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2012 overview

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2012 
Outfall Monitoring Overview 
Massachusetts Water Resources Authority 
Environmental Quality Department 
Report 2013-14

Citation: 
Werme C, Keay KE, Hall MP, Leo WS, Mickelson MJ, Taylor DI, Rex AC, Libby,
PS. 2013. 2012 outfall monitoring overview . Boston: Massachusetts Water
Resources Authority. Report 2013-14. 68 p.

2012 
Outfall Monitoring Overview 
prepared by 
Christine Werme 
Independent Consultant 
Berkeley, CA 94705 
and 
Kenneth E. Keay, Maurice P. Hall, Wendy S. Leo,
Michael J. Mickelson, David I. Taylor, Andrea C. Rex 
Massachusetts Water Resources Authority 
Environmental Quality Department 
100 First Avenue 
Charlestown Navy Yard 
Boston, MA 02129 
and 
P. Scott Libby 
Battelle 
397 Washington Street 
Duxbury, MA 02332 
October 10, 2013

2012 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: Benjamin Cowie-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: Vivi en Li

i 
Table of Contents 
Summary ....................................................................................................................... v 
1. Introduction ............................................................................................................... 1 
2. Effluent ..................................................................................................................... 2 
2012 Characterization ............................................................................................... 2 
Contingency Plan Thresholds ................................................................................... 9 
3. Water Column ......................................................................................................... 10 
Physical Conditions ................................................................................................ 11 
Water Quality .......................................................................................................... 16 
Phytoplankton Communities ................................................................................... 23 
Zooplankton Communities...................................................................................... 26 
Stellwagen Bank National Marine Sanctuary ......................................................... 30 
Contingency Plan Thresholds ................................................................................. 37 
4. Sea Floor ................................................................................................................. 39 
Sediment Characteristics and Tracers ..................................................................... 41 
Soft-bottom Communities ....................................................................................... 43 
Sediment-profile Imaging ....................................................................................... 45 
Stellwagen Bank National Marine Sanctuary ......................................................... 46 
Contingency Plan Thresholds ................................................................................. 48 
5. Fish and Shellfish .................................................................................................... 50 
Flounder Health ...................................................................................................... 51 
Fish and Shellfish Chemistry .................................................................................. 52 
Contingency Plan Thresholds ................................................................................. 56 
6. Special Studies ........................................................................................................ 57 
Marine Debris Observations ................................................................................... 57 
Continuous Monitoring Data .................................................................................. 59 
Primary Productivity Model Evaluations................................................................ 61 
Cape Cod Bay Studies ............................................................................................ 63 
Eutrophication Studies in Boston Harbor ............................................................... 64 
References ................................................................................................................... 66 
List of Acronyms ........................................................................................................ 68

ii 
List of Figures 
Figure 2-1. Annual rainfall in Boston in 1950–2012 and mean for the period ............. 2 
Figure 2-2. Annual primary-blended and full secondary effluent flows ...................... 3 
Figure 2-3. Monthly primary-blended and full secondary effluent flows during 2012 3 
Figure 2-4. Annual solids discharges ............................................................................ 4 
Figure 2-5. Annual biochemical oxygen demand ......................................................... 5 
Figure 2-6. Annual nitrogen discharges ........................................................................ 6 
Figure 2-7. Annual metals discharges ........................................................................... 7 
Figure 2-8. Annual mercury discharges ........................................................................ 7 
Figure 2-9. Annual PCBs and pesticides discharges .................................................... 8 
Figure 3-1. Water-column monitoring stations ........................................................... 10 
Figure 3-2. Flows of the Merrimack and Charles rivers were low throughout much of
the year, reflecting the relatively dry year .................................................................. 12 
Figure 3-3. Average wind stress at NDCB Buoy 44013 ............................................. 12 
Figure 3-4. Nearfield surface- and bottom-water temperature ................................... 13 
Figure 3-5. Nearfield surface- and bottom-water salinity........................................... 14 
Figure 3-6. Nearfield surface- and bottom-water dissolved oxygen concentrations .. 14 
Figure 3-7. Bottom-water dissolved oxygen concentration at stations in Massachusetts
and Cape Cod bays during the nine surveys conducted in 2012................................. 15 
Figure 3-8. Bottom-water dissolved oxygen concentrations at NERACOOS Buoy
A01 near Cape Ann and nearby MWRA stations, 2010–2012 ................................... 16 
Figure 3-9. Mean nutrient concentrations at Station N18 in 2012, compared to 2011
and other prior years ................................................................................................... 17 
Figure 3-10. Depth-averaged ammonium by station in Massachusetts and Cape Cod
bays ............................................................................................................................. 18 
Figure 3-11. (Top) Surface- and bottom-water ammonium on March 20, 2012 at the
monitoring stations during mixed conditions. (Bottom) Cross-sections of
concentrations at other depths along transects connecting selected stations, showing
that the plume reached surface waters ........................................................................ 19 
Figure 3-12. (Top) Surface- and bottom-water ammonium on May 15, 2012 at the
monitoring stations during stratified conditions. (Bottom) Cross-sections of
concentrations at other depths along transects connecting selected stations .............. 20 
Figure 3-13. Surface-water chlorophyll fluorescence by station in Massachusetts and
Cape Cod bays ............................................................................................................ 21 
Figure 3-14. Moderate Resolution Imaging Spectroradiometer satellite imagery of
surface chlorophyll concentrations in 2012 ................................................................ 22 
Figure 3-15. Phaeocystis pouchetii abundance during the 2012 bloom ..................... 23 
Figure 3-16. Mean nearfield abundance of Phaeocystis pouchetii, 1992–2012 ......... 24 
Figure 3-17. Alexandrium fundyense bloom in 2012 .................................................. 25 
Figure 3-18. Nearfield abundance of Alexandrium fundyense, 1992–2012................ 25 
Figure 3-19. Total zooplankton abundance in 2012 ................................................... 27

iii 
Figure 3-20. Nearfield abundance of total zooplankton, Oithona similis , and Calanus
finmarchicus in 2011 and 2012 compared to past years ............................................. 28 
Figure 3-21. Long-term trend in zooplankton abundance and multi-year mean derived
from a time-series analysis.......................................................................................... 29 
Figure 3-22. Bottom water dissolved oxygen concentrations in Stellwagen Basin in
2012 compared to the previous years of monitoring .................................................. 30 
Figure 3-23. Location of west-east transect from Deer Island, across MWRA outfall,
through Stellwagen Bank, for modeled water-quality parameters presented in Figures
3-24 through 3-27 ....................................................................................................... 31 
Figure 3-24. Modeled dissolved oxygen concentration on the west-east transect across
the MWRA outfall and Stellwagen Bank National Marine Sanctuary at the end of
each month from January through December 2012 .................................................... 32 
Figure 3-25. Modeled percent dissolved oxygen saturation on the west-east transect
across the MWRA outfall and Stellwagen Bank National Marine Sanctuary at the end
of each month from January through December in 2012 ........................................... 33 
Figure 3-26. Modeled dissolved inorganic nitrogen concentrations on the west-east
transect across the MWRA outfall and Stellwagen Bank National Marine Sanctuary at
the end of each month from January through December in 2012 ............................... 34 
Figure 3-27. Modeled chlorophyll concentrations on the west-east transect across the
MWRA outfall and Stellwagen Bank National Marine Sanctuary at the end of each
month from January through December in 2012 ........................................................ 35 
Figure 3-28. Surface-water phytoplankton abundance and composition at MWRA
Cape Cod Bay stations, including Station F29 near Stellwagen Bank National Marine
Sanctuary..................................................................................................................... 36 
Figure 3-29. Zooplankton abundance and composition at MWRA Cape Cod Bay
stations, including Station F29 near Stellwagen Bank National Marine Sanctuary. .. 37 
Figure 4-1. Soft-bottom monitoring stations .............................................................. 39 
Figure 4-2. Sediment-profile imaging stations ........................................................... 40 
Figure 4-3. Concentrations of Clostridium perfringens spores, normaled for sediment
grain size, in 2012 ....................................................................................................... 42 
Figure 4-4. Mean concentrations of Clostridium perfringens spores during the
baseline and outfall-discharge years ........................................................................... 42 
Figure 4-5. Mean infaunal abundance per sample in four areas of Massachusetts Bay,
1992–2012................................................................................................................... 43 
Figure 4-6. Mean abundance per sample of five dominant species and total abundance
at nearfield stations, 1992–2012 ................................................................................. 44 
Figure 4-7. Annual apparent color RPD depth for data from nearfield stations ......... 45 
Figure 4-8. Thumbnail images from Station NF24, located within two kilometers of
the outfall .................................................................................................................... 46 
Figure 4-9. Soft-bottom community data superimposed on a non-metric
multidimensional scaling plot, a multivariate analyses tool ....................................... 47 
Figure 4-10. Annual community parameters with nearfield Contingency Plan
thresholds .................................................................................................................... 49 
Figure 5-1. Fish-and-shellfish monitoring stations ..................................................... 50

iv 
Figure 5-2. Annual prevalence of centrotubular hydropic vacuolation, corrected for
age ............................................................................................................................... 52 
Figure 5-3. PCBs in flounder fillets, 1995–2012 ........................................................ 53 
Figure 5-4. PCBs in flounder livers, 1995–2012 ........................................................ 53 
Figure 5-5. PCBs in lobster meat, 1994–2012 ............................................................ 54 
Figure 5-6. PCBs in deployed mussels, 1991–2012 ................................................... 55 
Figure 5-7. Lead in deployed mussels, 2012 .............................................................. 55 
Figure 6-1. Net used for sampling floatable marine debris ........................................ 57 
Figure 6-2. Marine debris in net tow samples, 2000–2012......................................... 58 
Figure 6-3. Temperature and dissolved oxygen at the NERACOOS Buoy A01, NDBC
Buoy 44013, and during water quality surveys, June 2009 – December 2012 ........... 60 
Figure 6-4. Areal productivity and BZpI0 for individual stations ............................... 62 
Figure 6-5. Areal productivity and BZpI0 for monitoring seasons .............................. 62 
Figure 6-6. The Center for Coastal Studies monitors its own eight stations and three
MWRA stations in and near Cape Cod Bay ............................................................... 63 
Figure 6-7. Right whale sightings in Cape Cod Bay, 1998–2012 .............................. 64 
Figure 6-8. Time series plots of Boston Harbor water quality, 1994–2012 ............... 65 
List of Tables 
Table i. Effluent Contingency Plan thresholds and exceedances ................................. v 
Table ii. Water column Contingency Plan thresholds and exceedances ..................... vii 
Table iii. Sea floor Contingency Plan thresholds and exceedances ........................... viii 
Table iv. Fish and shellfish Contingency Plan thresholds and exceedances ............... ix 
Table 2-1. Contingency Plan threshold values and 2012 results for effluent
monitoring ..................................................................................................................... 9 
Table 3-1. Contingency Plan threshold values and 2012 results for water-column
monitoring ................................................................................................................... 38 
Table 4-1. Contingency Plan threshold values and 2012 results for sea-floor
monitoring ................................................................................................................... 48 
Table 5-1. Contingency Plan threshold values and 2012 results for fish-and-shellfish
monitoring ................................................................................................................... 56

v 
Summary 
Each year, the Massachusetts Water Resources Authority (MWRA) prepares this report,
an overview of environmental monitoring related to the discharge of municipal effluent
from the Deer Island Treatment Plant through its Massachusetts Bay outfall. The report
presents monitoring results and information relevant to the MWRA’s permit-required
Contingency Plan, including threshold exceedances and permit violations, responses,
and corrective actions. The overview also includes monitoring results relevant to the
Stellwagen Bank National Marine Sanctuary and information on special studies. 
The 2012 report marks the twenty-first year of MWRA’s monitoring program, including
almost nine years of baseline monitoring and more than twelve years of “outfall-
discharge” monitoring, covering the years since MWRA ceased discharge of sewage
effluent to the relatively confined waters of Boston Harbor and began to discharge into
deeper water in Massachusetts Bay. The monitoring program reports on results from
effluent, water-column, sea-floor, and fish-and-shellfish monitoring in the outfall
nearfield and at reference stations and on results from special studies. 
Operations at the Deer Island Treatment Plant continued to be exceptional in 2012,
earning MWRA a second consecutive National Association of Clean Water Agencies
(NACWA) Platinum Peak Performance Award. This NACWA award recognizes
facilities with 100% permit compliance for five consecutive years. 
Ambient monitoring results from 2012 were consistent with predictions and past results.
There were exceedances of Contingency Plan “caution level” thresholds 1 (Tables i
through iv) for presence of Phaeocystis pouchetii , a nuisance algal species that is poor
food for zooplankton; Alexandrium fundyense , a nuisance algal species that can cause
paralytic shellfish poisoning; and for two soft-bottom benthic community parameters,
Shannon-Wiener diversity and Pielou’s evenness. No “warning level” exceedances were
observed in 2012 
These exceedances have been reviewed for evidence of whether they were or were not
caused or exacerbated by the outfall discharge. Blooms of Phaeocystis pouchetii are
greatly influenced by temperature patterns and have not been found to be influenced by
the outfall. Presence and abundance of Alexandrium fundyense is controlled by the
presence and extent of seed beds to the northeast of Massachusetts Bay and on 
1 MWRA’s NPDES permit includes Contingency Plan threshold indicators that may indicate a need for action. The
thresholds are based on permit limits, state water quality standards, and expert judgment. “Caution level” thresholds
generally indicate a need for a closer look at the data to determine the reason for an observed change. “Warning level”
thresholds are a higher level of concern, and the permit requires a series of steps to evaluate whether adverse impacts
occurred and if so, whether they were related to the discharge. If caused by the discharge, MWRA may need to
implement corrective action. Thresholds based on effluent discharge permit limits are only “warning level.” Some
ambient parameters have both “caution” and “warning” level thresholds, and others have only “caution level”
thresholds.

vi 
temperature, wind, and current patterns in the spring. The pattern of Alexandrium 
abundance in 2012 was unusual. In 2012 highest cell abundances were observed in
Boston Harbor, the western portions of the nearfield, and along the Boston south shore,
while counts in northern Massachusetts Bay were consistently much lower (i.e. the
bloom did not begin in the north and move south as previous blooms have). Evaluation
of the 2012 Alexandrium bloom found no evidence effluent nutrients played a major
role, and indicates the unusual pattern may have resulted from the mild wind and weak
currents that occurred during the bloom. However, the available data do not allow
conclusions to be drawn as to the causes of the bloom. The exceedances in the benthic
community parameter thresholds, which occurred for a third consecutive year, were
indications of a somewhat more diverse community, resulting from normal cycles of
relative abundance in the animal populations. Increased diversity is not considered to be
environmentally adverse, and the changes are not thought to be related to the outfall. 
Table i. Effluent Contingency Plan thresholds and exceedances.  = no exceedance, NA = not applicable,
W = warning level exceedance 
Effluent Parameter
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
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 NA NA NA 
Oil and grease             

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Table ii. Water column Contingency Plan thresholds and exceedances.  = no exceedance, NA = not
applicable, C = caution level exceedance 
Water Column Parameter
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012 
Nearfield bottom water 
Dissolved oxygen concentration              
Dissolved oxygen saturation C             
Dissolved oxygen depletion rate NA             
Stellwagen Basin bottom water 
Dissolved oxygen concentration              
Dissolved oxygen saturation C             
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      C 
Autumn              
Nearfield nuisance algae Pseudonitzchia 
Winter/spring NA             
Summer NA             
Autumn              
Nearfield nuisance algae Alexandrium 
Any sample      C C  C C  C C 
Farfield shellfish 
PSP toxin extent              
Plume 
Initial dilution NA  Complete

viii 
Table iii. Sea floor Contingency Plan thresholds and exceedances.  = no exceedance, NA = not applicable,
C = caution level exceedance 
Sea Floor Parameter
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012 
Nearfield sediment 
Acenaphthene NA   NA NA  NA NA  NA NA  NA 
Acenaphylene NA   NA NA  NA NA  NA NA  NA 
Anthracene NA   NA NA  NA NA  NA NA  NA 
Benzo(a)anthracene NA   NA NA  NA NA  NA NA  NA 
Benzo(a)pyrene NA   NA NA  NA NA  NA NA  NA 
Cadmium NA   NA NA  NA NA  NA NA  NA 
Chromium NA   NA NA  NA NA  NA NA  NA 
Chrysene NA   NA NA  NA NA  NA NA  NA 
Copper NA   NA NA  NA NA  NA NA  NA 
Dibenzo(a,h)anthracene NA   NA NA  NA NA  NA NA  NA 
Fluoranthene NA   NA NA  NA NA  NA NA  NA 
Fluorene NA   NA NA  NA NA  NA NA  NA 
Lead NA   NA NA  NA NA  NA NA  NA 
Mercury NA   NA NA  NA NA  NA NA  NA 
Naphthalene NA   NA NA  NA NA  NA NA  NA 
Nickel NA   NA NA  NA NA  NA NA  NA 
p,p’-DDE NA   NA NA  NA NA  NA NA  NA 
Phenanthrene NA   NA NA  NA NA  NA NA  NA 
Pyrene NA   NA NA  NA NA  NA NA  NA 
Silver NA   NA NA  NA NA  NA NA  NA 
Total DDTs NA   NA NA  NA NA  NA NA  NA 
Total HMW PAH NA   NA NA  NA NA  NA NA  NA 
Total LMW PAH NA   NA NA  NA NA  NA NA  NA 
Total PAHs NA   NA NA  NA NA  NA NA  NA 
Total PCBs NA   NA NA  NA NA  NA NA  NA 
Zinc NA   NA NA  NA NA  NA NA  NA 
Sediment RPD depth NA             
Nearfield soft-bottom benthic diversity 
Species per sample NA             
Fisher’s log-series alpha NA             
Shannon diversity NA          C C C 
Pielou’s evenness NA          C C C 
Nearfield soft-bottom species composition 
Percent opportunists NA            

ix 
Table iv. Fish and shellfish Contingency Plan thresholds and exceedances.  = no exceedance, NA
= not applicable, C = caution level exceedance 
Fish and Shellfish
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012 
Nearfield flounder tissue 
Total PCBs NA    NA NA  NA NA  NA NA  
Mercury NA     NA  NA NA  NA NA  
Chlordane NA    NA NA  NA NA  NA NA  
Dieldrin NA    NA NA  NA NA  NA NA  
Total DDTs NA    NA NA  NA NA  NA NA  
Nearfield flounder disease 
Liver disease (CHV) NA             
Nearfield lobster tissue 
Total PCBs NA    NA NA  NA NA  NA NA  
Mercury NA    NA NA  NA NA  NA NA  
Chlordane NA    NA NA  NA NA  NA NA  
Dieldrin NA    NA NA  NA NA  NA NA  
Total DDTs NA    NA NA  NA NA  NA NA  
Nearfield mussel tissue 
Total PCBs NA    NA NA  NA NA  NA NA  
Lead NA    NA NA  NA NA  NA NA  
Mercury NA    NA NA  NA NA  NA NA  
Chlordane NA C C  NA NA  NA NA  NA NA  
Dieldrin NA    NA NA  NA NA  NA NA  
Total DDTs NA    NA NA  NA NA  NA NA  
Total PAHs NA C C C NA NA  NA NA  NA NA 

x

1 
1. Introduction 
Since its creation by the Massachusetts state legislature in 1984, the Massachusetts
Water Resources Authority (MWRA) has worked to minimize the effects of
wastewater discharge on the marine environment. The mission of what became
known as MWRA’s Boston Harbor Project included reducing inflow of contaminants
into the waste stream, ending biosolids discharge, improving wastewater treatment
facilities, and providing better dilution of the sewage effluent discharge. Throughout
MWRA’s early years, scientists conducted environmental monitoring in Boston
Harbor and also in Massachusetts Bay, at the (then future) location of a relocated
sewage effluent discharge. 
In 2000, most of the Boston Harbor Project had been completed, including the
relocated effluent outfall, which diverted sewage effluent from Boston Harbor to the
deeper, less confined waters of Massachusetts Bay. The outfall operates under a
National Pollutant Discharge Elimination System (NPDES) permit for the Deer Island
Treatment Plant (DITP) constructed as part of Boston Harbor Project. The permit
was issued jointly by the U.S. Environmental Protection Agency (EPA) and the
Massachusetts Department of Environmental Protection (MADEP). 
The NPDES permit includes requirements for ongoing monitoring of the sewage
effluent and for ambient monitoring of the receiving waters. Monitoring assesses
compliance with specific permit conditions and additional conditions specified by a
permit-required Contingency Plan. Background information on the monitoring
program can be found in Werme et al. (2012), an updated document that describes
monitoring revisions implemented in 2011. The background document, monitoring
plans (MWRA 1991, 1997a, 2004, 2010), the Contingency Plan (MWRA 1997b,
2001), and area-specific technical reports are available on the technical report list at
MWRA’s website, http://www.mwra.state.ma.us/harbor/enquad/trlist.html. 
Results from most baseline years and for each year since the outfall began to
discharge have been documented in reports such as this one, the annual outfall
monitoring overview. Since the Massachusetts Bay outfall came on line in 2000, the
reports have included information relevant to permit requirements, including
Contingency Plan threshold exceedances, responses, and corrective actions. Reports
also include information relevant to the Stellwagen Bank National Marine Sanctuary. 
This year’s outfall monitoring overview presents results for 2012, marking the
twenty-first year of MWRA’s monitoring program, including more than twelve years
of outfall-discharge monitoring. Measurements include effluent, water-column, sea-
floor, and fish-and-shellfish parameters, as well as special studies conducted in
response to permit conditions and environmental concerns. Data specifically related
to the Stellwagen Bank National Marine Sanctuary are included in the overview’s
water-column and sea-floor sections.

2 
2. Effluent 
2012 Characterization 
As in past years, DITP continued to operate as designed through 2012, earning
MWRA the National Association of Clean Water Agencies (NACWA) Platinum Peak
Performance Award for a second consecutive year. The Platinum Award is
NACWA’s highest award recognizing compliance with NPDES permit limits and is
reserved for facilities that have had no permit violations for five consecutive years. 
It was a relatively dry year in the Boston area in comparison to other years since the
outfall came on line in 2000, with precipitation about 20% below the long-term
average (Figure 2-1). Total effluent flow was lower in 2012 than in any year since
the outfall came on line, and virtually all the flow, 99.6%, received full primary and
secondary treatment (Figure 2-2). There were no extreme or protracted storms, and
consequently, storm-related discharges of primary-only effluent blended with effluent
receiving full secondary treatment were relatively small and brief (Figure 2-3). 
Figure 2-1. Annual rainfall in Boston in 1950–2012 (black line) and mean (red line) for the
period. Rainfall in 2012 was about 20% below the long-term average (red line). 
0
10
20
30
40
50
60
70 
Inches

3 
Figure 2-2. Annual primary-blended and full secondary effluent flows. In 2012, 99.6% of effluent
flow received full secondary treatment. (During large storms, flow exceeding the secondary capacity of
the plant is diverted around the secondary process to prevent washing out the essential microbes that
carry out secondary treatment. These diverted flows are combined with full-secondary flows before
disinfection; all discharges meet permit limits.) 
Figure 2-3. Monthly primary-blended and full secondary effluent flows during 2012. Total flow
was below average (about 350 million gallons per day) in every month throughout 2012, and there
were only small amounts of primary-blended flow. 
0
50
100
150
200
250
300
350
400
450
500
1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 
Million gallons per day 
Primary-blended f lows
Secondary f lows 
0
50
100
150
200
250
300
350
400
450
500
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 
Million gallons per day 
Primary-blended f lows
Secondary f lows

4 
The total suspended solids load to Massachusetts Bay was just less than 10 tons per
day, the lowest level recorded (Figure 2-4). Carbonaceous biochemical oxygen
demand (BOD) was also at a record low in 2012, remaining well below levels that
might be expected to affect ambient waters at the discharge site (Figure 2-5).
Nitrogenous BOD (also shown in Figure 2-5), which is a result of the biological
processes in secondary treatment and not a permit limit or Contingency Plan
parameter, was lower than any level measured since 2001. 
Figure 2-4. Annual solids discharges . Solids discharges reached a record low in 2012. 
0
5
10
15
20
25
30
35
1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 
Tons per day

5 
Figure 2-5. Annual biochemical oxygen demand (BOD). MWRA’s permit limits carbonaceous
BOD, which reached a record low in 2012. Nitrogenous BOD is the result of microbiological
breakdown that occurs during secondary treatment and is not regulated by the permit. 
Total nitrogen loads were also lower in 2012, remaining below the permit limits
(Figure 2-6). The portion of the load made up of ammonium increased slightly.
About 10% of the ammonium in the sewage influent is removed by secondary
treatment, but the biological treatment process converts some organic forms of
nitrogen to ammonium. Also, ammonium-rich liquids from the biosolids pelletizing
(fertilizer) plant, built as part of the Boston Harbor Project, are reintroduced to DITP
for treatment, adding to the ammonium load. As required by its permit, MWRA
continually evaluates nitrogen-removal technologies, so that it could be quickly
implemented, should a need arise (Bigornia-Vitale and Wu 2012). Because nitrogen
loads have remained below the Contingency Plan caution threshold, and there have
not been nitrogen-related adverse environmental impacts, nitrogen removal has not
been required or implemented. 
0
5
10
15
20
25
30
35
1998 2000 2002 2004 2006 2008 2010 2012 2014 
Tons per day 
Carbonaceous BOD
Nitrogenous BOD

6 
Figure 2-6. Annual nitrogen discharges. Most of the nitrogen in the effluent is in the form of
ammonium. 
Metals loads also decreased to record low levels in 2012 (Figure 2-7). Metals
discharges are now only a small fraction of what they were before the Boston Harbor
Project, when more than seven hundred fifty pounds of metals were discharged to
Boston Harbor each day. Most metals meet water quality criteria in the effluent itself,
while copper meets the criteria after initial dilution at the Massachusetts Bay outfall. 
Mercury loads were also low (Figure 2-8). Although sensitive methods have been
adopted for mercury analysis, mercury is now only rarely detected in effluent
samples, the consequence of efforts on the part of MWRA and the New England
states and New York to reduce mercury use, handle workplace spills, and discourage
disposal practices that introduce mercury into the sewer system. Most mercury
entering New England waters is from atmospheric deposition. 
0
3000
6000
9000
12000
15000
1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 
Metric tons per year 
Caution Threshold Other Nitrogen Species
Nitrite/Nitrate Ammonium

7 
Figure 2-7. Annual metals discharges. Except for copper, the metals meet receiving water quality
criteria in the effluent, even without the dilution provided by the outfall. 
Figure 2-8. Annual mercury discharges. Mercury is only rarely detected in the effluent, and fewer
than ten pounds were discharged in 2012. (Note that prior years’ outfall monitoring overviews reported
loads in pounds per day.) 
0
50
100
150
200
250
1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 
Average pounds per day 
Silver
Nickel
Chromium
Lead
Copper
Zinc 
0
10
20
30
40
50
60
1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 
Pounds per year

8 
Polychlorinated biphenyl (PCB) and pesticide loads also decreased in 2012 and were
similar to loads discharged in 2007 and 2009 (Figure 2-9). About two pounds of
PCBs and two pounds of pesticides were discharged. All contaminant loads remained
well below those that had been anticipated during the planning process for the
relocated outfall. Those predictions had been that more than 10 pounds of the
pesticide DDT and its breakdown products and more than 100 pounds of PCBs would
be discharged each year. 
Figure 2-9. Annual PCBs and pesticides discharges. New methods were implemented in 2006 to
detect these compounds, which are present at very low levels. PCBs and the pesticides DDT and
chlordane were banned in the 1970s and 1980s but persist in the environment (4-4’ DDE is a DDT
breakdown product and the only form detected in the effluent). (Note that prior years’ outfall
monitoring overviews reported loads in pounds per day.) 
0
1
2
3
4
5
6
7
2006 2007 2008 2009 2010 2011 2012 
Pounds per year 
PCB congeners
4-4' DDE
Chlordane

9 
Contingency Plan Thresholds 
DITP had no permit violations, and there were no exceedances of the Contingency
Plan effluent thresholds in 2012 (Table 2-1). For a second consecutive year, DITP
achieved the NACWA Platinum Award for facilities having five consecutive years
with 100% permit compliance. 
Table 2-1. Contingency Plan threshold values and 2012 results for effluent monitoring. cBOD =
carbonaceous biological oxygen demand, NOEC = no observable effect concentration, LC50 = 50%
mortality concentration, NA = not applicable 
Parameter Caution Level Warning Level 2012 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 None 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

10 
3. Water Column 
The water-column monitoring program measures physical processes and water
quality and studies phytoplankton and zooplankton at stations at the mouth of Boston
Harbor, in Massachusetts Bay, and in Cape Cod Bay (Figure 3-1). 
Figure 3-1. Water-column monitoring stations. Also shown are two instrumented buoys, one
operated by the Northeastern Regional Association of Coastal and Ocean Observing Systems
(NERACOOS) and the other by the National Data Buoy Center (NDBC); the MWRA outfall diffuser;
and the Stellwagen Bank National Marine Sanctuary.

11 
The revised water-column monitoring plan implemented in 2011 (MWRA 2010,
Werme et al. 2012) includes nine annual surveys at fourteen stations. Monitoring
includes sampling for vertical profiles of physical, chemical, and biological
characteristics in the area around the outfall (the nearfield), where some effects of the
effluent were expected and have been observed. Similar measurements are carried
out at farfield reference stations, including stations in Cape Cod Bay and near the
Stellwagen Bank National Marine Sanctuary. Additional surveys are conducted and
stations sampled in response to Alexandrium fundyense red tide blooms. The field
monitoring program is augmented by measurements on two instrumented buoys, the
Northeastern Regional Association of Coastal and Ocean Observing Systems
(NERACOOS) Buoy A01 and the National Oceanic and Atmospheric
Administration’s National Data Buoy Center (NDBC) Buoy 44013, and by satellite
imagery. 
The program also benefits from collaboration with the Center for Coastal Studies at
Provincetown, which conducts a monitoring program in Cape Cod Bay (see Section
6, Special Studies). The Center for Coastal Studies also conducts MWRA’s
monitoring at stations in Cape Cod Bay and the Stellwagen Bank National Marine
Sanctuary. Regulators have set a target that, whenever possible, sampling in Cape
Cod Bay should occur within 48 hours of MWRA Massachusetts Bay sampling and
that any failure to meet that schedule should be reported in the annual outfall
monitoring overview. Except for one survey, in the first two years of sampling under
the new monitoring plan, sampling in Cape Cod Bay was completed within 24 hours
of sampling in Massachusetts Bay. For that one survey (May 14–20, 2011),
inclement weather delayed sampling in Massachusetts Bay until six days after the
Cape Cod Bay survey had been completed. All 2012 sampling was completed within
the regulatory schedule. 
Physical Conditions 
Monitoring has shown 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 key to interpreting the annual monitoring data. 
The year 2012 was notably drier than other recent years (noted in Section 2, Effluent),
with an unusually warm winter, a mixing event in June, and Hurricane Sandy in the
fall. The relatively dry conditions followed a period of wetter years in the Boston
area and resulted in river discharges that were below average compared to 1992–2011
(Libby et al. 2013). Flows from both the Merrimack and Charles rivers were below
average in every season and especially lower than average during the spring months
(Figure 3-2).

12 
Figure 3-2. Flows of the Merrimack (top) and Charles (bottom) rivers were low throughout
much of the year, reflecting the relatively dry year. Flows from both rivers were low, especially
during April–June, with flows translating to only the 12 th percentile for flows throughout the period.
Even lower flows translated to higher percentiles during July–August, because flows are more
typically low in the summer. 
Wind conditions promoted strong upwelling conditions in May, July, August, and
September (Figure 3-3). In early June, a storm with winds from the northeast broke
that pattern. Strong downwelling conditions late October and early November were
caused by Hurricane Sandy, which reached the region on October 29. 
Figure 3-3. Average wind stress at NDBC Buoy 44013. Positive values indicate winds from the
south or southwest, which result in upwelling-favorable conditions; negative values indicate winds
from the north or northeast, which favor downwelling. The dip in June corresponds to a storm with
winds from the northeast, and the strong decline in the fall corresponds to Hurricane Sandy. 
12 th 36 th
percentile
26 th 45 th
12 th 21 st
percentile
31 st 21 st

13 
Nearfield surface- and bottom-water temperatures were higher than average
throughout the late winter and spring, setting record highs for some surveys (Figure
3-4). Warm, calm weather heated surface waters in late May. Then in early June, a
storm mixed warm surface waters down to the bottom, causing a strong spike in the
temperature of bottom waters. The persistent upwelling following that event kept
temperatures lower through the rest of the year, within the range for the monitoring
program. 
Figure 3-4. Nearfield surface- and bottom-water temperature. Water temperatures were
particularly warm, during the early part of the year, reaching record highs for the monitoring program
during some surveys . 
Surface- and bottom-water salinities began the year within normal ranges but,
because of the dry conditions, did not show the typical drop during the spring, when
runoff usually introduces fresh water to the bays (Figure 3-5). Record high salinities
were recorded for May, and relatively high levels persisted throughout the duration of
field sampling for the year. 
Dissolved oxygen concentrations were lower than normal in the winter, and in May,
bottom water dissolved oxygen levels reached record lows for that month (Figure 3-6,
3-7). Upwelling in late May and the mixing event in June may have prevented further
drops, and through the rest of the summer and fall, concentrations were low but
falling at a typical rate. The time-series data from the NERACOOS A01 buoy
located off Cape Ann corresponded well with the survey data and documented the
continued decline in bottom-water levels through mid-October (Figure 3-8). For
much of Massachusetts Bay, stratification persisted until Hurricane Sandy reached the
area on October 29. Another storm, with winds from the northeast, followed the
hurricane, and by early November, the water column was well-mixed.

14 
Figure 3-5. Nearfield surface- and bottom-water salinity . Salinity was high due to the relatively dry
conditions throughout the year. 
Figure 3-6. Nearfield surface- and bottom-water dissolved oxygen concentrations. Dissolved
oxygen concentrations were relatively low, although even lower values would be expected based on
the warmer than average bottom temperatures and higher than average bottom salinity measurements.

15 
Figure 3-7. Bottom-water dissolved oxygen concentration (mg/L) at stations in Massachusetts
and Cape Cod bays during the nine surveys conducted in 2012. Several panels show additional data
from MWRA’s in-house Boston Harbor monitoring surveys when those surveys were within a few
days of the outfall monitoring surveys. 
Feb 06 Mar 20 Apr 10 
May 15 Jun 19 Jul 26 
Aug 21 Sep 06 Oct 23 
4 5 6 7 8 9 
mg/L

16 
Figure 3-8. Bottom-water dissolved oxygen (DO) concentrations at NERACOOS Buoy A01 near
Cape Ann and nearby MWRA stations, 2010–2012. Buoy and survey data were in good agreement
during all three years. In 2012, the buoy data showed a continual decline in bottom water dissolved
oxygen concentrations until mid-October and a return to mixed conditions by early November. 
Water Quality 
Water quality measurements for 2012, including quantification of nutrients and
phytoplankton biomass (measured as chlorophyll), followed typical annual cycles and
continued to confirm predictions that although there would be a measureable increase
in levels of some parameters at stations very near the outfall, there would be no
unexpected adverse effects (Libby et al. 2013). Nutrient concentrations were
somewhat lower than most years during the February and March surveys, possibly
due to the dry year with limited runoff, but overall, concentrations of the major
nutrients important to phytoplankton growth fell into the ranges observed throughout
the monitoring program (Figure 3-9). 
5
6
7
8
9
10
11
12 
Oxygen concentration (mg/l) 
Cape Ann (NERACOOS A01, 50 m)
Survey deep DO (stations near Cape
Ann buoy, 40-60 m)

17 
Figure 3-9. Mean nutrient concentrations at Station N18 in 2012 (black ), compared to 2011 (red)
and other prior years. Spring concentrations of nitrate and silicate were low compared to 2011 and
other years, probably largely because it was a much drier year, with low runoff from rivers. and
possibly also due to phytoplankton blooms prior to the first MWRA survey in March. 
Elevated ammonium levels were apparent at the outfall in most surveys (Figure 3-10),
consistent with the results from prior years. The furthest southern extent that plume-
related elevated ammonium concentrations were detected was Station F15 in May.
Elevated levels were seen at Station N01, to the northwest of the outfall, in September
and October. 
As has been typical since the outfall began to discharge, the plume was found in
surface waters during the winter and spring (Figure 3-11) but was confined beneath
the pycnocline during the summer, stratified season (Figure 3-12). The upwelling
conditions present in May brought nutrients into the upper portions of the water
column, although surface nutrient levels remained low. The detectable ammonium
plume did not reach the surface, but it was apparent in the nearfield. 
Jan Mar May Jul Sep Nov Jan
0
5
10
15 
μ M
Jan Mar May Jul Sep Nov Jan
0
5
10
15 
μ M
Jan Mar May Jul Sep Nov Jan
0
5
10
15 
μ M
SIO4
Jan Mar May Jul Sep Nov Jan
0
0.5
1
1.5 
μ M
PO4 
nitrate ammonium
silicate phosphate

18 
Figure 3-10. Depth-averaged ammonium (μM) by station in Massachusetts and Cape Cod bays. 
Several panels show additional data from MWRA’s in-house Boston Harbor monitoring surveys when
those surveys were within a few days of the outfall monitoring surveys. 
Feb 06 Mar 20 Apr 10 
May 15 Jun 19 Jul 26 
Aug 21 Sep 06 Oct 23 
0 2 4 6 8 10
μM

19 
Figure 3-11. (Top) Surface- and bottom-water ammonium on March 20, 2012 at the monitoring
stations during mixed conditions. (Bottom) Cross-sections of concentrations at other depths
along transects connecting selected stations, showing that the plume reached surface waters. 
Mar 20 Mar 20 
N N
S S
W W
E E 
Mar 20
surface
Mar 20
bottom 
Distance (km)
Depth (m)
0 5 10 15 20 25 30
-70
-60
-50
-40
-30
-20
-10
0 
F23 N21 N04 F22
Parameter: NH4
Survey: WN122
Date: 20-Mar-2012
Distance (km)
Depth (m)
0 5 10 15 20 25 30 35
-35
-30
-25
-20
-15
-10
-5
0 
N01 N21 N18 F15 F10 F06 
W E
N S 
0 2 4 6 8 10
μM

20 
Figure 3-12. (Top) Surface- and bottom-water ammonium on May 15, 2012 at the monitoring
stations during stratified conditions. (Bottom) Cross-sections of concentrations at other depths
along transects connecting selected stations. 
May 15 May 15 
N N
S S
W W
E E 
May 15
surface
May 15
bottom 
Distance (km)
Depth (m)
0 5 10 15 20 25 30
-70
-60
-50
-40
-30
-20
-10
0 
F23 N21 N04 F22
Parameter: NH4
Survey: WN124
Date: 15-May-2012
Distance (km)
Depth (m)
0 5 10 15 20 25 30 35
-35
-30
-25
-20
-15
-10
-5
0 
N01 N21 N18 F15 F10 F06 
W E
N S 
0 2 4 6 8 10
μM

21 
Survey surface-water chlorophyll levels peaked on March 20 (Figure 3-13). High
chlorophyll levels were observed two weeks before the survey date in satellite
imagery from early March (Figure 3-14), suggesting that a winter-spring bloom began
before the March 7 image was made. Chlorophyll fluorescence data from the
NERACOOS Buoy A01 near station F22 off Cape Ann suggested that there could
have been two early chlorophyll peaks. 
Chlorophyll levels were also elevated in the late summer and early fall, consistent
with typical fall phytoplankton bloom patterns. The satellite imagery suggests an
early fall bloom, which ended by mid September, and a later bloom in late September
and October. The imagery also shows high chlorophyll levels later in the year, after
the survey season was complete, particularly in the shallow waters of Cape Cod Bay. 
Figure 3-13. Surface-water chlorophyll fluorescence by station in Massachusetts and Cape Cod
bays. The highest chlorophyll concentrations were recorded during the March 20, 2012 survey, when
concentrations of particulate organic carbon were also high. 
Feb 06 Mar 20 Apr 10 
May 15 Jun 19 Jul 26 
Aug 21 Sep 06 Oct 23 
0 2 4 6 8 10
μg/L

22 
Figure 3-14. Moderate Resolution Imaging Spectroradiometer satellite imagery of surface
chlorophyll concentrations in 2012. The stars show the timing of the nine MWRA surveys, and the
circles highlight blooms. The imagery shows that the spring bloom detected during the March survey
began before March 7. Chlorophyll levels were high throughout the bays in late August and much of
the fall. Note that these images are heavily weather dependent and do not represent consistent intervals
of time. 
Jan 05 Jan 18 Jan 24 Feb 09 Feb 18 Feb 20 Mar 07 Mar 18 
Mar 21 Mar 30 Apr 07 Apr 16 Apr 25 May 07 No Data 
Jul 22 Jul 30 Aug 13 Aug 26 Aug 30 Sep 03 Sep 16 Sep 24 
Sep 27 Oct 13 Oct 25 Nov 04 Nov 10 Nov 22 Dec 06 Dec 24

23 
Phytoplankton Communities 
Total abundance of phytoplankton in 2012 was near the long-term mean for the
monitoring program (Libby et al. 2013). The phytoplankton communities followed
typical progressions throughout the year, with two notable pulses: a predominantly
offshore bloom of Phaeocystis pouchetii in March and a coastal pulse of centric
diatoms ( Skeletonema spp.) in September. As in other years, microflagellates
comprised the numerically dominant group. 
Spring blooms of the colonial flagellate Phaeocystis pouchetii have occurred every
year in Massachusetts Bay over the past decade, but the 2012 bloom was unique in its
early start and early peak abundance, in March rather than in April (Figure 3-15).
The bloom persisted, at a low level, into the early summer. Total microflagellate
abundance also peaked earlier than usual, and it is possible that both these groups
were affected by the unusually warm winter. Overall, Phaeocystis abundance was
somewhat high in comparison to past years (Figure 3-16). 
Figure 3-15. Phaeocystis pouchetii abundance during the 2012 bloom . The bloom began earlier
than in some past years, in March rather than in April, and it persisted into May. Note difference in
scale for May survey . 
Mar 20 Apr 10 May 15 
0 2 4 6 8 10 0 5 10 15 20 25
Million cells L -1 Thousands cells L -1

24 
Figure 3-16. Mean nearfield abundance of Phaeocystis pouchetii, 1992–2012 . (Top) winter-spring.
(Bottom) summer. 
Centric diatom abundance peaked in September or October in all regions except the
northern, offshore stations, where abundance was highest in June. No large winter-
spring diatom bloom occurred in any region, but the September bloom, dominated by 
Skeletonema spp., was large enough that annual centric diatom abundance was near
the long-term mean. The June bloom in northern waters was dominated by 
Thalassiosira spp. and Chaetoceros spp., primarily Chaetoceros socialis . That bloom
exceeded past Chaetoceros abundances in that region. 
Dinoflagellate abundances in 2012 were also approximately equal to the long-term
mean. The toxic dinoflagellate Alexandrium fundyense occurred at low levels in
April and June, but bloomed in May (Figure 3-17). Alexandrium fundyense blooms
have occurred regularly in Massachusetts Bay since 2005 (Figure 3-18). Levels in
2012 reached above the 100 cells/L limit that triggers Alexandrium rapid-response
surveys. 
1
10
100
1,000
10,000
100,000
1,000,000
10,000,000 
Winter-spring Phaeocystis (cells/l) 
1
10
100
1,000
10,000
100,000
1,000,000 
Summer Phaeocystis (cells/l) 
baseline outfall discharge caution threshold

25 
Figure 3-17. Alexandrium fundyense bloom in 2012. The late spring storm ended the bloom rather
than bringing cells in from the Gulf of Maine. 
Figure 3-18. Nearfield abundance of Alexandrium fundyense, 1992–2012. 
1
10
100
1,000
10,000
100,000 
Alexandrium per sample (cells/l +1 ) 
baseline outfall discharge caution threshold

26 
While the timing and relatively low magnitude of the 2012 bloom on a New England-
wide scale had been forecast by Woods Hole researchers (based on measurements of
cyst abundance in the fall of 2011), the spatial pattern in Alexandrium abundance and
in paralytic shellfish poisoning (PSP) toxicity in Massachusetts Bay was unusual.
The normal progression for Alexandrium blooms is that they develop in coastal
Maine waters when cysts germinate and begin to multiply. The bloom then follows
coastal currents south to New Hampshire and Cape Ann. If wind conditions are right,
a bloom in those coastal waters can be swept into Massachusetts Bay. 
In 2012 the highest cell abundances were observed in Boston Harbor, the western
portions of the nearfield, and along the Boston south shore, while counts in northern
Massachusetts Bay were consistently much lower (i.e. the bloom did not begin in the
north and move south). Also, while the bloom caused PSP toxicity and closed beds
from Salem to Duxbury, there were no closures on the north shore. 
When MWRA discussed the bloom and the Contingency Plan threshold exceedance
with regulators and OMSAP at its April 1, 2013 meeting, Panel members requested
MWRA review the available data further to address whether effluent nutrients might
have contributed to the unusual spatial pattern of the bloom. That review found no
evidence effluent nutrients played a major role in causing the bloom. Effluent
nutrient loading before and during the bloom were well within historic ranges for that
time of year including the loading of ammonium, the effluent nutrient most
immediately available to stimulate phytoplankton growth. The temporal and spatial
patterns of nutrients before and during the 2012 Alexandrium bloom were well within
the ranges observed during previous years, including years in which Alexandrium 
bloomed in Massachusetts Bay and years when it did not. High concentrations of
nutrients did not extend further south from the outfall than is normally observed (~10-
20 km). 
As noted previously, 2012 was a dry year, with lower river discharges during the
spring than occurs most years. Coupled with the weak and upwelling favorable winds
experienced around the time of the bloom, this may have slowed circulation and
increased residence times of the early season pulse of cells within Massachusetts Bay,
allowing time for the small population of cells to grow to bloom levels. These weak
winds also prevented transportation south of elevated cell abundances seen off the
coast of Maine in late May. Unfortunately, the available data do not allow
conclusions to be drawn as to the causes of this unusual bloom. It is important to note
that even for an organism like Alexandrium , which has been extensively studied for
decades because of its impacts on the shellfish industry, gaps remain in our
understanding of all the factors involved in a bloom. 
Zooplankton Communities 
The 2012 abundances, species composition, and seasonal progressions of the
zooplankton communities fell within the general patterns of past years, with highest
abundances in June, July, and August (Figure 3-19) (Libby et al. 2013). Total
abundance during the first survey in February was somewhat higher than typical,

27 
possibly due to the warm, dry winter and possibly also an end result of an early,
undetected diatom bloom (Figure 3-20). 
Total zooplankton abundance in February and continuing through the year was
dominated by the small copepod Oithona similis and by total copepod nauplii,
copepodites, and adults. Oithona feeds primarily upon microzooplankton, mostly
protozoans, rather than on phytoplankton. The dominant abundance of this species in
Massachusetts Bay and in other ecosystems around the world has been recognized
only recently, because it is too small to be sampled by many conventional protocols. 
Figure 3-19. Total zooplankton abundance in 2012. 
Feb 06 Mar 20 Apr 10 
May 15 Jun 19 Jul 26 
Aug 21 Sep 06 Oct 23 
0 30000 60000 90000 120000 150000
Individuals m -3

28 
Figure 3-20. Nearfield abundance of total zooplankton, Oithona similis , and Calanus
finmarchicus in 2011 (dashed red line) and 2012 (solid black line) compared to past
years . Total zooplankton, dominated by Oithona similis , were relatively abundant in 2012. 
Calanus finmarchicus was almost absent in 2012, following a relatively abundant year in
2011. 
Jan Mar May Jul Sep Nov Jan
0
2
4
6
8
10
12
14
16
10,000 individuals/m3
TOTAL ZOOPLANKTON 
Jan Mar May Jul Sep Nov Jan
0
1
2
3
4
5
6
7
8
10,000 individuals/m3
Oithona 
Jan Mar May Jul Sep Nov Jan
0
0.5
1
1.5
2
10,000 individuals/m3
Calanus finmarchicus 
Total zooplankton 
Oithona similis 
Calanus finmarchicus

29 
Larger abundant zooplankton taxa typically include Calanus finmarchicus , Acartia 
spp., and barnacle nauplii. Calanus finmarchicus and Acartia spp. were almost
absent in the nearfield in 2012, following a year in which they were relatively
abundant. Acartia spp. were abundant only in Boston Harbor. The dearth of Calanus
finmarchicus , a known food for right whales, did not appear to affect whale
abundance, as sightings by the Center for Coastal Studies remained relatively high
(see Section 6, Special Studies). 
Time-series analysis of the zooplankton abundance data have shown that there was a
decline throughout the bays during 2001–2006, but populations have rebounded since
that period (Figure 3-18). Total abundance is now greater than the long-term mean.
The 2001–2006 decline in total zooplankton largely reflected lower numbers of
copepods during those years. Total copepod abundance has rebounded along with
total zooplankton abundance. Reasons for such long-term trends are not well
understood but occur on broad regional scales. There is no suggestion that the outfall
discharge has affected zooplankton abundance or species composition in
Massachusetts Bay. 
Figure 3-21. Long-term trend in zooplankton abundance and multi-year mean derived from a
time-series analysis. Data are from Stations N04 and N18. 
0
10000
20000
30000
40000
50000
60000
70000
1995 2000 2005 2010 2015 
Total zooplankton (animals m -3 ) Trend
Multi-year mean

30 
Stellwagen Bank National Marine Sanctuary 
The NPDES permit to discharge from DITP into Massachusetts Bay requires annual
reporting on results that are relevant to the Stellwagen Bank National Marine
Sanctuary. Two stations are most relevant to the sanctuary, Station F22 in Stellwagen
Basin to the northwest of the sanctuary and Station F29 on the sanctuary’s southern
boundary. 
MWRA monitors dissolved oxygen concentration and saturation in Stellwagen Basin
as Contingency Plan requirements. Bottom dissolved oxygen concentrations were
low throughout 2012, the lowest measured during the monitoring program in late
spring and early summer (Figure 3-22) (Libby et al. 2013). These levels reflected the
warm, saline conditions found throughout the region in 2012. 
Figure 3-22. Bottom water dissolved oxygen concentrations in Stellwagen Basin in 2012
compared to the previous years of monitoring. 
Besides survey data, buoy data and model outputs are useful in determining water
quality conditions throughout Massachusetts Bay, including the sanctuary. Data from
the deep oxygen sensor on the NERACOOS Buoy A01, within the sanctuary,
documented the return to oxygenated conditions with fall mixing (see Figure 3-8 and
Section 6, Special Studies). 
Figure 3-23 shows the location of a transect running west to east across the
Massachusetts Bay outfall and Stellwagen Bank, and Figures 3-24 through 3-27
depict modeled water quality parameters, including dissolved oxygen, dissolved
oxygen saturation, dissolved inorganic nitrogen, and chlorophyll, along that transect.

31 
Figure 3-23. Location of west-east transect from Deer Island, across MWRA outfall, through
Stellwagen Bank, for modeled water-quality parameters presented in Figures 3-24 through 3-27. 
The model outputs supported predictions that there would be no indication of any
effect of the outfall for most parameters, even in the nearfield, and no evidence of
effects on the sanctuary. The model projects no effects of the outfall on dissolved
oxygen concentration or saturation in any month. Elevated levels of dissolved
inorganic nitrogen can be detected but only in the immediate vicinity of the outfall,
with no influence on the sanctuary. Modeled chlorophyll levels show increased
levels across the region in March at the time of the Phaeocystis bloom but no relation
with the outfall. Note that the model tends to show less variation in chlorophyll
values (such as a lower peak during the spring bloom and less difference from surface
to bottom) than the field observations, but it generally captures the seasonal and
geographic patterns.

32 
Figure 3-24. Modeled dissolved oxygen concentration (mg/L) on the west-east transect across the
MWRA outfall and Stellwagen Bank National Marine Sanctuary at the end of each month from
January through December 2012.

33 
Figure 3-25. Modeled percent dissolved oxygen saturation on the west-east transect across the
MWRA outfall and Stellwagen Bank National Marine Sanctuary at the end of each month from
January through December in 2012.

34 
Figure 3-26. Modeled dissolved inorganic nitrogen concentrations ( μ M) on the west-east transect
across the MWRA outfall and Stellwagen Bank National Marine Sanctuary at the end of each
month from January through December in 2012.

35 
Figure 3-27. Modeled chlorophyll concentrations (μg/L) on the west-east transect across the
MWRA outfall and Stellwagen Bank National Marine Sanctuary at the end of each month from
January through December in 2012.

36 
The Center for Coastal Studies monitoring program in Cape Cod Bay includes
MWRA Station F29, on the southern boundary of the sanctuary as well as MWRA
stations F01 and F02 in Cape Cod Bay. Major groups of phytoplankton and
zooplankton followed similar abundance patterns at all three stations throughout the
year (Figures 3-28 and 3-29). Phytoplankton samples showed dominance of
microflagellates at all three stations during much of the year. Samples also confirmed
the fall diatom bloom. 
Cape Cod Bay zooplankton sampling focuses on larger species than targeted by
Massachusetts Bay sampling. The sampling techniques do not capture smaller
copepods, such as the Oithona similis seen in MWRA’s Massachusetts Bay samples,
but focuses on larger species, which are favored whale prey. Abundances of several
larger species were lower than in 2011. Similar to the MWRA program, the large
species Calanus finmarchicus was not abundant in any month. 
Figure 3-28. Surface-water phytoplankton abundance and composition at MWRA Cape Cod Bay
stations, including Station F29 near Stellwagen Bank National Marine Sanctuary. (Data from the
Center for Coastal Studies) 
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
F01
F02
F29
F01
F02
F29
F01
F02
F29
F01
F02
F29
F01
F02
F29
F01
F02
F29
F01
F02
F29
F01
F02
F29
F01
F02
F29 
Million cells per liter 
Microf lagellate
Dinof lagellate
Cryptophyte
Pennate Diatom
Centric Diatom 
Feb Mar Apr May Jun Jul Aug Sep Oct

37 
Figure 3-29. Zooplankton abundance and composition at MWRA Cape Cod Bay stations,
including Station F29 near Stellwagen Bank National Marine Sanctuary. ( Data from the Center
for Coastal Studies) 
Contingency Plan Thresholds 
Most water-quality parameters were within normal ranges throughout 2012. Bottom
water dissolved oxygen concentrations were consistent with the normal seasonal
pattern but were low in comparison to past years, reaching minima that were only
slightly above the Contingency Plan threshold baselines (Table 3-1). The low levels
were due to the warm, dry conditions found in 2012 and not affected by the outfall.
There were two exceedances of nuisance phytoplankton species thresholds, when
samples collected in May exceeded the Phaeocystis pouchetii summer and 
Alexandrium fundyense caution levels. The Phaeocystis exceedance resulted from the
early bloom lingering into May (which is considered summer for threshold
calculation). The Alexandrium exceedance had been anticipated, based on
information on overwintering Alexandrium cysts in the sediments off the coast of
Maine and spring measurements of Alexandrium cells in coastal waters of Maine and
New Hampshire. Results from rapid-response surveys indicated that the bloom
proceeded in a pattern that was different from historic progressions, but the available
data do not allow conclusions to be drawn as to the causes of this unusual bloom. 
0
1000
2000
3000
4000
5000
6000
F01
F02
F29
F01
F02
F29
F01
F02
F29
F01
F02
F29
F01
F02
F29
F01
F02
F29
F01
F02
F29
F01
F02
F29
F01
F02
F29 
Individuals per m3 
Acartia
Temora
Pseudocalanus
Centropages
Calanus 
Feb Mar Apr May Jun Jul Aug Sep Oct

38 
Table 3-1. Contingency Plan threshold values and 2012 results for water-column monitoring . 
DO = dissolved oxygen 
Location/ 
Parameter 
Specific
Parameter Baseline Caution Level Warning
Level 
2012 
Results 
Bottom water
nearfield 
Dissolved
oxygen
concentration 
Background 5 th
percentile 
6.05 mg/L 
Lower than 6.5
mg/L for any
survey (June-
October) unless
background
conditions are
lower 
Lower than 6.0
mg/L for any
survey (June-
October) unless
background
conditions are
lower 
Lowest survey
mean = 6.19 mg/L 
Dissolved
oxygen percent
saturation 
Background 5 th
percentile 
65.3% 
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 = 67.5% 
Bottom water
Stellwagen
Basin 
Dissolved
oxygen
concentration 
Background 5 th
percentile 
6.23 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 = 6.6 
mg/L 
Dissolved
oxygen percent
saturation 
Background 5 th
percentile 
67.2% 
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 = 70.4% 
Bottom water
nearfield 
DO depletion
rate (June-
October) 
0.024 mg/L/d 0.037 mg/L/d 0.049 mg/L/d 0.022 mg/L/d 
Chlorophyll
nearfield 
Annual 72 mg/m 2 108 mg/m 2 144 mg/m 2 96 mg/m 2 
Winter/spring 50 mg/m 2 199 mg/m 2 None 144 mg/m 2 
Summer 51 mg/m 2 89 mg/m 2 None 69 mg/m 2 
Autumn 90 mg/m 2 239 mg/m 2 None 78 mg/m 2 
Nuisance
algae
nearfield 
Phaeocystis
pouchetii 
Winter/spring 622,000 cells/L 2,860,000 cells/L None 1,690,000 cells/L, 
Summer 72 cells/L 357 cells/L None 
1,120 cells/L, 
caution level
exceedance 
Autumn 370 cells/L 2,960 cells/L None Absent 
Nuisance
algae
nearfield 
Pseudo-
nitzschia 
Winter/spring 6,735 cells/L 17,900 cells/L None 526 cells/L 
Summer 14,635 cells/L 43,100 cells/L None 388 cells/L 
Autumn 10,050 cells/L 27,500 cells/L None 2,820 cells/L 
Nuisance
algae
nearfield 
Alexandrium
fundyense 
Any nearfield
sample 
Baseline
maximum = 
163 cells/L 
100 cells/L None 
3,731 cells/L,
caution level
exceedance 
Farfield PSP toxin
extent Not applicable New incidence None No new incidence

39 
4. Sea Floor 
Sea-floor monitoring in 2012 included soft-bottom sampling for sediment conditions
and infauna at 14 stations and sediment-profile imaging at 23 stations (Figures 4-1
and 4-2). 
Figure 4-1. Soft-bottom monitoring stations. Fourteen stations were sampled for benthic community
parameters and sediment characteristics. Also shown are the instrumented buoys, the MWRA outfall
diffuser, and the Stellwagen Bank National Marine Sanctuary.

40 
Figure 4-2. Sediment-profile imaging stations. Twenty-three stations are monitored. Also shown are
the NDBC buoy and the MWRA outfall diffuser.

41 
Sampling for grain-size composition, total organic carbon, the effluent tracer 
Clostridium perfringens spores, and benthic infauna was completed during August,
following the revised monitoring plan implemented in 2011 (MWRA 2010, Werme et
al. 2012). Sediment and infauna sampling included one station in the “transition”
area, located between Boston Harbor and the nearfield stations (FF12); four nearfield
stations located within two kilometers of the outfall (NF13, NF14, NF17, NF24); six
nearfield stations located within Massachusetts Bay but farther than two kilometers
from the outfall (NF04, NF10, NF12, NF20, NF21, NF22); and three farfield
reference stations located in Massachusetts Bay and Cape Cod Bay (FF01A, FF04,
and FF09). For the purposes of threshold testing, “nearfield” includes the transition
station, as well as both groups of nearfield stations, for a total of eleven stations. The
new design provides greater consistency than the one it replaced, in which different
sets of soft-bottom stations were sampled in alternate years. 
Sediment-profile images were made on August 12. The images were used to measure
the apparent reduction-oxidation (redox) potential discontinuity (RPD) depth,
apparent successional stage of the community, and an organism sediment index which
is derived from the RPD depth and the successional stage. 
Sediment Characteristics and Tracers 
Grain-size distributions of sediment samples in 2012 remained consistent with results
from past years, ranging from silt and clay at some stations to mostly sand at others
(Nestler et al. 2013). Percent organic carbon content in the samples was also
consistent with past results at most stations, with higher mean total organic carbon
concentrations at stations with finer sediments. Total organic carbon concentrations
showed no signs of organic enrichment from the effluent discharge, even at stations
closest to the outfall. 
As in past years since the outfall came on line (except 2006), it was possible to detect
elevated levels of the effluent tracer, Clostridium perfringens spores, at the stations
located closest to the outfall, although even at these stations, concentrations fell
within the baseline range (Figures 4-3 and 4-4). Concentrations of Clostridium
perfringens spores were highest at Stations NF13 and NF24, both located within two
kilometers of the outfall. Overall, there has been a large decline in Clostridium
perfringens spores at the transition station FF12 since the baseline period. A smaller
decline may also be apparent in the nearfield samples farther from the outfall, while
concentrations at farfield locations have remained stable. A concurrent monitoring
program for Boston Harbor has documented declines in Clostridium spore counts
throughout the Boston Harbor Project, with 2012 spore counts remaining consistently
below historic levels (Pembroke et al. 2013).

42 
Figure 4-3. Concentrations of Clostridium perfringens spores, normalized for sediment grain size,
in 2012. 
Figure 4-4. Mean concentrations of Clostridium perfringens spores during the baseline and
outfall-discharge years. Tran = transition area, stations located between Boston Harbor and the
nearfield; NF<2km = stations within 2 km of the outfall; NF>2km = nearfield stations greater than 2
km from the outfall; FF = farfield stations offshore from the outfall

43 
Soft-bottom Communities 
The soft-bottom communities continued to show no response to the outfall relocation
(Nestler et al. 2013). Monitoring has shown that community structure is determined
primarily by grain-size distribution of the sediments and by natural fluctuations in
populations. Data from 2012 were consistent with past years’ results. 
Sampling and analysis of the 14 samples taken in 2012 yielded 27,114 organisms,
classified into 210 species and 30 other taxonomic groups. The numbers of
organisms per sample were higher than found in 2010 and 2011 in all regions and
comparable to the historic means (Figure 4-5). Relative abundances of the five
dominant species in the samples, those contributing at least 5% to total abundance
numbers, were low in 2012, as they has been for several years (Figure 4-6). In
particular, the polychaete Prionospio steenstrupi , which was the numerically
dominant species during much of the 1990s and 2000s, was present in low numbers. 
Figure 4-5. Mean infaunal abundance per sample in four areas of Massachusetts Bay, 1992–2012. 
Tran = transition area, stations located between Boston Harbor and the nearfield; NF<2km = stations
within 2 km of the outfall; NF>2km = nearfield stations greater than 2 km from the outfall; FF =
farfield stations offshore from the outfall 
Total Abundance
0
500
1000
1500
2000
2500
3000
3500
4000
4500 Outfall Startup
1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012
Tran
NF <2km
NF >2km
FF

44 
Figure 4-6. Mean abundance per sample of five dominant species and total abundance at
nearfield stations, 1992–2012. 
A series of multivariate analyses assessed spatial and temporal patterns in the
communities and found no particular species or type of community that could be
specifically associated with the outfall. A cluster analysis, which identified six
separate faunal assemblages in the region, found that three of those species groups
occurred at stations within two kilometers of the outfall but also at stations farther
away. Species distributions were largely determined by sediment types. 
Temporal analyses suggested that species assemblages have varied little since 1992
and that samples were most similar to others collected from the same station over
time. These analyses are discussed further under in the subsection addressing
Stellwagen Bank National Marine Sanctuary below.

45 
Sediment-profile Imaging 
Sediment-profile imaging measurements continued to show no adverse effects of the
outfall (Nestler et al. 2013). Monitoring has shown that physical processes, such as
storms and storm-induced sediment transport, are the primary stressors on the sea
floor. The dominance of physical forces may be considered typical of outfalls that
have been located in high-energy areas that promote rapid dispersion of effluent. 
The RPD depth (the depth to which oxygen penetrates into sediments as determined
by color changes) remained deeper than the baseline mean, as it has been during most
outfall-discharge years (Figure 4-7). The environmental concern before the outfall
came on line was that the RPD depth would become shallower, so a deeper RPD
depth continues to indicate that there has been no adverse effect from the discharge. 
Figure 4-7. Annual apparent color RPD depth for data from nearfield stations. The mean RPD for
the outfall-discharge years is slightly deeper than the baseline mean, indicating that there has been no
adverse effect from the discharge. SD = standard deviation 
The sediment-profile images also found no indications of organic carbon
accumulation and no adverse effects on the types of organisms inhabiting the
sediments. There is no evidence of organic carbon accumulation, even at stations
located close to the outfall (Figure 4-8). If organic carbon concentrations were
increasing in the sediments, the images would show increased darkening at the
sediment surface, but the images continue to show light-colored, oxygenated surface
sediment. 
-6
-5
-4
-3
-2
-1
0 
RPD (cm) 
Mean RPD Depth +/- 1SD
Outf all Startup
Threshold

46 
Figure 4-8. Thumbnail images from Station NF24, located within two kilometers of the
outfall. There are no indications of increased organic carbon content or other outfall effects.
Black hash marks are at five-centimeter intervals in images made prior to 2006 (many are
quite faint). Hash marks in recent images are at one-centimeter intervals. 
Stellwagen Bank National Marine Sanctuary 
The NPDES permit to discharge from DITP into Massachusetts Bay requires annual
reports on results that are relevant to the Stellwagen Bank National Marine Sanctuary.
One MWRA sea-floor station lies within the sanctuary, in Stellwagen Basin, which is
a long-term sediment sink (FF04, see Figure 4-1). Station FF09 is adjacent to the
basin, southeast of the outfall diffusers. A third sea-floor station (FF01A) is just
northwest of the sanctuary boundary. No large or unexpected changes in bottom-
community parameters have been measured within or near the sanctuary since the
outfall came on line.

47 
Sediment conditions have not changed at Station FF04, and the deep-water station
continued to support infaunal communities typical of the monitoring program (Nestler
et al. 2013). As would be expected because of its depth, there are some differences
from the shallower communities in the nearfield and elsewhere in Massachusetts Bay.
Multivariate analyses of soft-bottom fauna showed that Station FF04 has consistently
contained a somewhat distinct infaunal community, in that its samples group together,
apart from samples from other stations (Figure 4-9). Community differences at
Station FF04 in 2010, 2011, and 2012 compared to earlier years may reflect the
decreases in the abundant polychaete Prionospio steenstrupi , which has decreased in
numbers throughout the region. 
The separate grouping reflects Station FF04’s deepwater, silty sediment, typical for
Stellwagen Basin, whereas many shallower stations are sandier. Monitoring during
1992–2010 showed the faunal community currently found at Station FF04 to be
widespread throughout deeper waters, with similar faunal assemblages occurring at
all stations with water depths greater than 70 meters. 
Figure 4-9. Soft-bottom community data superimposed on a non-metric multidimensional scaling
plot, a multivariate analyses tool. Each point represents one sample collected during 1992–2012.
Similarity of species composition is indicated by proximity of the points on the plot. Station FF04
(located within Stellwagen Basin and almost 30 km southeast of the outfall), has consistently
maintained a unique fauna in comparison to sandier stations NF13 (about 2 km north of the outfall),
NF24 (less than 2 km south of the outfall), and FF01A (more than 20 km northeast of the outfall).

48 
Contingency Plan Thresholds 
RPD depth was more than twice as deep as the caution level, and percent opportunists
among the soft-bottom community remained far below caution and warning levels.
However, for a third consecutive year, there were Contingency Plan threshold
exceedances for sea-floor community parameters (Table 4-1). Values for two
threshold parameters, Shannon-Wiener diversity and Pielou’s evenness, were higher
than the caution-level ranges (Figure 4-10). Two other community threshold
parameters, total number of species per sample and Fisher’s log-series alpha, were
within the caution-level ranges. 
Similar exceedances of Shannon-Wiener diversity and Pielou’s evenness thresholds
were observed in 2010 and 2011 and evaluated in consultation with the Outfall
Monitoring Science Advisory Panel (OMSAP). Those evaluations found that the
2010 and 2011 exceedances probably resulted from natural fluctuations in the
communities and that they were not related to any outfall effect. 
Spatial and temporal analyses showed that the increases in Shannon-Wiener diversity
and Pielou’s evenness did not result from changes at the stations closest to the outfall.
Instead, the threshold exceedances were driven by data from nearfield stations that
are farther away, more than two kilometers from the outfall and less likely to be
influenced by the discharge. Region-wide declines in the abundance of the
numerically dominant species, particularly the spionid polychaete Prionospio
steenstrupi , are likely important factors in the recent increases. 
Increases in Shannon-Wiener diversity and Pielou’s evenness can be a signal of
improvements rather than degradation in environmental conditions. However, the
Contingency Plan community measures thresholds were selected to be triggered by
any results that would indicate a change from baseline conditions, and consequently,
they have upper as well as lower bounds. 
Table 4-1. Contingency Plan threshold values and 2012 results for sea-floor monitoring. 
Location/
Parameter
Type 
Parameter Caution Level Warning Level 2012 Results 
Nearfield RPD depth <1.18 cm None 3.441 cm 
Even years, 
benthic
diversity,
nearfield 
Species per sample 442.99 or >81.85 None 73.45 
Fisher’s log-series
alpha <9.42 or >15.8 None 15.68 
Shannon-Wiener
diversity <3.37 or >3.99 None 4.36, caution level
exceedance 
Pielou’s evenness <0.57 or >0.67 None 0.70, caution level
exceedance 
Benthic
opportunists % opportunists >10% >25% 0.16 %

49 
Figure 4-10. Annual community parameters with nearfield Contingency Plan thresholds. The
varied symbols represent differences in the stations sampled over the years of the program. Results
were tested against thresholds calculated for each sampling design, but only the current threshold
values are shown. Except for the percent opportunists threshold, which is based on levels in Boston
Harbor, thresholds have both upper and lower bounds show potentially meaningful changes from the
baseline. SD = standard deviation 
30
50
70
90 Species per sample 
6
10
14
18 Fisher's log-series alpha 
2.5
3.0
3.5
4.0
4.5
5.0 Shannon-Wiener diversity 
0.4
0.5
0.6
0.7
0.8 Pielou's evenness 
0
3
6
9
12 Percent opportunists
Baseline mean Thresholds
Mean +/-1SD Outfall startup

50 
5. Fish and Shellfish 
Each year MWRA monitors the health of winter flounder from Deer Island Flats in
Boston Harbor, off Nantasket Beach just outside the harbor, the Massachusetts Bay
outfall site, and eastern Cape Cod Bay. Every three years, including 2012,
monitoring includes chemistry measurements in flounder fillets and liver, lobster
meat and hepatopancreas, and blue mussel tissue. Lobsters are sampled from Deer
Island Flats, the outfall site, and Cape Cod Bay. Mussels are deployed at two sites
near the outfall, at Deer Island Light, and in Boston’s inner harbor (Figure 5-1). 
Figure 5-1. Fish-and-shellfish monitoring stations. Also shown are the two instrumented buoys, the
MWRA outfall diffuser, and the boundaries of the Stellwagen Bank National Marine Sanctuary.

51 
Flounder Health 
Annual flounder monitoring focuses on the presence of early liver disease and liver
neoplasms (tumors). Other indications of health are also documented. In April 2012,
50 sexually mature flounder were collected from each site (Moore et al. 2012). Catch
per unit effort remained low near the outfall and off Nantasket Beach, as has been
typical, and there was a small decrease in eastern Cape Cod Bay, although the catches
there remained the highest of the regions. Catch per unit effort increased at Deer
Island Flats to the highest levels observed since 2005. Abandoned fishing gear
continued to interfere with catches at the outfall site and Deer Island Flats. 
Average ages, lengths, and weights of the winter flounder collected from near the
outfall site in 2012 were lower than in most years. Average age fell at all locations
except Deer Island Flats, but remained within the historic range for the monitoring
program. As they have been throughout most of the monitoring program, the catches
continued to be dominated by females. The percent females increased at all sites, to
more than 95% at Nantasket Beach and eastern Cape Cod Bay. 
External condition measures also fell within historic ranges. Prevalence of fin
erosion, a condition that can be indicative of elevated concentrations of ammonium
and other pollutants, was highest at Deer Island Flats and within the historic range of
the monitoring program, continuing to be much lower than had been observed in
other studies during the 1980s. The greatest percentage of another common
condition, bent fin ray, also occurred at Deer Island Flats. Incidence of blind-side
ulcers, which were first noted in 2003, decreased substantially from 2011 and were
present only at Nantasket Beach and the outfall site. 
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 studies during
the 1980s. Neoplasia has never been observed in a 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. Incidence of CHV, corrected for age, continued to drop in fish taken
near the outfall site after a gradual increase observed during 2005–2010 (Figure 5-2).
CHV incidence in fish from Deer Island Flats remained lower than the relatively high
baseline levels and about the same as was measured in 2011. Average severity of
CHV also remained lower than baseline levels.

52 
Figure 5-2. Annual prevalence of centrotubular hydropic vacuolation (CHV), corrected for age. 
DIF = Deer Island Flats, NB = Nantasket Beach, OS = Outfall site, ECCB = Eastern Cape Cod Bay 
Fish and Shellfish Chemistry 
Samples for chemical analyses of winter flounder tissues were taken from the same
April collections made for the health assessments (Hall et al. 2013). 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 and polycyclic aromatic hydrocarbons (PAHs). 
Lobsters were collected by local lobstermen in August and October. Three replicates
of lobster meat and hepatopancreas were composed of tissues from seven lobsters
from each site and were analyzed for PCBs, pesticides, and mercury. Hepatopancreas
samples were also analyzed for metals and PAHs. 
Mussels were collected in June from a reference location at Pemaquid Point, Maine,
and deployed in cages for 60 days, ending in late August. Mussel tissues were
analyzed for PCBs, pesticides, PAHs, mercury, and lead. 
Concentrations of organic compounds in flounder fillets and livers remained low, as
they have been throughout the monitoring program. Concentrations of the banned
organochlorine pesticides, DDT and chlordane, and their breakdown products
continued to show long, slow, region-wide declines in most samples. Concentrations
of PCBs in fillet samples from Deer Island Flats, Nantasket Beach, and the outfall site
were higher than in most past years, but within the range for the monitoring program
(Figure 5-3). PCB levels also increased in liver samples but were lower than those
measured in 1995 at all sites (Figure 5-4). 
0%
2%
4%
6%
8%
10%
12%
14%
1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 
%CHV/mean age 
DIF
NB
OS
ECCB 
outf all startup

53 
Figure 5-3. PCBs in flounder fillets, 1995–2012. DIF = Deer Island Flats, NB = Nantasket Beach, 
OS = Outfall site, ECCB = Eastern Cape Cod Bay 
Figure 5-4. PCBs in flounder livers, 1995–2012. DIF = Deer Island Flats, NB = Nantasket Beach, 
OS = Outfall site, ECCB = Eastern Cape Cod Bay 
0
200
400
600
800
1,000
1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 
ng/g dry wt 
DIF
NB
OS
ECCB
outf all startup 
0
2,000
4,000
6,000
8,000
10,000
12,000
1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 
ng/g dry wt 
DIF
NB
OS
ECCB
outf all startup

54 
In contrast, PCB levels in lobster tissues were among the lowest measured throughout
the monitoring program. PCB concentrations in lobster meat samples were low at all
three sites (Figure 5-5). Concentrations in hepatopancreas samples were similarly
low. Concentrations of other organic contaminants in lobster samples were also very
low, continuing to reflect long, slow declines, while metals levels continued to have
less predictable spatial and temporal patterns. 
Figure 5-5. PCBs in lobster meat, 1994–2012. DIF = Deer Island Flats, OS = Outfall site, ECCB =
Eastern Cape Cod Bay 
Deployed mussels also showed historically low levels of PCBs (Figure 5-6).
Concentrations of other organic compounds were also low. Total chlordane, which
was not detected in the source mussels, bioaccumulated at all sites, but to similarly
low levels except the Boston inner harbor. Mussels from the inner harbor also
accumulated higher levels of DDT, PAHs, mercury, and lead. Lead levels at all sites
except the inner harbor were very low, even lower than detected in the source mussels
(Figure 5-7). 
0
200
400
600
800
1,000
1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 
ng/g dry wt 
DIF
OS
ECCB
outf all startup

55 
Figure 5-6. PCBs in deployed mussels, 1991–2012. DIL = Deer Island Light; OSM = Outfall site,
four locations just south of the diffuser heads; LNB = Buoy B, one kilometer south of the outfall 
Figure 5-7. Lead in deployed mussels, 2012. Levels at the outfall site were lower than those found at
the reference site. PE = reference site at Pemaquid Point, Maine; LNB = Buoy B, one kilometer south
of the outfall; OSM = Outfall site, four locations at the edge of the mixing zone; DIF = Deer Island
Flats; IH = Boston inner harbor 
0
100
200
300
400
1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 
ng/g dry wt 
DIL
OSM
LNB
outf all startup 
0
1
2
3
4
PE LNB OSM DIF IH 
μg/g dry wt

56 
Contingency Plan Thresholds 
There were no Contingency Plan threshold exceedances for fish and shellfish in 2012
(Table 5-1). Incidence of CHV, the most common indicator of liver disease in the
winter flounder of the region, was 12% in fish taken from the vicinity of the outfall
site, lower than the caution threshold and less than half the baseline average.
Chemistry threshold parameters values were lower than the thresholds for every
parameter and also lower than baseline averages for every parameter except for PCBs
in flounder fillets. 
Table 5-1. Contingency Plan threshold values and 2012 results for fish-and-shellfish monitoring. 
Parameter
Type/ 
Nearfield 
Parameter Baseline Caution
Level 
Warning
Level 
2012
Results 
Flounder disease Liver disease
(CHV) 24.4% 44.9% None 12% 
Flounder meat 
PCB 0.033 ppm 1 ppm 
wet weight 
1.6 ppm 
wet weight 0.0413 ppm 
Mercury 0.074 ppm 0.5 ppm 
wet weight 
0.8 ppm 
wet weight 0.0646 ppm 
Flounder liver 
lipid normalized 
Chlordane 242 ppb 484 ppb None 73.6 ppb 
Dieldrin 63.7 ppb 127 ppb None 0 ppb 
DDT 775.9 ppb 1552 ppb None 369 ppb 
Lobster meat 
PCB 0.015 ppm 1 ppm 
wet weight 
1.6 ppm 
wet weight 0.0086 ppm 
Mercury 0.148 ppm 0.5 ppm 
wet weight 
0.8 ppm 
wet weight 0.115 ppm 
Lobster
hepatopancreas 
lipid normalized 
Chlordane 75 ppb 150 ppb None 0 ppb 
Dieldrin 161 ppb 322 ppb None 0 ppb 
DDT 341.3 ppb 683 ppb None 45.1 ppb 
Mussel tissue 
PCB 0.011 ppm 1 ppm 
wet weight 
1.6 ppm 
wet weight 0.0024 ppm 
Lead 0.415 ppm 2 ppm 
wet weight 
3 ppm 
wet weight 0.216 ppm 
Mercury 0.019 ppm 0.5 ppm 
wet weight 
0.8 ppm 
wet weight 0.0161 ppm 
Mussel tissue 
lipid normalized 
Chlordane 102.3 ppb 205 ppb None 40.5 ppb 
Dieldrin 25 ppb 50 ppb None 0 ppb 
DDT 241.7 ppb 483 ppb None 33 ppb 
PAH 1080 ppb 2160 ppb None 1020 ppb

57 
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. Special studies in 2012 included evaluation of marine debris observations
at the outfall site in 2000–2012; continuous monitoring results from instrumented
buoys; evaluation of primary productivity models; Center for Coastal Studies
monitoring in Cape Cod Bay; and changes in eutrophication indicators in Boston
Harbor. 
Marine Debris Observations 
One environmental concern for the outfall was aesthetics, specifically that the outfall
would discharge unsightly, floating debris. After the outfall came on line in
September 2000 and through 2010, MWRA conducted visual observations and
sampled debris at the outfall and a reference site during all water-column surveys.
Sampling was made by net tows (Figure 6-1). 
Figure 6-1. Net used for sampling floatable marine debris. The net measures 1 x 2 meters, with
500-μm mesh.

58 
Routine sampling by nets ended with revisions to the monitoring plan in 2010. The
revised plan called for net tows following events in which some primary-only treated
effluent is blended with effluent that received full primary and secondary treatment
before discharge. The new plan also called for analyzing debris captured by the net
for organochlorine pesticides, PCBs, PAHs, and mercury. Four tows were conducted
in response to blending events in March 2011 and May and July 2012. 
From September 2000 through July 2012, MWRA conducted 136 marine debris
surveys, collecting 135 samples at a reference site and 134 samples at the outfall (Rex
and Delaney 2013). Debris was found at both the reference site and the outfall but
was detected in more samples from the outfall (Figure 6-2). In particular, fat particles
were more frequently detected at the outfall, with 49% of the samples from the outfall
having fat particles compared to only 5% at the reference site. Other types of debris
were found in more similar numbers in both the outfall and the reference tows.
Sightings of sewage-related floatable debris, such as tampon applicators and
condoms, were rare. 
Figure 6-2. Marine debris in net tow samples, 2000–2012. Different types of debris were sometimes
present in the same sample. “Plastic” includes plastic and latex-like material; “Paper” includes paper,
cellophane, string, and fabric. 
Chemical analyses of the fat particles did not detect significant quantities of
pesticides, PCBs, PAHs, or mercury. Even using conservative assumptions and
calculations, MWRA estimated that only small fractions of the already low total
effluent loadings of these contaminants to the bay could have come from the fat
particles. 
0
10
20
30
40
50
60
70
80
90
100
Plastic Paper Fat
Particles
Total with
debris
Total no
debris 
Number of samples 
Control
Outfall

59 
Based on the results from these studies, EPA and MADEP agreed to end net tows and
chemical analyses. Visual observations of floating debris continue. 
Continuous Monitoring Data 
In 2007, MWRA partnered with the National Data Buoy Center (NDBC) to add water
quality and oceanographic sensors to the NDBC Buoy 44013, a weather buoy located
seven kilometers southeast of the outfall, just east of MWRA’s water-column station
N07 (see Figure 3-1 in Section 3, Water Column). MWRA’s regulators, EPA and
MADEP, wanted continuous data from moored sensors communicated or
“telemetered” back to shore in real time as a method of “filling the gaps” between
surveys. 
The active shipping lanes into Boston Harbor pass right over the outfall, making ship
strikes a possibility for the surface buoy and antenna required for telemetered data.
However, the weather buoy is in a protected traffic-separation corridor and well-
known to ship operators. At the time of partnering with MWRA, NDBC was already
conducting a pilot study to add water quality and oceanographic sensors to selected
buoys nationwide, so adding sensors to Buoy 44013 met needs of both groups. 
Deployment of new sensors was completed in June 2009. During the spring through
fall months of 2009–2012, hourly temperature, salinity, water clarity, dissolved
oxygen, and chlorophyll fluorescence data were telemetered to NDBC. The water
quality sensors were not designed to survive freezing temperatures and were removed
in the winter. A subset of parameters was measured through the winter using
submerged sensors, but those data were not telemetered to shore. Despite its
protected location, a ship strike disabled NDBC Buoy 44013 for much of 2012. 
Comparisons of data from the NDBC Buoy 44013, from the other instrumented buoy
in the region (NERACOOS Buoy A01 off Cape Ann), and from surveys generally
showed good correspondence. Temperature (Figure 6-3, top) and salinity (not
shown) data from the buoys corresponded well with survey data. Dissolved oxygen
measurements from the NDBC buoy through 2011 tended to be slightly lower than
the shipboard survey data but showed the typical seasonal cycle (Figure 6-3, bottom).
Correspondence between the NERACOOS Buoy A01, which added dissolved oxygen
sensors at the end of 2011, and the survey data was relatively good. The limited
available 2012 data from both buoys compared relatively well with survey data. 
Except for their collaboration with MWRA, NDBC’s pilot study for adding
instruments to weather buoys ended in 2009. Their support for the MWRA
partnership ended in December 2012. MWRA, its regulators, and OMSAP are
determining the need for continuous monitoring data closer to the outfall.
Meanwhile, measurements at the NERACOOS Buoy A01 continue.

60 
Figure 6-3. Temperature (top) and dissolved oxygen (bottom) at the NERACOOS Buoy A01,
NDBC Buoy 44013, and during water quality surveys, June 2009 – December 2012. WC = water
column 
0
4
8
12
16
20
24 
Temperature (ºC) 
7
8
9
10
11
12
13 
Oxygen concentration (mg/l) 
NERACOOS Buoy A (2 m) WC stations (near Buoy A)
NDBC Buoy 44013 (0.5 m) WC stations (near Buoy 44013) 
NDBC Buoy 44013 (2.4 m)

61 
Primary Productivity Model Evaluations 
Through 2010, MWRA measured primary productivity at three stations, one at the
mouth of Boston Harbor (F23), one several kilometers to the northeast of the outfall
(N04), and one a kilometer to the south of the outfall (N18). (See Figure 3-1 in
Section 3, Water Column, for station locations.) In 2009, MWRA proposed ending
that special study, because the measurements were costly and results had found that
the relocated discharge did not result in detectable increased productivity near the
outfall. Regulators and their science advisory panel (OMSAP) concurred, but
requested that MWRA evaluate other, less costly approaches to assessing primary
productivity in marine waters. 
One alternative approach was to use a simple light-biomass model, known as BZpI0,
which had been developed for estuaries. BZpI0 multiplies the chlorophyll biomass
present in the photic zone (the BZp term) by the intensity of the sunlight hitting the
ocean surface (the I0 term). BZpI0 has been found to be a suitable replacement for
direct productivity measurements in many well-mixed coastal systems where the
amount of available light limits algal growth. 
Comparisons between BZpI0 and productivity measurements had already been
included in MWRA reports for 1992–2000. Those results were mixed, with good
correlations for some stations in some years but poor correlations for other stations
and years. 
A new evaluation of data from 2001–2010 found similar mixed results (Keay et al.
2013). Comparison of annual results found that some years showed a good
correlation between BZpI0 and field measurements, but others did not. Spatially, the
correlation was better for data from the station at the mouth of Boston Harbor than it
was for the offshore stations (Figure 6-4). Spring and fall data correlated better than
summer data (Figure 6-5). 
Overall, BZpI0 did not reflect the measured primary productivity well enough to
consider its use as a replacement for direct measurements. The variability in results
was not surprising, because BZpI0 is a simple model with assumptions that are
sometimes not met in Boston Harbor or Massachusetts Bay.

62 
Figure 6-4. Areal productivity and BZpI0 for individual stations. (a) F23, (b) N04, (c) N18 
Figure 6-5. A real productivity and BZpI0 for monitoring seasons. (a) Winter-spring: February –
April, (b) Summer: May – August, (c) Autumn: September – December 
R² = 0.4906
0
3000
6000
9000
12000
15000
0 1000 2000 3000 4000 5000 
BZpI0
Areal productivity
a 
R² = 0.462
0
3000
6000
9000
12000
15000
0 1000 2000 3000 4000 5000 
BZpI0
Areal productivity
c 
R² = 0.2037
0
3000
6000
9000
12000
15000
0 1000 2000 3000 4000 5000 
BZpI0
Areal productivity
b 
R² = 0.5251
0
3000
6000
9000
12000
15000
0 1000 2000 3000 4000 5000 
BZpI0
Areal productivity
a 
R² = 0.1061
0
3000
6000
9000
12000
15000
0 1000 2000 3000 4000 5000 
BZpI0
Areal productivity
b 
R² = 0.3881
0
3000
6000
9000
12000
15000
0 1000 2000 3000 4000 5000 
BZpI0
Areal productivity
c

63 
Cape Cod Bay Studies 
Since 2011, MWRA has collaborated with the Center for Coastal Studies at
Provincetown, which has had an extensive program to monitor Cape Cod Bay and its
shorelines since 2006. MWRA’s focus is on the portion of the program that provides
offshore water quality and plankton measurements. The Center for Coastal Studies
also has an inshore measurement component, which employs citizen volunteers to
monitor areas not accessible by boat. Overall, the program provides additional detail
for the region, with a focus on information relevant to the whale populations that visit
the area each year. The Center for Coastal Studies also makes observations of whales
in the region, including aerial surveys and shipboard observations. Some of the Cape
Cod Bay program results have been reported on in Section 3, Water Column. 
In 2012, the Center for Coastal Studies completed 16 surveys of eleven stations in
Cape Cod Bay and the southwestern corner of Stellwagen Bank, including three
MWRA stations (F01, F02, F29) (Figure 6-6). Those surveys found typical
hydrographic and water quality patterns. Phytoplankton communities were
dominated by microflagellates. The zooplankton community was somewhat different
from past years, including unusual free-swimming gastropods (pteropods), possibly
due to intrusion of water from offshore. 
Figure 6-6. The Center for Coastal Studies monitors its own eight stations and three MWRA
stations (F01, F02, and F29) in and near Cape Cod Bay. (Figure from the Center for Coastal
Studies)

64 
Numbers of Center for Coastal Studies whale sightings have been relatively high
since 2007, with 2012 numbers lower than 2011 but greater than 2010 (Figure 6-7).
In 2012, whales entered the bay and reached peak abundance earlier than is typical of
most years, with the last whales sighted in April. The early arrival may have been
related to warm water temperatures. 
Figure 6-7. Right whale sightings in Cape Cod Bay, 1998–2012. IPUE = individuals per unit effort
(Figure from the Center for Coastal Studies) 
In March 2012, a bowhead whale was sighted off Cape Cod, the first such recorded
sighting. Bowhead whales typically live farther north in the Atlantic, Pacific, and
Arctic oceans and had never been sighted so far south. 
Eutrophication Studies in Boston Harbor 
While studies in Massachusetts Bay have confirmed predictions that any outfall-
related changes would be minor and localized, comparable measurements in Boston
Harbor have documented improvements resulting from the Boston Harbor Project
(Figure 6-8). Average 2012 summer and winter levels of dissolved inorganic
nitrogen, chlorophyll, and transparency (measured as a light-attenuation coefficient),
were similar to those in 2011, continuing conditions observed in recent years.
Minimum dissolved oxygen concentrations in the inner and outer regions of the
harbor were also similar to previous years. 
Over the course of the Boston Harbor Project, inputs of nitrogen, phosphorus, and
organic carbon declined by 65–90%, most of which was due to the ending of sewage
effluent discharge to the harbor. A recent report (Taylor 2013) documents the
improvements through 2009, changes that reversed the historic eutrophic conditions.
These improvements have been maintained since the diversion of discharge to
Massachusetts Bay. 
0
1
2
3
4
5
6
1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 
IPUE

65 
Figure 6-8. Time series plots of Boston Harbor water quality, 1994–2012 . DIN=dissolved
inorganic nitrogen, CHL-A=chlorophyll

66 
References 
Bigornia-Vitale G, Wu D. 2012. Technical survey of nitrogen removal alternatives of
the Deer Island Treatment Plant. Boston: Massachusetts Water Resources Authority.
Report 2012-01. 35 p. 
Hall M, Lao Y, Moore M. 2013. 2012 fish and shellfish report. Boston:
Massachusetts Water Resources Authority. Report 2013-08. 47 p. 
Keay KE, Taylor, DI, Hall MP, Leo WS, Libby PS. 2013. Comparisons of measured
productivity and the composite parameter BZpI0 in Massachusetts Bay: 2001–2010.
Boston: Massachusetts Water Resources Authority. Report 2013-10. 15 p. 
Libby PS, Borkman DG, Geyer WR, Turner JT, Costa AS. 2013. 2012 water column
monitoring results. Boston: Massachusetts Water Resources Authority. Report 2013-
15. 50 p. 
MWRA. 1991. Massachusetts Water Resources Authority effluent outfall monitoring
plan: Phase I baseline studies. Boston: Massachusetts Water Resources Authority.
Report 1991-ms-02. 95 p. 
MWRA. 1997a. Massachusetts Water Resources Authority effluent outfall
monitoring plan: Phase II post discharge monitoring. Boston: Massachusetts Water
Resources Authority. Report 1997-ms-44. 61 p. 
MWRA. 1997b. Massachusetts Water Resources Authority Contingency Plan.
Boston: Massachusetts Water Resources Authority. Report 1997-ms-069. 41 p. 
MWRA. 2001. Massachusetts Water Resources Authority Contingency Plan revision
1. Boston: Massachusetts Water Resources Authority. Report 2001-ms-071. 47 p. 
MWRA. 2004. Massachusetts Water Resources Authority effluent outfall ambient
monitoring plan Revision 1, March 2004. Boston: Massachusetts Water Resources
Authority. Report 2004-ms-092. 65 p. 
MWRA. 2010. Ambient monitoring plan for the Massachusetts Water Resources
Authority effluent outfall Revision 2, July 2010. Boston: Massachusetts Water
Resources Authority. Report 2010-04. 107 p. 
Moore MJ, Nestler EC, Pembroke AE. 2012. Flounder monitoring report: 2012
results. Boston: Massachusetts Water Resources Authority. Report 2012-12. 17 p. 
Nestler EC, Diaz RJ, Hecker B, Pembroke AE. 2013. Outfall benthic monitoring
report: 2012 results. Boston: Massachusetts Water Resources Authority. Report 2013-
12. 36 p.

67 
Pembroke AE, Diaz RJ, Nestler EC. 2013. Harbor benthic monitoring report: 2012
results. Boston: Massachusetts Water Resources Authority. Report 2013-13. 41 p. 
Rex A, Delaney M. 2013. Summary of marine debris observations at MWRA’s Deer
Island Treatment Plant effluent discharge site in Massachusetts Bay, 200–2012.
Boston: Massachusetts Water Resources Authority. Report 2013-01. 10 p. 
Taylor DI. 2013. The Boston Harbor Project and the reversal of eutrophication of
Boston Harbor. Boston: Massachusetts Water Resources Authority. Report 2013-07.
33 p. 
Werme C, Rex AC, Hunt, C. 2012. Outfall monitoring overview background: 2012
update. Boston: Massachusetts Water Resources Authority. Report 2012-02. 59 p.

68 
List of Acronyms 
BOD Biochemical oxygen demand 
cBOD Carbonaceous biochemical oxygen demand 
CHL-A Chlorophyll 
CHV Centrotubular hydropic vacuolation 
DDE Dichlorodiphenyldichloroethylene 
DDT Dichlorodiphenyltrichloroethane 
DIF Deer Island Flats 
DIN Dissolved inorganic nitrogen 
DITP Deer Island Treatment Plant 
ECCB Eastern Cape Cod Bay 
EPA U.S. Environmental Protection Agency 
FF Farfield 
HMW High molecular weight 
IAAC Inter-Agency Advisory Committee 
IH Inner Harbor 
IPUE Individuals per unit effort 
LC50 50% mortality concentration 
LMW Low molecular weight 
LNB Outfall site B 
MADEP Massachusetts Department of Environmental Protection 
MWRA Massachusetts Water Resources Authority 
NA Not analyzed/not applicable 
NACWA National Association of Clean Water Agencies 
NB Nantasket Beach 
NERACOOS Northeastern Regional Association of Coastal Ocean Observing
Systems 
NDBC National Data Buoy Center 
NF Nearfield 
NOEC No observed effects concentration 
NPDES National Pollutant Discharge Elimination System 
OMSAP Outfall Monitoring Science Advisory Panel 
OS Outfall site 
OSM Outfall site 
PAH Polycyclic aromatic hydrocarbon 
PCB Polychlorinated biphenyl 
PE Pemaquid Point, Maine 
PIAC Public Interest Advisory Committee 
PSP Paralytic shellfish poisoning 
RPD Redox potential discontinuity 
T Temperature 
WC Water column

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

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