants in the tissues
of fish and shellfish around the outfall
changed since discharge began? 
There has been no substantial change in
flounder or lobster contaminant body
burdens, with concentrations remaining very
low. There have been detectable increases in
concentrations of some contaminants in
mussel arrays deployed within the mixing
zone 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? 
There have been no changes that would pose
a threat to human health. Regional patterns
have persisted since the baseline period, and
there appears to be a general long-term
downward trend for most contaminant levels. 
Are the contaminant levels in fish and
shellfish different between the outfall,
Boston Harbor, and a reference site? 
Differences were documented during baseline
monitoring. Regional patterns have persisted
since the diversion, with concentrations being
highest in Boston Harbor and lowest in Cape
Cod Bay. 
Has the incidence of disease and/or
abnormalities in fish or shellfish changed? 
There have been no increases in disease or
abnormalities in response to the outfall; there
has been a long-term downward trend in liver
disease in fish from near Deer Island and
near the outfall.

2009 OUTFALL MONITORING OVERVIEW 67 
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2009 OUTFALL MONITORING OVERVIEW 69 
List of Acronyms 
BACI Before-After, Control-Impact analysis 
BEM Bays Eutrophication Model 
BOD Biochemical oxygen demand 
cBOD Carbonaceous biochemical oxygen demand 
BWQM Bay Water Quality Monitoring 
CHV Centrotubular hydropic vacuolation 
DDE Dichlorodiphenylethylene 
DDT Dichlorodiphenyltrichloroethane 
DEP Massachusetts Department of Environmental Protection 
DIF Deer Island Flats 
DIL Deer Island Light 
DITP Deer Island Treatment Plant 
DO Dissolved oxygen 
ECCB Eastern Cape Cod Bay 
EPA U.S. Environmental Protection Agency 
ER-L Effects range-low 
FF Farfield 
FVCOM Finite Volume Coastal Ocean Model 
GoMOOS Gulf of Maine Ocean Observation System 
GOMTOX Gulf of Maine Toxicity 
HMW High molecular weight 
IAAC Inter-Agency Advisory Committee 
LC50 50% mortality concentration 
LMW Low molecular weight 
LNB Outfall site B Buoy 
MB Massachusetts Bay 
MGD Million gallons per day 
MWRA Massachusetts Water Resources Authority 
NA Not analyzed/not applicable 
NERACOOS Northeastern Regional Association of Coastal Ocean Observing Systems 
NB Nantasket Beach 
NDBC National Data Buoy Center 
NF Nearfield 
NOAA National Oceanic and Atmospheric Administration 
NOEC No observed effects concentration 
NPDES National Pollutant Discharge Elimination System 
OMSAP Outfall Monitoring Science Advisory Panel 
OS Outfall site 
OSI Organism sediment index 
OSM Outfall site 
PAH Polycyclic aromatic hydrocarbon 
PCB Polychlorinated biphenyl 
PIAC Public Interest Advisory Committee 
PSP Paralytic shellfish poisoning 
RPD Redox potential discontinuity 
SBNMS Stellwagen Bank National Marine Sanctuary 
SEIS Supplemental Environmental Impact Statement 
SPI Sediment profile imagery 
TKN Total Kjeldahl nitrogen 
WHOI Woods Hole Oceanographic Institution

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

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