2014 overview

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2014 Outfall monitoring overview 
1 
Massachusetts Water Resources Authority 
Environmental Quality Department 
Report 2015-11

Citation : 
Werme C, Keay KE, Libby PS, Wu DC, Taylor DI, Codiga DL, Coughlin K. 2015. 
2014 outfall monitoring overview . Boston: Massachusetts Water Resources
Authority. Report 2015-11. 70 p.

2014 
Outfall Monitoring Overview 
prepared by 
Christine Werme 
Independent Consultant 
Berkeley, CA 94705 
Kenneth E. Keay 
Massachusetts Water Resources Authority 
Environmental Quality Department 
100 First Avenue 
Charlestown Navy Yard 
Boston, MA 02129 
P. Scott Libby 
Battelle 
157 Park Row 
Brunswick, ME 04011 
David C. Wu, David I. Taylor, Daniel L. Codiga, Kelly Coughlin 
Massachusetts Water Resources Authority 
Environmental Quality Department 
100 First Avenue 
Charlestown Navy Yard 
Boston, MA 02129 
October 13, 2015

2014 Outfall Monitoring Panel and Committees 
Outfall Monitoring Science Advisory Panel (OMSAP) 
Andrew Solow (chair), Woods Hole Oceanographic Institution 
Robert Beardsley, Woods Hole Oceanographic Institution 
Robert Kenney, 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 
Geoffrey Trussell, Northeastern University Marine Science Center 
Juanita Urban-Rich, University of Massachusetts, Boston 
Inter-Agency Advisory Committee (IAAC) 
US Geological Survey 
Massachusetts Coastal Zone Management 
US Army Corps of Engineers 
Stellwagen Bank National Marine Sanctuary 
US Environmental Protection Agency 
Massachusetts Division of Marine Fisheries 
Massachusetts Department of Environmental Protection 
Public Interest Advisory Committee (PIAC) 
Save the Harbor/Save the Bay 
MWRA Wastewater Advisory Committee 
Conservation Law Foundation 
Massachusetts Audubon Society 
MWRA Advisory Board 
Association to Preserve Cape Cod 
Safer Waters in Massachusetts 
The Boston Harbor Association

i 
Table of Contents 
Summary ...................................................................................................................... vi 
1. Introduction ............................................................................................................... 1 
2. Effluent ..................................................................................................................... 2 
2014 Characterization ............................................................................................... 2 
Contingency Plan Thresholds ................................................................................... 9 
3. Water Column ......................................................................................................... 10 
Physical Conditions ................................................................................................ 11 
Water Quality .......................................................................................................... 14 
Phytoplankton Communities ................................................................................... 19 
Zooplankton Communities...................................................................................... 24 
Stellwagen Bank National Marine Sanctuary ......................................................... 26 
Boston Harbor ......................................................................................................... 30 
Contingency Plan Thresholds ................................................................................. 32 
4. Sea Floor ................................................................................................................. 34 
Sediment Characteristics and Tracers ..................................................................... 37 
Sediment Contaminants .......................................................................................... 40 
Soft-bottom Communities ....................................................................................... 41 
Sediment-profile Imaging ....................................................................................... 44 
Hard-bottom Communities ..................................................................................... 45 
Stellwagen Bank National Marine Sanctuary ......................................................... 46 
Boston Harbor ......................................................................................................... 47 
Contingency Plan Thresholds ................................................................................. 51 
5. Fish and Shellfish .................................................................................................... 54 
Flounder Health ...................................................................................................... 55 
Boston Harbor ......................................................................................................... 57 
Contingency Plan Thresholds ................................................................................. 58 
6. Special Studies ........................................................................................................ 59 
Boston Harbor Bacterial Water Quality.................................................................. 59 
Massachusetts Bay Water-Quality Modeling ......................................................... 61 
Cape Cod Bay Studies ............................................................................................ 64 
References ................................................................................................................... 68 
List of Acronyms ........................................................................................................ 70

ii 
List of Figures 
Figure 2-1. Annual rainfall in Boston, 1950–2014 ....................................................... 2 
Figure 2-2. Annual primary-blended and full secondary effluent flows, 1999–2014 .. 3 
Figure 2-3. Monthly primary-blended and full secondary effluent flows during 2014
....................................................................................................................................... 3 
Figure 2-4. Annual solids discharges, 1990–2014 ........................................................ 4 
Figure 2-5. Annual carbonaceous biochemical oxygen demand, 1999–2014 .............. 5 
Figure 2-6. Annual nitrogen discharges, 1999–2014 .................................................... 6 
Figure 2-7. Annual metals discharges, 1999–2014. ...................................................... 7 
Figure 2-8. Annual mercury discharges, 1999–2014 .................................................... 7 
Figure 2-9. Annual PAH discharges, 2006–2014 ......................................................... 8 
Figure 3-1. Water-column monitoring stations ........................................................... 10 
Figure 3-2. Flows of the Merrimack and Charles rivers ............................................. 12 
Figure 3-3. Nearfield surface-water temperature at the NDBC Buoy 44013 ............. 13 
Figure 3-4. Average wind stress at NDBC Buoy 44013 ............................................. 13 
Figure 3-5. Mean depth-averaged nutrient concentrations at nearfield station N18 in
2014, compared to prior years .................................................................................... 14 
Figure 3-6. Depth-averaged ammonium concentrations by station in Massachusetts
and Cape Cod bays...................................................................................................... 15 
Figure 3-7. (Left) Surface- and bottom-water ammonium on June 14, 2014 at the
monitoring stations during stratified conditions. (Right) Cross-sections of
concentrations at the five depths sampled at each station along the two transects. .... 16 
Figure 3-8. Average areal chlorophyll by station in Massachusetts Bay, 2014. ......... 17 
Figure 3-9. Moderate Resolution Imaging Spectroradiometer satellite imagery of
surface chlorophyll concentrations in 2014. ............................................................... 18 
Figure 3-10. Bottom water dissolved oxygen concentrations in the nearfield and
offshore in 2014 compared to earlier years................................................................. 19 
Figure 3-11. Annual mean abundance of total phytoplankton, centric diatoms, and
pennate diatoms, 1992–2014 ...................................................................................... 20 
Figure 3-12. Total phytoplankton abundance at selected stations in 2014 compared to
baseline (Harbor Outfall) and post-discharge (Bay Outfall) monitoring years. ......... 21 
Figure 3-13. Mean nearfield abundance Phaeocystis pouchetii, 1992–2014 ............. 22 
Figure 3-14. Nearfield abundance of Alexandrium fundyense, 1992–2014................ 23 
Figure 3-15. Long-term average zooplankton abundance .......................................... 24 
Figure 3-16. Total zooplankton abundance at selected stations in 2014 compared to
baseline (Harbor Outfall) and post-discharge (Bay Outfall) monitoring years ......... 25 
Figure 3-17. Annual total phytoplankton versus total zooplankton at nearfield stations
N04 and N18, 1998–2014 ........................................................................................... 26 
Figure 3-18. Deep and near-bottom water dissolved oxygen concentrations at Station
F22 and the NERACOOS Mooring A01, inside Stellwagen Bank Marine Sanctuary.
..................................................................................................................................... 27

iii 
Figure 3-19. Location of an east-west transect from Deer Island, across MWRA
outfall, through Stellwagen Bank, for modeled water-quality parameters. ................ 28 
Figure 3-20. Modeled increases in ammonium concentrations due to MWRA
discharge, on the east-west transect across the MWRA outfall and into Stellwagen
Bank National Marine Sanctuary for six months in 2013........................................... 29 
Figure 3-21. Ammonium levels at Station F23 in Boston Harbor .............................. 30 
Figure 3-22. Acartia spp. abundance at Station F23 in Boston Harbor ...................... 31 
Figure 3-23. Acartia hudsonica and Acartia tonsa abundance at Station F23 in Boston
Harbor ......................................................................................................................... 32 
Figure 4-1. Soft-bottom monitoring stations .............................................................. 34 
Figure 4-2. Sediment-profile imaging stations ........................................................... 35 
Figure 4-3. Hard-bottom stations ................................................................................ 36 
Figure 4-4. Percent total organic carbon by region, during the baseline, other post-
diversion years, and 2014 ........................................................................................... 38 
Figure 4-5. Concentrations of Clostridium perfringens spores, corrected for sediment
grain size, in 2014 ....................................................................................................... 39 
Figure 4-6. Mean concentrations of Clostridium perfringens spores during the
baseline and outfall-discharge years ........................................................................... 39 
Figure 4-7. Mean concentration of mercury during the baseline and outfall-discharge
years ............................................................................................................................ 40 
Figure 4-8. Mean PCB concentration by region, during the baseline, other post-
diversion years, and 2014 ........................................................................................... 41 
Figure 4-9. Mean infaunal abundance per sample in four areas of Massachusetts Bay,
1992–2014................................................................................................................... 42 
Figure 4-10. Mean abundance per sample of five dominant species compared to total
abundance at nearfield stations, 1992–2014 ............................................................... 42 
Figure 4-11. Percent fine sediments superimposed on ordination plot of the 2014
infauna samples ........................................................................................................... 43 
Figure 4-12. Annual apparent color RPD depth for data from nearfield stations. ...... 44 
Figure 4-13. Lush growth on active diffuser in 2014 ................................................. 45 
Figure 4-14. Mean concentrations of mercury at selected stations, 1992–2014 ......... 46 
Figure 4-15. Mean concentrations of total PCBs at selected stations, 1992–2014 .... 47 
Figure 4-16. Soft-bottom sampling stations in Boston Harbor ................................... 48 
Figure 4-17. Ordination plot of 2014 Boston Harbor infauna samples ...................... 49 
Figure 4-18. Sediment profiles from Station T02, in President Roads, near Deer
Island Flats, 1992–2014 .............................................................................................. 50 
Figure 4-19. Annual community parameters with nearfield Contingency Plan
thresholds .................................................................................................................... 53 
Figure 5-1. Flounder sampling sites............................................................................ 54 
Figure 5-2. “Ghost” lobster gear brought up in a flounder trawl. ............................... 55 
Figure 5-3. Annual prevalence of centrotubular hydropic vacuolation corrected for
age ............................................................................................................................... 56 
Figure 5-4. Incidence of liver tumor precursors and liver tumors in winter flounder
from Deer Island Flats in Boston Harbor, 1987–2014 ................................................ 57

iv 
Figure 6-1. Bacterial water quality prior to the Boston Harbor Project and after
completion of the treatment plant and most CSO projects ......................................... 60 
Figure 6-2. Modeled dissolved inorganic nitrogen concentrations in bottom waters at
selected stations. ......................................................................................................... 62 
Figure 6-3. Modeled dissolved inorganic nitrogen concentrations in surface waters at
selected stations .......................................................................................................... 63 
Figure 6-4. The Center for Coastal Studies monitors its own eight stations and three
MWRA stations in and near Cape Cod Bay ............................................................... 64 
Figure 6-5. Water quality measurements and zooplankton and phytoplankton
abundance in Cape Cod Bay in 2014 .......................................................................... 65 
Figure 6-6. Zooplankton abundance and whale sightings in Cape Cod Bay, January –
April 2014 ................................................................................................................... 66 
Figure 6-7. Right whale sightings in Cape Cod Bay, 1998–2014 .............................. 67

v 
List of Tables 
Table i. Contingency Plan threshold values and 2014 results for effluent monitoring.
..................................................................................................................................... vii 
Table ii. Contingency Plan threshold values and 2014 results for water-column
monitoring. ................................................................................................................. viii 
Table iii. Contingency Plan threshold values and 2014 results for sea-floor
monitoring. ................................................................................................................... ix 
Table iv. Contingency Plan threshold values and 2014 result for fish-and-shellfish
monitoring. .................................................................................................................... x 
Table 2-1. Contingency Plan threshold values and 2014 results for effluent
monitoring. .................................................................................................................... 9 
Table 3-1. Contingency Plan threshold values and 2014 results for water-column
monitoring. .................................................................................................................. 33 
Table 4-1. Contingency Plan threshold values and 2014 results for sea-floor
monitoring. .................................................................................................................. 52 
Table 5-1. Contingency Plan threshold values and 2014 result for fish-and-shellfish
monitoring. .................................................................................................................. 58

vi 
Summary 
Each year, the Massachusetts Water Resources Authority (MWRA) prepares an
overview of environmental monitoring related to the discharge of municipal wastewater
effluent from Deer Island Treatment Plant through an offshore outfall tunnel into
Massachusetts Bay. The report presents monitoring results and information relevant to
MWRA’s permit-required Contingency Plan, including threshold exceedances and
permit violations, responses, and, if needed, corrective actions. The overview also
includes monitoring results relevant to the Stellwagen Bank National Marine Sanctuary
and information on special studies conducted in response to specific permit
requirements, scientific questions, or public concerns. 
This 2014 report marks more than fourteen years of “outfall-discharge” monitoring,
covering the years since September 2000, when MWRA ceased discharge of wastewater
effluent to the relatively confined waters of Boston Harbor and began to discharge into
deeper water in Massachusetts Bay. Before September 2000, MWRA had completed
almost nine years of baseline monitoring. This report includes results of effluent
analyses; water-column, sea-floor, and fish-and-shellfish monitoring in the outfall
nearfield and at reference stations; and results pertinent to Stellwagen Bank and to
Boston Harbor. This year’s report on special studies focuses on bacterial water quality
in Boston Harbor, modeling results, and ongoing Cape Cod Bay studies. 
Operations at the Deer Island Treatment Plant continued to be exceptional in 2014,
earning MWRA a National Association of Clean Water Agencies (NACWA) Platinum 8
Peak Performance Award. This NACWA award recognizes facilities with 100% permit
compliance for eight consecutive years. Nearfield and reference-station monitoring
results from 2014 were consistent both with predictions made during the outfall-siting
process and with past results, showing no unanticipated effects of the discharge (Tables i
through iv). No Contingency Plan “warning-level” exceedances were observed, but
“caution-level” exceedances * occurred for one water-column and two soft-bottom sea-
floor parameters: summer levels of the nuisance algal species Phaeocystis pouchetii and
two benthic-community parameters, Shannon-Wiener diversity and Pielou’s evenness.
The exceedances have been analyzed and are not thought to be related to the outfall.
The summer Phaeocystis exceedance resulted from a cool spring, which delayed the
annual phytoplankton cycles. The benthic community exceedances resulted from normal
variability in relative abundances of animal populations. 
* MWRA’s discharge 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 exceedances were related to the discharge,
MWRA might need to implement corrective action. All thresholds based on effluent discharge permit limits are
“warning-level.” Some ambient parameters have both “caution” and “warning” level thresholds, and others have only
“caution-level” thresholds.

vii 
Table i. Contingency Plan threshold values and 2014 results for effluent monitoring. 
Parameter Baseline Caution Level Warning Level 2014 Results 
pH NA None <6 or >9 Not exceeded 
Fecal coliform NA None 14,000 fecal
coliforms/100 mL Not exceeded 
Chlorine, residual NA None 631 μg/L daily, 
456 μg/L monthly Not exceeded 
Suspended solids NA None 45 mg/L weekly 
30 mg/L monthly Not exceeded 
cBOD NA None 40 mg/L weekly, 
25 mg/L monthly Not exceeded 
Acute toxicity NA None LC50 <50% Not exceeded 
Chronic toxicity NA None NOEC <1.5%
effluent Not exceeded 
PCBs NA Aroclor=0.045 ng/L None Not exceeded 
Plant performance NA 5 violations/year Compliance <95%
of the time Not exceeded 
Flow NA None >436 MGD
average dry days Not exceeded 
Total nitrogen load NA 12,500 mtons/year 14,000 mtons/year Not exceeded 
Oil and grease NA None 15 mg/L weekly Not exceeded 
NA = not applicable 
cBOD = carbonaceous biological oxygen demand 
LC50 = 50% mortality concentration 
NOEC = no observable effect concentration 
PCB = polychlorinated biphenyl 
Plant performance = compliance with permit conditions

viii 
Table ii. Contingency Plan threshold values and 2014 results for water-column monitoring. 
Parameter Baseline Caution Level Warning Level 2014 Results 
Dissolved oxygen* 
Nearfield
concentration 6.05 mg/L 6.5 mg/L 6.0 mg/L 7.19 mg/L 
Nearfield percent
saturation 65.3% 80% 75% 81.6% 
Stellwagen
concentration 6.23 mg/L 6.5 mg/L 6.0 mg/L 6.76 mg/L 
Stellwagen percent
saturation 67.2% 80 75% 75.0% 
Nearfield depletion
rate 0.024 mg/L/d 0.037 mg/L/d 0.049 mg/L/d 0.015 mg/L/d 
Chlorophyll 
Annual 72 mg/m 2 108 mg/m 2 144 mg/m 2 66 mg/m 2 
Winter/spring 50 mg/m 2 199 mg/m 2 None 75 mg/m 2 
Summer 51 mg/m 2 89 mg/m 2 None 68 mg/m 2 
Autumn 90 mg/m 2 239 mg/m 2 None 50 mg/m 2 
Nuisance algae Phaeocystis pouchetii 
Winter/spring 622,000 cells/L 2,860,000 cells/L None 27,800 cells/L 
Summer 72 cells/L 357 cells/L None 
395,000 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 106 cells/L 
Summer 14,635 cells/L 43,100 cells/L None Absent 
Autumn 10,050 cells/L 27,500 cells/L None 270 cells/L 
Nuisance algae nearfield Alexandrium fundyense 
Any nearfield
sample 
Baseline maximum 
163 cells/L 100 cells/L None 20 cells/L 
PSP toxin extent NA New incidence None No new incidence 
*Dissolved oxygen caution and warning levels represent numerical criteria, with the caveat “unless
background conditions are lower.” Results are therefore compared to the baseline rather than to the
caution and warning levels. 
PSP = paralytic shellfish poisoning 
NA = not applicable

ix 
Table iii. Contingency Plan threshold values and 2014 results for sea-floor monitoring. 
Parameter Baseline Caution Level Warning Level 2014 Results 
Polycylclic aromatic hydrocarbons (PAHs) (ng/g dry weight) 
Acenaphthene 22.7 – 43.5 None 500 28.3 
Acenaphylene 30.3 – 43.1 None 640 11.1 
Anthracene 101 – 159 None 1,100 77.3 
Benzo(a)anthracene 206 – 302 None 1,600 176 
Benzo(a)pyrene 204 – 298 None 1,600 182 
Chrysene 164 – 296 None 2,800 172 
Dibenzo(a,h)anthracene 27.8 – 38.3 None 260 26.7 
Fluoranthene 422 – 621 None 5,100 389 
Fluorene 35.5 – 66.6 None 540 32.5 
Naphthalene 53.6 – 103 None 2,100 31.6 
Phenanthrene 273 – 431 None 1,500 247 
Pyrene 412 – 579 None 2,600 362 
Total HMW PAH 2,790 – 3,850 None 9,600 2,440 
Total LMW PAH 1,390 – 1,630 None 3,160 814 
Total PAHs 4,180 – 5,400 None 44,792 3,260 
Other organic contaminants (ng/g dry weight) 
p,p’-DDE 0.386 – 1.00 None 27 0.37 
Total DDTs 2.51 – 5.69 None 46.1 0.79 
Total PCBs 10.2 – 20.2 None 180 7.17 
Metals (μg/g dry weight) 
Cadmium 0.0727 – 0.185 None 9.6 0.11 
Chromium 59.2 – 79.9 None 370 47.6 
Copper 19.1 – 25.2 None 270 22.9 
Lead 41.1 – 46.3 None 218 32.7 
Mercury 0.159 – 0.353 None 0.71 0.12 
Nickel 15.7 – 17.2 None 51.6 8.46 
Silver 0.335 – 0.485 None 3.7 0.17 
Zinc 49.5 – 57.5 None 410 41.5 
Sediment parameters 
RPD depth NA <1.18 cm None 4.01 cm 
Benthic community parameters 
Species per
sample NA <42.99 or >81.85 None 62.73 
Fisher’s log-series
alpha NA <9.42 or >15.8 None 13.35 
Shannon diversity NA <3.37 or >3.99 None 4.03, caution level
exceedance 
Pielou’s evenness NA <0.57 or >0.67 None 0.68, caution level
exceedance 
% opportunists NA >10% >25% 0.12% 
HMW = high molecular weight; LMW = low molecular weight 
NA = not applicable; RPD = redox potential discontinuity

x 
Table iv. Contingency Plan threshold values and 2014 result for fish-and-shellfish monitoring. 
Parameter Baseline Caution Level Warning Level 2014 Results 
Liver disease CHV 24.4% 44.9% None 10% 
CHV = centrotubular hydropic vacuolation

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
municipal 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 wastewater-
effluent discharge. Throughout MWRA’s early years, scientists conducted
environmental monitoring in Boston Harbor and also in Massachusetts Bay, at what
would become the site of a relocated wastewater-effluent discharge. 
By the end of 2000, most of the Boston Harbor Project had been completed, including
the relocated outfall, which diverted wastewater 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 the 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 wastewater
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). That document, as well as 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 from each year since the outfall began to
discharge have been documented in annual outfall monitoring overviews. The reports
have included information relevant to permit requirements, including Contingency
Plan threshold exceedances, responses, and corrective actions. Reports have also
included information relevant to the Stellwagen Bank National Marine Sanctuary. 
This outfall monitoring overview presents results from 2014, marking the twenty-
third year of MWRA’s monitoring program, including more than fourteen 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, and additional information from MWRA’s in-
house Boston Harbor monitoring is included in the water-column, sea-floor, and
flounder monitoring sections.

2 
2. Effluent 
2014 Characterization 
As in past years, DITP continued to operate as designed through 2014, earning
MWRA the National Association of Clean Water Agencies (NACWA) Platinum 8
Peak Performance Award. This NACWA award recognizes facilities with 100%
permit compliance over eight consecutive years. 
The Boston area received about 40.5 inches of rain in 2014, wetter than 2012 or 2013
and slightly rainier than the long-term average (Figure 2-1). Total effluent flow in
2014 was slightly higher than flow in 2012 or 2013, but lower than in all other years
since the Massachusetts Bay outfall came on line in 2000 (Figure 2-2). Virtually all
the flow received full primary and secondary treatment, with only small discharges of
primary-only effluent blended with fully treated effluent prior to discharge, mostly
during March and December storms (Figure 2-3). 
Figure 2-1. Annual rainfall in Boston, 1950–2014. 
0
10
20
30
40
50
60
70 
Inches

3 
Figure 2-2. Annual primary-blended and full secondary effluent flows, 1999–2014. (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 primary-treated
flows are then combined (“blended”) with full secondary flows before disinfection and discharge. All
discharges in 2014 met permit limits.) 
Figure 2-3. Monthly primary-blended and full secondary effluent flows during 2014. S mall
discharges of primary-blended flow in any month correspond to rainfall, most notably during March
and December storms. 
0
50
100
150
200
250
300
350
400
450
500
99 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 
Million gallons per day 
Primary-blended flows
Secondary flows 
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 flows
Secondary flows

4 
The total suspended solids load to Massachusetts Bay remained well below the loads
discharged to Boston Harbor before the outfall came on line in 2000 and similar to
loads measured since 2006 (Figure 2-4). Carbonaceous biological demand, a measure
of the amount of oxygen consumed by microorganisms, also remained low, well
below levels that would be expected to affect dissolved oxygen at the discharge
(Figure 2-5). 
Figure 2-4. Annual solids discharges, 1990–2014 . Solids discharges remained low in 2014, less than
20 tons per day. (Ending biosolids (sludge) disposal and effluent discharge to the southern portion of
the harbor from Nut Island, and the addition of secondary treatment were important steps in the Boston
Harbor Project. All effluent discharge was diverted from Boston Harbor to Massachusetts Bay in
September 2000.) 
0
20
40
60
80
100
120
140
160
180
90 91 92 93 94 95 96 97 98 99 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 
Tons per day 
Sludge
Nut Island
Deer Island

5 
Figure 2-5. Annual carbonaceous biochemical oxygen demand, 1999–2014. 
The total nitrogen load also remained below its threshold in 2014 (Figure 2-6). In
1996, during construction, DITP discharged more than 12,700 metric tons of
nitrogen, while discharges in 2014 were about 12,200 metric tons. The portion of the
load made up of ammonium also increased, as it has since earlier years of the Boston
Harbor Project. About 10% of the ammonium in the wastewater 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 to end biosolids
discharge to the harbor, are reintroduced to DITP for treatment, adding to the
ammonium load. The high total nitrogen and ammonium loads in 2014 may
correspond to low flow in the system throughout the summer months. As required by
its permit, MWRA continually evaluates nitrogen-removal technologies, so that
removal could be quickly implemented, should a need arise (Smolow et al. 2015).
Because nitrogen loads have remained below the Contingency Plan caution threshold,
and there have not been adverse environmental effects due to nitrogen, 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

6 
Figure 2-6. Annual nitrogen discharges, 1999–2014. Most of the nitrogen in the effluent is in the
form of ammonium. 
Metals loads remained low in 2014, 112 pounds per day, but were higher than past
years since 2006 (Figure 2-7). Zinc and copper continued to comprise most of the
annual discharge. The increase in 2014 could be traced to a storm on December 9–
11, which corresponded by chance with effluent-sampling times. Without those wet-
weather data points, the calculated loads would have totaled 90 pounds per day, with
particularly large differences in the mercury and lead loads. Even with the higher
values, metals discharges are now only a small fraction of what they were before the
Boston Harbor Project began, when more than 750 pounds of metals were discharged
to Boston Harbor each day. Except for copper, metals meet water quality criteria
prior to discharge, while copper meets the criteria after initial dilution at the
Massachusetts Bay outfall. Once considered a sewage tracer, silver is no longer
detected in the effluent in appreciable amounts, a result of removal efficiencies and
the change from film to digital photography. 
Annual mercury discharges in 2014 were also higher than those in 2012 or 2013, but
far below the discharges of the late 1990s (Figure 2-8). Mercury discharges are only
a small fraction of what had been anticipated during the outfall-planning process, and
most mercury inputs to New England waters come from atmospheric deposition. 
0
3000
6000
9000
12000
15000
99 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 
Metric tons per year 
Caution Threshold Other Nitrogen Species
Nitrite/Nitrate Ammonium

7 
Figure 2-7. Annual metals discharges, 1999–2014. Total metals discharges were higher than in
recent years, but remained low. 
Figure 2-8. Annual mercury discharges, 1999–2014. 
0
50
100
150
200
250
99 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 
Average pounds per day
Silver
Chromium
Lead
Nickel
Copper
Zinc 
0
5
10
15
20
25
30
35
40
45
50
99 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 
Pounds per year

8 
Polycyclic aromatic hydrocarbon (PAH) and other organic contaminant loads also
increased in 2014 in comparison to 2013 (Figure 2-9), but remained well below levels
that had been projected during the outfall-planning process. In 1988, MWRA
projected annual discharges of about 3,100 pounds of total PAHs per year with full
secondary treatment, while 2014 discharges were less than 15% of that total,
approximately 420 pounds. 
Figure 2-9. Annual PAH discharges, 2006–2014 . LMW PAH = low molecular weight PAHs,
generally derived from petroleum; HMW PAH = high molecular weight PAHs, generally derived from
combustion processes 
0
50
100
150
200
250
300
350
400
450
500
2006 2007 2008 2009 2010 2011 2012 2013 2014 
Pounds per year 
LMW PAH HMW PAH

9 
Contingency Plan Thresholds 
DITP had no permit violations, and there were no exceedances of the Contingency
Plan effluent thresholds in 2014 (Table 2-1). 
Table 2-1. Contingency Plan threshold values and 2014 results for effluent monitorin g. 
Parameter Caution Level Warning Level 2014 Results 
pH None <6 or >9 Not exceeded 
Fecal coliform None 14,000 fecal coliforms/100 mL Not exceeded 
Chlorine, residual None 631 μg/L daily, 
456 μg/L monthly Not exceeded 
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 
Acute toxicity None LC50 <50% Not exceeded 
Chronic toxicity None NOEC <1.5% effluent Not exceeded 
PCBs Aroclor=0.045 ng/L None Not exceeded 
Plant performance 5 violations/year Compliance <95% of the time Not exceeded 
Flow None >436 MGD average dry days Not exceeded 
Total nitrogen load 12,500 mtons/year 14,000 mtons/year Not exceeded 
Oil and grease None 15 mg/L weekly Not exceeded 
NA = not applicable 
cBOD = carbonaceous biological oxygen demand 
LC50 = 50% mortality concentration 
NOEC = no observable effect concentration 
PCB = polychlorinated biphenyl 
Plant performance = compliance with permit conditions

10 
3. Water Column 
The water-column monitoring program evaluates relevant physical-oceanographic
processes, water quality, and phytoplankton and zooplankton communities at stations
in Massachusetts Bay, at the mouth of Boston Harbor, 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 
Sampling during nine surveys at fourteen stations in 2014 included 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
and at farfield reference stations, including stations in Cape Cod Bay and near the
Stellwagen Bank National Marine Sanctuary. Analyses included data from ten
additional stations, sampled as part of MWRA’s Boston Harbor water-quality
monitoring program when sampling dates were close. In some years, special surveys
are conducted in response to Alexandrium fundyense red tide blooms, but no
additional surveys were necessary in 2014. However, additional stations were added
to the June survey, as a precaution in the event that Alexandrium had been transported
into the bay. While no bloom was detected in the bay, the additional data collected at
those stations were included in analyses. 
The program continued to benefit from collaboration with the Center for Coastal
Studies at Provincetown, which conducts a monitoring program in Cape Cod Bay.
The Center for Coastal Studies samples MWRA’s monitoring 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 this annual outfall monitoring overview. In 2014, all
Cape Cod Bay sampling was completed within the required time frame. 
The field monitoring program was augmented by measurements on two instrumented
buoys, the Northeastern Regional Association of Coastal and Ocean Observing
Systems (NERACOOS) Mooring A01 and the National Oceanic and Atmospheric
Administration’s National Data Buoy Center (NDBC) Buoy 44013. The National
Aeronautics and Space Administration provided Moderate Resolution Imaging
Spectroradiometer (MODIS-Aqua) satellite imagery for chlorophyll and for sea-
surface temperature. 
Physical Conditions 
Monitoring has shown that the water quality 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 2014 was wetter than 2012 and 2013 (See Figure 2-1 in Section 2, Effluent,
for annual rainfall in Boston). River discharges from both the Merrimack and Charles
rivers were lower than average in January through March, with no strong spring peaks
in runoff (Figure 3-2; Libby et al. 2015). Discharges from the Merrimack River were
somewhat higher than average for the remainder of the year. Discharges from the
Charles River remained low until the last months of the year, when flows were high
following an early December storm.

12 
Figure 3-2. Flows of the Merrimack (top) and Charles (bottom) rivers. Flows from both rivers
were about average over the year, with no strong spring peaks. Flow from the Charles River was
relatively high in the last quarter of the year, translating to the 72 nd percentile for all years of the
monitoring program. 
January surface-water temperatures were close to the long-term average (Figure 3-3).
By mid-March, water temperatures had cooled and were close to the minima
observed during the monitoring program at the NDBC Buoy 44013 and nearby
Station N18. Although there was brief warming at the NDBC Buoy in early April,
water temperatures remained cold throughout the region into May, when rapid
warming brought them closer to typical levels, where they remained through the
summer. Temperatures were warmer than average in the fall. 
Wind conditions promoted strong downwelling in February and March (Figure 3-4).
Upwelling conditions persisted through the summer and were particularly strong in
July. Stratification, the difference in density between surface and bottom waters,
developed later than in many years (not shown). Destratification, the re-mixing of the
water column that occurs as waters cool in the autumn, was early, with the return to
downwelling conditions in the fall. 
63 rd 20 th
percentile 63 rd 63 rd
37 th 20 th
percentile
24 th 72 nd

13 
Figure 3-3. Nearfield surface-water temperature at the NDBC Buoy 44013. Surface-water
temperatures were relatively cool in March and April and warm during the much of the later months of
2014. 
Figure 3-4. 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 strongest summer upwelling since 1994
was measured in July.

14 
Water Quality 
Water quality measurements for 2014 included quantification of nutrients,
phytoplankton biomass (measured as chlorophyll and particulate organic carbon), and
dissolved oxygen. Results continued to confirm predictions of measureable outfall
influence in some parameters at stations very near the outfall but no unexpected
adverse effects (Libby et al. 2015). 
Nitrate, ammonium, silicate, and phosphate concentrations at Station N18 near the
outfall averaged through the water column were lower than most previous years
during the first survey in February (Figure 3-5). Similar low concentrations have
been observed since 2012 and may have been caused by continual phytoplankton
production over the winter or by early phytoplankton blooms that occurred prior to
the start of the sampling season. Ammonium is the largest fraction of the total
nitrogen in wastewater and provides a tracer to identify possible effects of the outfall.
Throughout the year, depth-averaged ammonium concentrations greater than 4μM
were observed only at Station N21 at the outfall and those stations immediately to the
south (Figure 3-6). 
Figure 3-5. Mean depth-averaged nutrient concentrations at nearfield station N18 in 2014,
compared to prior years. February nutrient concentrations were lower than other years, possibly due
to phytoplankton blooms prior to the first MWRA survey in February. (Station N18 is immediately
southwest of the outfall. Note difference in scale for phosphate.) 
J F M A M J J A S O N D
0
5
10
15 
μ M
NO3
J F M A M J J A S O N D
0
5
10
15 
μ M
SIO4
J F M A M J J A S O N D
0
0.5
1
1.5 
μ M
PO4
J F M A M J J A S O N D
0
5
10
15 
μ M
NH4 Nitrate 
Harbor Outfall
Bay Outfall 
2014
Phosphate
Ammonium
Silicate

15 
Figure 3-6. Depth-averaged ammonium concentrations (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.
Elevated ammonium levels are detected near the outfall throughout the year. 
As has been typical since the offshore outfall began to discharge, the ammonium
signature of the plume was found in surface waters during the winter and spring (not
shown), but was confined beneath the pycnocline during the summer, stratified
season (Figure 3-7). The ammonium signature could be detected within 10–20
kilometers of the outfall in both well-mixed and stratified seasons. 
.

16 
Figure 3-7. (Left) Surface- and bottom-water ammonium (μM) on June 14, 2014 at the
monitoring stations during stratified conditions. (Right) Cross-sections of concentrations at the
five depths sampled at each station along the two transects. No ammonium signal was detected at
Station N04, 7.1 kilometers to the northeast, or Station F10, 20 kilometers to the south of the outfall.
Station F10 is the farthest station at which detectable effects of the outfall were anticipated. 
Despite the elevated levels of ammonium that have been typical near the outfall, there
has been no detectable increase in phytoplankton biomass, measured as chlorophyll or
particulate organic carbon. Overall, both chlorophyll and particulate organic carbon
levels were low throughout 2014. Even at Station N18 near the outfall, chlorophyll
levels were at the low end of the historic range during most surveys. Broadly, survey
data showed the possible remnants of a bloom during the February survey, an
increase in chlorophyll levels in the north and east in May, and elevated chlorophyll
concentrations at the entrance to Boston Harbor and shallower stations in the coastal
waters of Massachusetts Bay in July and August (Figure 3-8).

17 
Figure 3-8. Average areal chlorophyll (mg/m 2 ) by station in Massachusetts Bay, 2014. 
Satellite imagery showed that phytoplankton were relatively productive prior to the
February 2014 survey, particularly inshore and in Cape Cod Bay (Figure 3-9), as they
had been in November and December of 2013. Levels were low in February and into
March, then relatively elevated in April and May, corresponding to the Phaeocystis
pouchetii bloom (discussed in the Phytoplankton Communities section below), and
again in the fall, corresponding to a mixed diatom bloom.

18 
Figure 3-9. Moderate Resolution Imaging Spectroradiometer satellite imagery of surface
chlorophyll concentrations in 2014. These images are heavily weather dependent and do not
represent consistent intervals of time. The numbers show the timing of the nine MWRA surveys.
Survey 2 was on the same day as one image; other surveys occurred between image dates.

19 
Nearfield and farfield bottom-water dissolved oxygen concentrations were in the
middle of the historic range in February through May (Figure 3-10). Levels were at
the low end of the range in the nearfield during June to September. As is typical,
mixing during September and October storms re-oxygenated bottom waters. Fall
oxygen minima were moderate in 2014 compared to past years and continued to show
no effects of the discharge. 
Figure 3-10. Bottom water dissolved oxygen concentrations in the nearfield (Station N18) and
offshore (Station F22) in 2014 compared to earlier years. Sampling now ends in October; in earlier
years it continued until December. The dashed lines show the 6 mg/L Massachusetts water-quality
standard and Contingency Plan warning-level threshold. 
Phytoplankton Communities 
Total abundance of phytoplankton was low in 2014, ranking lowest of 23 years of
monitoring (Figure 3-11, Libby et al. 2015), a result that is thought to be bay-wide
and not related to the outfall. The low annual abundance reflected decreases in
abundances of all major taxonomic groups, including the centric diatoms, pennate
diatoms, dinoflagellates, cryptophytes, and microflagellates. Long-term declines
(1992–2014) of centric and pennate diatoms are statistically significant. Abundance
of centric diatoms, a major component of the Massachusetts Bay winter/spring flora,
was particularly reduced in 2014, with an annual mean abundance in the nearfield the
lowest since 2009. Microflagellate, dinoflagellate and cryptophyte abundance
showed no linear trends, but long-term mean abundance patterns of those groups
suggested there may be cycles in their abundance.

20 
Figure 3-11. Annual mean abundance of total phytoplankton, centric diatoms, and pennate
diatoms, 1992–2014. (Data are mean for all samples from all stations ± standard deviation). Declines
in centric and pennate diatoms were statistically significant, linear regression lines shown.) 
Total phytoplankton abundances were low throughout the year and throughout
Massachusetts Bay (Figure 3-12). The survey data did not detect winter/spring
blooms. Interestingly, cold-water centric diatoms, Detonula confervacea, Porosira
glacialis and Lauderia annulata , which often comprise the earliest species in the
winter/spring, were abundant during March and April 2014. The most abundant of
the three species, D. confervacea , is typically abundant in cold and boreal waters,
with temperatures lower than 5ºC. The delay in springtime warming may have
influenced population growth in 2014. 
0.0
0.5
1.0
1.5
2.0
2.5
3.0
1990 1995 2000 2005 2010 2015
Total Phytoplankton
(milion cells L -1 ) 
R² = 0.37
0.0
0.2
0.4
0.6
0.8
1.0
1990 1995 2000 2005 2010 2015
Centric diatoms
(milion cells L -1 ) 
R² = 0.48
0.00
0.05
0.10
0.15
1990 1995 2000 2005 2010 2015
Pennate Diatoms
(milion cells L -1 ) 
Pennate diatoms 
Total phytoplankton 
Centric diatoms

21 
Figure 3-12. Total phytoplankton abundance at selected stations in 2014 compared to baseline
(Harbor Outfall) and post-discharge (Bay Outfall) monitoring years. 
To some degree, low annual phytoplankton abundance may reflect the timing of the
MWRA surveys as well as actual declines. There have been indications of
phytoplankton productivity prior to the first surveys of the year in recent years. The
satellite imagery in Figure 3-9 above showed, for example, that there was increased
chlorophyll between the dates of the April and May surveys. 
Even accounting for the artifacts of sampling times, there are indications of region-
wide declines, which are unrelated to the outfall. One factor that may have limited
phytoplankton abundance in 2014 is grazing by zooplankton. The abundances of
total zooplankton and many dominant taxa were at or above maxima for the
monitoring program at many of the stations in Massachusetts Bay (see Zooplankton
Communities, below). 
J F M A M J J A S O N D
0
2
4
6
8
10 x 10 6
cells/L
TOTAL PHYTOPLANKTON
J F M A M J J A S O N D
0
2
4
6
8
10 x 10 6
cells/L
TOTAL PHYTOPLANKTON
J F M A M J J A S O N D
0
2
4
6
8
10 x 10 6
cells/L
TOTAL PHYTOPLANKTON
J F M A M J J A S O N D
0
2
4
6
8
10 x 10 6
cells/L
TOTAL PHYTOPLANKTON
J F M A M J J A S O N D
0
2
4
6
8
10 x 10 6
cells/L
TOTAL PHYTOPLANKTON 
Harbor Outfall
Bay Outfall 
2014
F22
N04
N18
F06
F23
J F M A M J J A S O N D
0
2
4
6
8
10 x 10 6
cells/L
TOTAL PHYTOPLANKTON
F13

22 
Abundance of the nuisance species Phaeocystis pouchetii was moderate to low in the
nearfield in winter/spring 2014, but elevated to above the Contingency Plan caution
threshold for the summer (Figure 3-13). Annual abundance was relatively low
compared to other years since blooms began to occur regularly just before the outfall
came on line in 2000. The cold winter/spring period apparently delayed the onset of
the bloom in 2014. The rapid warming in May contributed to rapid senescence,
quickly ending the summer bloom. The short-lived bloom was not particularly
strong, but because it peaked in May, later than typical for Phaeocystis blooms, it fell
within the “summer” Contingency Plan threshold season. The summer Phaeocystis 
threshold is extremely low, so the moderate bloom resulted in an exceedance. 
Figure 3-13. Mean nearfield abundance Phaeocystis pouchetii, 1992–2014 . (Top) Winter/spring.
(Bottom) Summer. Note difference in scale for winter/spring and summer. (No Phaeocystis were
detected in years with no symbol.) 
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

23 
Similar to 2013, abundance of the toxic dinoflagellate Alexandrium fundyense in 2014
was lower than it had been in recent years, with only a small bloom (Figure 3-14).
Cell counts were at the lowest levels reported since before 2005. The cold
winter/spring and a lack of storms with winds from the northeast when waters were
warmer in late May and June may have contributed to the modest Alexandrium bloom
in Massachusetts Bay. Elevated abundances and paralytic shellfish poisoning (PSP)
toxicity were observed in the Gulf of Maine in late May and early June, later than the
April and early May storms that could have transported cells into Massachusetts Bay.
Consequently, 2014 marked a second consecutive year with no shellfishing closures
due to PSP toxicity in Massachusetts Bay. 
Figure 3-14. Nearfield abundance of Alexandrium fundyense, 1992–2014. 
1
10
100
1000
10000
100000 
Alexandrium per sample (CELLS/L +1 ) 
baseline outfall discharge caution threshold

24 
Zooplankton Communities 
The abundances of total zooplankton and many dominant species groups were
relatively high in 2014, continuing a trend of greater abundances since lows in 2005
(Figure 3-15, Libby et al. 2015). Increases in abundances of a wide variety of
species, including adults and copepodites of Pseudocalanus spp., Temora longicornis , 
Oithona similis , and Calanus finmarchicus , contributed to the increase in total
zooplankton abundance. 
The relatively high abundance of total zooplankton was observed throughout
Massachusetts Bay (Figure 3-16). Abundances of total zooplankton mostly peaked in
June or July, and with levels at or above maxima for the monitoring program at some
stations. 
Figure 3-15. Long-term average zooplankton abundance. The graph was derived from a time-series
analysis of data from Stations N04 and N18, 1998–2014. The long-term mean, shown as the dashed
line, is 38,000 animals per cubic meter. 
0
10,000
20,000
30,000
40,000
50,000
60,000
70,000
1998 2002 2006 2010 2014 
Total zooplankton (animals m -3 ) Trend
Multi-year mean

25 
Figure 3-16. Total zooplankton abundance at selected stations in 2014 compared to baseline
(Harbor Outfall) and post-discharge (Bay Outfall) monitoring years. Total zooplankton levels
were relatively high throughout Massachusetts Bay. 
Reasons for the relatively high zooplankton abundances in 2014 and the long-term
trends are not well understood, but the increased grazing by zooplankton may have
contributed to the long-term decline in phytoplankton abundance described above.
Linear-regression analyses suggested that annual mean zooplankton abundance
explains 30–40% of the variability in annual mean phytoplankton abundance at
nearfield stations (Figure 3-17). Large-scale regional patterns are likely a major
factor, but a lack of comparable data across the broader geographic region prevents a
direct comparison. 
J F M A M J J A S O N D
0
5
10
15
20
25
10,000 individuals/m3
TOTAL ZOOPLANKTON 
Harbor Outfall
Bay Outfall 
2014
J F M A M J J A S O N D
0
5
10
15
20
25
10,000 individuals/m3
TOTAL ZOOPLANKTON
J F M A M J J A S O N D
0
5
10
15
20
25
10,000 individuals/m3
TOTAL ZOOPLANKTON F22
N04
J F M A M J J A S O N D
0
5
10
15
20
25
10,000 individuals/m3
TOTAL ZOOPLANKTON
N18
J F M A M J J A S O N D
0
5
10
15
20
25
10,000 individuals/m3
TOTAL ZOOPLANKTON
F06
F23
J F M A M J J A S O N D
0
5
10
15
20
25
10,000 individuals/m3
TOTAL ZOOPLANKTON
F13

26 
Figure 3-17. Annual total phytoplankton versus total zooplankton at nearfield stations N04 and
N18, 1998–2014. 
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. Water-column Station F22 is in Stellwagen Basin, to the northwest of the
sanctuary and is considered to be representative of northern, offshore conditions. 
Ammonium levels have remained low at Station F22 since the outfall began to
discharge (see, for example, 2014 results in Figures 3-6 and 3-7, above). Levels have
also remained low at Station F06 located to the south and offshore. In contrast,
increased ammonium levels have been detected in the nearfield, at Station N18, while
decreases have been detected at representative harbor and coastal stations. 
Bottom-water dissolved oxygen concentrations at Station F22 were relatively low
throughout 2014 (Figure 3-18). These levels reflected the warm, saline conditions
found throughout the region. Data from the NERACOOS Mooring A01, located
within the sanctuary, documented the return to oxygenated conditions with fall
mixing.

27 
Figure 3-18. Deep and near-bottom water dissolved oxygen concentrations at Station F22 and the
NERACOOS Mooring A01, inside Stellwagen Bank Marine Sanctuary. The NERACOOS
measurement is at 51 m, the deep Station F22 at 54 m, and the near-bottom Station F22 at 78 m. 
DO = dissolved oxygen 
Potential influences of the MWRA outfall on Stellwagen Bank National Marine
Sanctuary were recently assessed using results from the numerical Bays
Eutrophication Model, which simulates and predicts the physical and biological
conditions in Massachusetts Bay (Zhao et al. 2015). Using 2013 conditions, modelers
compared ammonium concentrations along a 60-kilometer east-west transect, passing
over the outfall, and across Stellwagen Basin and Stellwagen Bank (Figure 3-19).
One model simulation used nutrient concentrations measured in outfall effluent, and a
comparison simulation set outfall nutrient inputs to zero. 
5
6
7
8
9
10
11
12
Oxygen concentration (mg/l)
NERACOOS Buoy A (51 m)
Deep DO station F22 (54 m)
Near-bottom DO station F22 (78 m)

28 
Figure 3-19. Location of an east-west transect from Deer Island, across MWRA outfall, through
Stellwagen Bank, for modeled water-quality parameters.

29 
As has also been observed from monitoring data, the model simulations using 2013
effluent data showed that increased ammonium concentrations from the outfall occur
mostly within 10 kilometers of the discharge and in the deepest part of the water
column (Figure 3-20). The simulations showed small increases (0.5–1.5 μM) in
ammonium concentrations extending into waters over Stellwagen Basin in some
months (August and October), but no such detectable changes in waters over the
Stellwagen Bank. 
Figure 3-20. Modeled increases in ammonium concentrations ( μ M) due to MWRA discharge, on
the east-west transect across the MWRA outfall and into Stellwagen Bank National Marine
Sanctuary for six months in 2013. The model simulations show small increases in ammonium levels
in Stellwagen Basin (the deepest waters) in August and October, but no changes on Stellwagen Bank
(the offshore shallower area). 
Ammonium is, as discussed in the Water Quality section above, the most sensitive
indicator of any outfall influence in the bay. Similar model simulations, comparing
actual discharge data so a scenario presuming no outfall inputs, showed only
negligible differences in chlorophyll and dissolved oxygen levels. 
(Additional model results are also presented in Section 6, Special Studies.) 
Feb
Apr
Jun
Aug
Dec
Oct 
μ M

30 
Boston Harbor 
Water quality in Boston Harbor has improved throughout the past 20 years, and those
improvements continued in 2014 (Taylor 2015). MWRA’s in-house Boston Harbor
monitoring program confirmed that harbor-wide concentrations of total nitrogen and
phosphorus remained low, as they have since discharges to the harbor ended. In
2015, total suspended solids increased and transparency decreased, but those changes
could be attributed to shoreline erosion rather than to wastewater inputs. Dissolved
oxygen concentrations remained high, as they have been since 2001. Concentrations
of the bacterial indicator Enterococcus were the lowest since routine monitoring
began in 1995. (Additional bacterial water-quality data are presented in Section 6,
Special Studies.) 
One of the most dramatic improvements in Boston Harbor has been the decrease in
ammonium levels (Figure 3-21; Libby et al. 2015). Ammonium concentrations
dropped dramatically as soon as effluent discharge was diverted from the harbor to
Massachusetts Bay in 2000, and they have remained low. In 2014, ammonium levels
at Station F23, at the mouth of Boston Harbor, were near the bottom of the historic
range in February through August and about average for the post-diversion years
throughout the fall. 
Figure 3-21. Ammonium levels at Station F23 in Boston Harbor. Red lines = Boston Harbor
discharge years, Blue lines = Massachusetts Bay discharge years. Black line = 2014 
J F M A M J J A S O N D
0
5
10
15 
μ M

31 
Total phytoplankton biomass, measured as chlorophyll, was slightly higher than
during many of the years since the discharges to the harbor ended but lower than
when effluent was discharged to the harbor (Taylor 2015). Total phytoplankton
abundance by counts was relatively low throughout the year, while total zooplankton
abundance was relatively high at Station F23, off Deer Island at the mouth of Boston
Harbor (Libby et al. 2015). 
While total zooplankton abundance peaked in June and July in Massachusetts Bay,
there were two peaks at Station F23, one in June and July and a second one in
September. The early peak was largely due to abundances of Acartia spp., which are
common in the lower-salinity waters found in the harbor (Figure 3-22). The May
peak in Acartia abundance reflects a long-term shift observed since 2001, which
coincided with the transfer of effluent discharge from the harbor to the bay. 
Figure 3-22. Acartia spp. abundance at Station F23 in Boston Harbor. Red lines = Boston Harbor
discharge years, Blue lines = Massachusetts Bay discharge years. Black line = 2014 
J F M A M J J A S O N D
0
1
2
3
4
5
10,000 individuals/m3

32 
J F M A M J J A S O N D
0
0.3
0.6
0.9
1.2
1.5
10,000 individuals/m3
ca t a udso ca 
The data suggest that the shift has been caused by an earlier peak in Acartia
hudsonica , which is the dominant of the two Acartia species that occur in the harbor. 
Acartia hudsonica populations are typically more abundant in the spring, while
populations of the other species present in the harbor, Acartia tonsa , peak later in the
year (Figure 3-23). It remains unknown whether the increased dominance of Acartia
hudsonica is a result of the decreased effluent loads to the harbor or whether it is a
result of broader regional changes. 
Figure 3-23. Acartia hudsonica and Acartia tonsa abundance at Station F23 in Boston Harbor. 
Red lines = Boston Harbor discharge years, Blue lines = Massachusetts Bay discharge years. Black
line = 2014 
Contingency Plan Thresholds 
All water-quality parameters were within normal ranges throughout 2014. There was,
however, a Contingency Plan caution-level threshold exceedance for one nuisance
algae measure, summer Phaeocystis pouchetii (Table 3-1). The exceedance has been
analyzed and found to be primarily due to cool temperatures in March and April,
which caused a delay in the annual phytoplankton cycle. The overall magnitude of
the Phaeocystis pouchetii bloom was moderate in 2014, but it peaked in May rather
than in March or April, which has been typical. No aesthetic or other adverse effects
were observed from the 2014 bloom, and abundance had dropped to much lower
levels by mid-June. 
J F M A M J J A S O N D
0
0.3
0.6
0.9
1.2
1.5
, 
Acartia hudsonica Acartia tonsa

33 
Table 3-1. Contingency Plan threshold values and 2014 results for water-column monitoring. 
Parameter Baseline Caution Level Warning Level 2014 Results 
Dissolved oxygen* 
Nearfield
concentration 6.05 mg/L 6.5 mg/L 6.0 mg/L 7.19 mg/L 
Nearfield percent
saturation 65.3% 80% 75% 81.6% 
Stellwagen
concentration 6.23 mg/L 6.5 mg/L 6.0 mg/L 6.76 mg/L 
Stellwagen percent
saturation 67.2% 80 75% 75.0% 
Nearfield depletion
rate 0.024 mg/L/d 0.037 mg/L/d 0.049 mg/L/d 0.015 mg/L/d 
Chlorophyll 
Annual 72 mg/m 2 108 mg/m 2 144 mg/m 2 66 mg/m 2 
Winter/spring 50 mg/m 2 199 mg/m 2 None 75 mg/m 2 
Summer 51 mg/m 2 89 mg/m 2 None 68 mg/m 2 
Autumn 90 mg/m 2 239 mg/m 2 None 50 mg/m 2 
Nuisance algae Phaeocystis pouchetii 
Winter/spring 622,000 cells/L 2,860,000 cells/L None 27,800 cells/L 
Summer 72 cells/L 357 cells/L None 
395,000 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 106 cells/L 
Summer 14,635 cells/L 43,100 cells/L None Absent 
Autumn 10,050 cells/L 27,500 cells/L None 270 cells/L 
Nuisance algae nearfield Alexandrium fundyense 
Any nearfield
sample 
Baseline maximum 
163 cells/L 100 cells/L None 20 cells/L 
PSP toxin extent NA New incidence None No new incidence 
*Dissolved oxygen caution and warning levels represent numerical criteria, with the caveat “unless
background conditions are lower.” Results are therefore compared to the baseline rather than to the
caution and warning levels. 
PSP = paralytic shellfish poisoning 
NA = not applicable

34 
4. Sea Floor 
Sea-floor monitoring in 2014 included sampling and analysis of soft-bottom sediment
conditions, tracers, contaminants, and infauna at 14 stations; sediment-profile
imaging at 23 stations; and video surveys at 23 hard-bottom stations, including one
active and one inactive outfall diffuser (Figures 4-1 through 4-3). 
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.

35 
Figure 4-2. Sediment-profile imaging stations. Images are taken at 23 stations and provide rapid
assessments of benthic habitats. Also shown are the NDBC buoy and the MWRA outfall diffuser. SPI
= sediment-profile imaging

36 
Figure 4-3. Hard-bottom stations. Video and still photographs are collected at 23 stations, including
one active diffuser and one inactive diffuser, which has not been opened.

37 
Soft-bottom sediment sampling was completed over two days in early August, with
samples analyzed for grain-size distribution, total organic carbon, the effluent tracer 
Clostridium perfringens spores, chemical contaminants, and benthic infauna. The 14
stations 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
nearfield groups, for a total of eleven stations. 
Sediment-profile imaging was also completed in August. Triplicate images from 23
stations 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. 
Video surveys of hard-bottom areas were performed in June, surveying 23 stations,
including an actively discharging diffuser head at the eastern end of the outfall and an
unopened diffuser at the western end of the outfall. 
Sediment Characteristics and Tracers 
Sediment grain-size distributions in 2014 varied broadly among stations, ranging
from silt and clay at some stations to mostly sand at others (Nestler et al. 2015).
Although sediment grain-size distributions have remained generally consistent at
individual stations over the years of the monitoring program, there were some notable
changes in 2014. In particular, some stations, which had become coarser following
early 2013 storms returned to more typical, siltier conditions. Overall, the percentage
of fine particles, silts and clays, making up the sediments was close to the historical
average. One exception was at Station NF24, which is located close to the outfall,
where percent fine material reached a record high. 
Percent organic carbon content, which tracks closely with fine material in the
samples, was 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 (Figure 4-4).

38 
Figure 4-4. Percent total organic carbon by region, during the baseline, other post-diversion
years, and 2014. (mean ± standard deviation) There have been no changes from the baseline;
variability for the farfield in 2014 resulted from there being only three stations, with widely varying
sediment grain size. ( Tran = transition area, stations located between Boston Harbor and the outfall;
NF<2km = nearfield stations located within 2 km of the outfall diffusers; NF>2km = nearfield stations
located further than 2 km from the diffusers; FF = farfield stations offshore from the outfall.) 
As in past years since the offshore outfall began to discharge (except 2006), it was
possible to detect elevated levels of the effluent tracer, Clostridium perfringens 
spores, at the stations located closest to the outfall (Figures 4-5 and 4-6). Past years’
statistical analyses have shown that these increases close to the outfall are statistically
significant and consistent with predictions made during the outfall-siting process. In
2014, there was a seemingly large increase in the number of spores normalized to the
percentage of fine material at the sites closest to the outfall. This increase resulted in
part from changing grain-size distributions at some stations. Some stations, with
higher than typical spore counts were especially sandy, so the spore count normalized
to percent fine material was especially high. Conversely, the siltiest station, where
spore counts are expected to be high, had record low spore counts. Outside the area
closest to the outfall, concentrations of Clostridium perfringens spores have declined
or remained comparable to the baseline throughout the duration of the monitoring
program. 
Baseline Post-diversion 2014
Mean Concentration (%)
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
4.0
Tran NF <2km NF >2km FF

39 
Figure 4-5. Concentrations of Clostridium perfringens spores, corrected for sediment grain size,
in 2014. 
Figure 4-6. Mean concentrations of Clostridium perfringens spores during the baseline and
outfall-discharge years. ( Tran = transition area, stations located between Boston Harbor and the
outfall; NF<2km = nearfield stations located within 2 km of the outfall diffusers; NF>2km = nearfield
stations located further than 2 km from the diffusers; FF = farfield stations offshore from the outfall.) 
Clostridium perfringens (cfu/g dry/%fines)
0
50
100
150
200
250
300
350 Outfall Startup
1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014
Tran
NF <2km
NF >2km
FF

40 
Sediment Contaminants 
In general, over the course of the monitoring program, concentrations of toxic
contaminants in sediments have remained stable or slowly declined. Similar to other
measures, concentrations of sediment contaminants tend to be higher in sediments
with finer grain-size distributions. That pattern remained evident in 2014, with the
finest-grained sediment stations having the highest levels of contaminants. Stations
closest to Boston Harbor, the major historic source of contaminants, tend to have
higher concentrations than those offshore. Statistical analyses have found no
indications of any effects of the outfall on Massachusetts Bay sediments (Nestler et
al. 2015). 
Concentrations of mercury, for example, showed no indications of any outfall effect
(Figure 4-7). Mercury concentrations at the stations closest to the outfall have
remained low, lower than baseline levels in most years. Levels at nearfield stations
farther from the outfall reached a historic low for the monitoring program in 2014. 
Figure 4-7. Mean concentration of mercury during the baseline and outfall-discharge years.
( Tran = transition area, stations located between Boston Harbor and the outfall; NF<2km = nearfield
stations located within 2 km of the outfall diffusers; NF>2km = nearfield stations located further than 2
km from the diffusers; FF = farfield stations offshore from the outfall.) 
Mercury Concentration (mg/kg dry)
0.0
0.1
0.2
0.3
0.4
0.5
0.6 Outfall Startup
1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014
Tran
NF <2km
NF >2km
FF

41 
Concentrations of total polychlorinated biphenyls (PCBs) provided the best indication
of the long, slow declines in levels of organic contaminants following bans in their
manufacture and use (Figure 4-8). Although the data are variable, there have been
some indications of declines in PCB concentrations throughout Massachusetts Bay. 
Figure 4-8. Mean PCB concentration by region, during the baseline, other post-diversion years,
and 2014. ( Tran = transition area, stations located between Boston Harbor and the outfall; NF<2km =
nearfield stations located within 2 km of the outfall diffusers; NF>2km = nearfield stations located
further than 2 km from the diffusers; FF = farfield stations offshore from the outfall.) 
Soft-bottom Communities 
The 14 soft-bottom samples collected and analyzed in 2014 yielded 21,863
organisms, classified into 183 species and 24 other discrete taxonomic groups
(Nestler et al. 2015). Infaunal abundance was within the range observed over the
monitoring program, but was appreciably higher than in 2013 in all regions except the
farfield (Figure 4-9). Relative abundances of the five dominant species in the
samples, those contributing at least 5% to total abundances, were low in 2014, as has
been observed for several years (Figure 4-10). In particular, the polychaete 
Prionospio steenstrupi , which was the numerically dominant species during much of
the 1990s and 2000s, continued to be present in relatively low numbers. 
Baseline Post-diversion 2014
Mean Concentration (ng/kg dry)
0
5
10
15
20
25
Tran NF <2km NF >2km FF

42 
Figure 4-9. Mean infaunal abundance per sample in four areas of Massachusetts Bay, 1992–2014. 
(Tran = transition area, stations located between Boston Harbor and Massachusetts Bay; 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) 
Figure 4-10. Mean abundance per sample of five dominant species compared to total abundance
at nearfield stations, 1992–2014. 
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 2014
Tran
NF <2km
NF >2km
FF 
Total abundance
0
500
1000
1500
2000
2500
3000
3500
4000 Outfall Startup
1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014
Aricidea catherinae
Mediomastus californiensis
Prionospio steenstrupi
Spio limicola
Tharyx acutus
Total abundance

43 
A series of multivariate analyses assessed spatial and temporal patterns in the soft-
bottom benthic communities and found no particular species or type of community
that could be specifically associated with the outfall. A cluster analysis identified two
main infaunal assemblages, with an outlier at Station FF04, which is offshore in
Stellwagen Basin and has consistently had a distinct community. An ordination
analysis demonstrated that species distributions were largely determined by sediment
type rather than by proximity to the outfall (Figure 4-11). 
Figure 4-11. Percent fine sediments superimposed on ordination plot of the 2014 infauna
samples. Each point on the plot represents one of the 14 samples; similarity of species composition is
indicated by proximity of points on the plot. Faunal assemblages (Groups I, II, and sub-groups)
identified by cluster analysis are circled on the plot.

44 
Sediment-profile Imaging 
Sediment-profile images continued to show no adverse effects of the outfall (Nestler
et al. 2015). Secondary treatment effectively reduces contaminants that might affect
the sediments, and monitoring has shown that physical processes, such as storms and
storm-induced sediment transport, are the primary stressors on the Massachusetts Bay
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 the
effluent discharge. 
The average RPD depth (the depth to which oxygen penetrates into sediments as
determined by color changes) was the deepest ever measured during the monitoring
program (Figure 4-12). The environmental concern before the outfall came on line
was that the RPD depth would become shallower, causing stress on sensitive
sediment-dwelling organisms, so a deeper RPD depth continued to indicate that there
has been no adverse effect from the discharge. 
Figure 4-12. Annual apparent color RPD depth for data from nearfield stations. (mean ± standard
deviation) The average RPD discharge-period mean has been deeper than the baseline mean,
continuing to indicate that there has been no adverse effect from the discharge. 
-6
-5
-4
-3
-2
-1
0 
RPD (cm) 
Mean RPD Depth +/- 1SD
Outfall Startup
Threshold

45 
Counter intuitively, the camera images detected a trend beginning in 2013 towards
increased numbers of “pioneering” or “Stage I” organisms. This finding would be
unexpected where there are deepening RPD depths. It was also not anticipated from
the infaunal organism analyses presented above, either from the identification of
individual animals or from the diversity and other community-parameter
measurements. The change appears to be related to a slight coarsening of sediment
grain-size and a resulting decline in visible biogenic structures in the sediment-profile
images, a factor in determining succession stage. 
Hard-bottom Communities 
Photographic coverage of the hard-bottom habitat in the vicinity of the outfall in 2014
included 13–28 minutes of video footage at each station. A total of 488 minutes of
video were viewed and analyzed. The footage was generally similar to that taken in
2011, the last time that hard-bottom communities were surveyed (Nestler et al. 2015).
The species and the number of species have remained relatively constant over the
course of the monitoring program. The distribution of the species has also remained
relatively constant. Coralline algae continued to be the most common and
widespread component of the hard-bottom benthic communities, being found at 18 of
the 23 stations. Lush growth continued to be found on the open diffuser head,
included as one of the stations (Figure 4-13). 
Figure 4-13. Lush growth on active diffuser in 2014.

46 
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.
MWRA’s deepwater reference station FF04 lies within the depositional part of the
sanctuary, in Stellwagen Basin, which is considered a long-term sediment sink. 
Sediment chemistry has not changed at Station FF04, where, because of its
depositional environment, some accumulation of contaminants might be expected to
occur. For example, mercury and PCB levels at Station FF04 have remained constant
throughout the duration of monitoring (Figures 4-14 and 4-15). 
Station FF04 is considered typical of the deep waters offshore from the outfall,
representative of a number of stations monitored in earlier years of the monitoring
program, and it continues to support infaunal communities typical of what was found
at the larger suite of deepwater stations. The deepwater stations, including Station
FF04, have always shown distinct differences from those found at shallower stations,
probably due to their depth, their fine-grained sediments (see Figure 4-11, above),
and their distance from shore. 
Figure 4-14. Mean concentrations of mercury at selected stations, 1992–2014. Station FF04 is
within Stellwagen Basin, a long-term sediment sink. 
Mercury Concentration (mg/kg dry)
0.0
0.2
0.4
0.6
0.8
1.0
1.2
Outfall Startup
1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014
FF04
NF12
NF17
NF21

47 
Figure 4-15. Mean concentrations of total PCBs at selected stations, 1992–2014 . Station FF04 is
within Stellwagen Basin, a long-term sediment sink. 
Boston Harbor 
While the chemistry and biology of the Massachusetts Bay sea floor have not been
affected by the relocated outfall, conditions have greatly improved and continue to
improve in Boston Harbor as a result of the Boston Harbor Project and more recent
improvements, including enhancements to treatment and remediation of combined
sewer overflows. MWRA has conducted ongoing sea-floor monitoring in Boston
Harbor since 1991. Annual sediment and infauna samples are taken from nine
stations (Figure 4-16). 
Total PCB Concentration (ng/kg dry)
0
10
20
30
40
50
60
70
80
Outfall Startup
1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014
FF04
NF12
NF17
NF21

48 
Figure 4-16. Soft-bottom sampling stations in Boston Harbor. Nine stations are sampled each year
for sediment characteristics and infauna analyses. 
Concentrations of total organic carbon and Clostridium perfringens spores have
declined over time, and infaunal diversity has increased. Multivariate analyses have
found two main faunal assemblages, one found throughout the harbor and a second
found in slightly more organically enriched sediments in the inner harbor and in
Quincy Bay (Figure 4-17). The station most different from others is T04, at the
mouth of Savin Hill Cove in Dorchester Bay. The infaunal assemblages likely reflect
a gradient in tidal flushing as well as differences in inputs of organic matter, nutrients,
and other possible contaminants.

49 
Figure 4-17. Ordination plot of 2014 Boston Harbor infauna samples (2 samples/station). Group I
comprises stations from the outer harbor; Group II includes Station C019 in the inner harbor and
Station T07 in Quincy Bay. The assemblage most different from others was found at Station T04, at
the mouth of Savin Hill Cove, in Dorchester Bay. 
Sediment-profile images have also documented improvements in Boston Harbor
sediments. An eelgrass bed has persisted at Deer Island Flats since 2008.
Improvements continued to be observed in 2014; for example, the RPD has deepened
at Station T02, in President Roads near Deer Island Flats (Figure 4-18). Tucker et al.
(2014) found that in the early 1990s, sediment oxygen demand and nutrient fluxes at
this station increased when macrofauna, particularly tube-building amphipods,
colonized the sediments. As reductions to loading to the harbor progressed, mean
rates of oxygen uptake and release of ammonium, nitrate, and phosphate decreased.
Higher sediment redox potential resulted in the deepening RPD.

50 
Figure 4-18. Sediment profiles from Station T02, in President Roads, near Deer Island Flats,
1992–2014. Improvements in habitat quality occurred from the 1990s to the late 2000s and persisted in
2014. Scales along the sides of each image are in cm.

51 
Contingency Plan Thresholds 
All sediment-contaminant concentrations remained well below Contingency Plan
thresholds in 2014, and RPD depth remained more than three times deeper than the
caution level. However, for a fifth consecutive year, there were Contingency Plan
threshold exceedances for two sea-floor community parameters (Table 4-1). Values
for Shannon-Wiener diversity and Pielou’s evenness, both diversity measures, were
higher than the upper caution-level ranges (Figure 4-19). Two other community
threshold parameters, total number of species per sample (species richness) and
Fisher’s log-series alpha, another diversity measure, were within the caution-level
ranges. Percent opportunists among the soft-bottom community remained far below
caution and warning levels. 
The exceedances of Shannon-Wiener diversity and Pielou’s evenness have been
shown to be driven by changes in abundances of a few dominant species (Nestler et
al. 2015). Analyses have found no patterns suggesting any effect of the outfall.
Spatial patterns have been consistent throughout the duration of the monitoring
program, and while species assemblages have changed somewhat over time, the
degree and pace of change have been similar throughout the region.

52 
Table 4-1. Contingency Plan threshold values and 2014 results for sea-floor monitoring . 
Parameter Baseline Caution Level Warning Level 2014 Results 
Polycylclic aromatic hydrocarbons (PAHs) (ng/g dry weight) 
Acenaphthene 22.7 – 43.5 None 500 28.3 
Acenaphylene 30.3 – 43.1 None 640 11.1 
Anthracene 101 – 159 None 1,100 77.3 
Benzo(a)anthracene 206 – 302 None 1,600 176 
Benzo(a)pyrene 204 – 298 None 1,600 182 
Chrysene 164 – 296 None 2,800 172 
Dibenzo(a,h)anthracene 27.8 – 38.3 None 260 26.7 
Fluoranthene 422 – 621 None 5,100 389 
Fluorene 35.5 – 66.6 None 540 32.5 
Naphthalene 53.6 – 103 None 2,100 31.6 
Phenanthrene 273 – 431 None 1,500 247 
Pyrene 412 – 579 None 2,600 362 
Total HMW PAH 2,790 – 3,850 None 9,600 2,440 
Total LMW PAH 1,390 – 1,630 None 3,160 814 
Total PAHs 4,180 – 5,400 None 44,792 3,260 
Other organic contaminants (ng/g dry weight) 
p,p’-DDE 0.386 – 1.00 None 27 0.37 
Total DDTs 2.51 – 5.69 None 46.1 0.79 
Total PCBs 10.2 – 20.2 None 180 7.17 
Metals (μg/g dry weight) 
Cadmium 0.0727 – 0.185 None 9.6 0.11 
Chromium 59.2 – 79.9 None 370 47.6 
Copper 19.1 – 25.2 None 270 22.9 
Lead 41.1 – 46.3 None 218 32.7 
Mercury 0.159 – 0.353 None 0.71 0.12 
Nickel 15.7 – 17.2 None 51.6 8.46 
Silver 0.335 – 0.485 None 3.7 0.17 
Zinc 49.5 – 57.5 None 410 41.5 
Sediment parameters 
RPD depth NA <1.18 cm None 4.01 cm 
Benthic community parameters 
Species per
sample NA <42.99 or >81.85 None 62.73 
Fisher’s log-series
alpha NA <9.42 or >15.8 None 13.35 
Shannon diversity NA <3.37 or >3.99 None 4.03, caution level
exceedance 
Pielou’s evenness NA <0.57 or >0.67 None 0.68, caution level
exceedance 
% opportunists NA >10% >25% 0.12% 
HMW = high molecular weight; LMW = low molecular weight 
NA = not applicable; RPD = redox potential discontinuity

53 
Figure 4-19. Annual community parameters with nearfield Contingency Plan thresholds. (mean ±
standard deviation) 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 to show potentially meaningful
changes from the baseline. 
30
50
70
90 Total species richness 
6
10
14
18 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
4
8
12 
Percent opportunists 
Baseline mean Thresholds
Mean +/-1SD Outfall startup

54 
5. Fish and Shellfish 
Each year MWRA monitors the health of winter flounder from the Massachusetts Bay
outfall site, Deer Island Flats in Boston Harbor, off Nantasket Beach just outside the
harbor, and eastern Cape Cod Bay (Figure 5-1). Every three years, most recently in
2012, monitoring includes chemistry measurements in flounder fillets and liver,
lobster meat and hepatopancreas, and cage-deployed blue mussels. Sampling and
analysis in 2014 was limited to winter flounder health. 
Figure 5-1. Flounder sampling sites. Also shown are the two instrumented buoys, the MWRA outfall
diffuser, and the boundaries of the Stellwagen Bank National Marine Sanctuary. OS=outfall site;
DIF=Deer Island Flats; NB=Nantasket Beach

55 
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 2014,
50 sexually mature flounder were collected from each site (Moore et al. 2014). Catch
per unit effort, which has varied through time, was moderate near the outfall,
approximately at the median for the monitoring program. Abandoned fishing gear,
sometimes referred to as “ghost gear,” continued to interfere with catches,
particularly in muddy depressions at the outfall and at Deer Island Flats (Figure 5-2). 
Figure 5-2. “Ghost” lobster gear brought up in a flounder trawl. 
Average ages of fish were relatively high in 2014. Lengths and weights were
somewhat lower than typically observed but remained within historic ranges at all
sites. As has been common throughout the duration of the monitoring program, the
catches were dominated by females. Skewed sex ratios are common in winter
flounder populations, possibly related to temperature, self-segregation by age and sex,
and different growth rates of males and females. There are no indications of any
effect of the Massachusetts Bay effluent discharge on sex ratios. Catches from
eastern Cape Cod Bay, the station farthest (75 km) from the outfall, have in many
years had the highest proportion of females.

56 
Measures of external condition, such as fin erosion and blind-side ulcers, also fell
within historic ranges. Prevalence of fin erosion, a condition that can be indicative of
elevated concentrations of ammonium and other pollutants, ranged from a low of 8%
at the outfall to a high of 26% at Deer Island Flats. 
Blind-side ulcers, which were first noted in 2003, were rare in 2014. Elevated
occurrence of ulcers occurred in 2003–2006 and again 2011. The pathology of the
ulcers has been studied but is not well understood. 
The incidence of centrotubular hydropic vacuolation (CHV), a mild condition
associated with exposure to contaminants and a neoplasia precursor, remained lower
than the baseline observations. Incidence of CHV, corrected for age, was slightly
lower at the outfall than in 2013 (Figure 5-3). CHV incidence in fish from Deer
Island Flats reached a record low, remaining well below the relatively high baseline
levels. Average severity of CHV (not shown) also remained lower than baseline
levels. 
Figure 5-3. Annual prevalence of centrotubular hydropic vacuolation (CHV), corrected for age. 
(DIF=Deer Island Flats, ECCB=Eastern Cape Cod Bay, NB=Nantasket Beach, OS=outfall site) 
No neoplasms (liver tumors) were observed in any fish from any site. Incidence of
neoplasia has been rare throughout the area since MWRA monitoring started in 1991,
although levels were higher in flounder taken from Boston Harbor for studies during
the 1980s (see below). Neoplasia has never been observed in a fish taken from the
vicinity of the outfall. 
% CHV/Mean Age
0
2
4
6
8
10
12
14 Outfall Startup
1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014
DIF
ECCB
NB
OS

57 
Boston Harbor 
While there have been no indications of adverse effects near the outfall, there have
been major improvements in flounder health in Boston Harbor. During the 1970s and
1980s, pollutant-related external abnormalities and liver disease were common in
winter flounder taken from Boston Harbor. Catches made by MWRA’s predecessor,
the Metropolitan District Commission, in 1979, found that almost half of the fish had
fin erosion. Incidence of fin erosion continues to be variable and greater in fish from
Deer Island Flats, near the former Boston Harbor outfall, than it is in fish from near
the Massachusetts Bay outfall or off Nantasket Beach, outside the harbor. 
Studies by the National Marine Fisheries Service in 1984 and 1985 found that
flounder from Deer Island Flats had a variety of cancerous tumors and pre-cancerous
conditions, such as CHV, with tumors present in 15% of the fish (Murchelano and
Wolke 1991). Routine sampling and analysis for liver disease in fish from Deer
Island Flats began in 1987 and found that more than half the fish had pre-cancerous
liver conditions. That sampling program, adopted by MWRA, has continued,
documenting substantial declines in tumors and tumor precursors (Figure 5-4). Liver
tumors were present in 12% of the flounder caught in 1988 but have not been seen
since 2004. Incidence of the most common tumor precursor, CHV, has dropped by
more than half, reaching a new low in 2014. 
Figure 5-4. Incidence of liver tumor precursors and liver tumors in winter flounder from Deer
Island Flats in Boston Harbor, 1987–2014. Incidence of the tumor precursor CHV has fallen,
reaching a new low in 2014, and tumors are now rare. 
0
10
20
30
40
50
60
70
80
1985 1990 1995 2000 2005 2010 2015 
% Flounder Affected 
Liver Tumor Precursors
Liver Tumors

58 
Contingency Plan Thresholds 
There was no exceedance of the one Contingency Plan threshold for fish and shellfish
in 2014 (Table 5-1). Incidence of CHV, the most common indicator of liver disease
in the winter flounder of the region, was 10% in fish taken from the vicinity of the
outfall, lower than the 44.9% caution threshold and the baseline average. CHV
incidence in flounder was the only threshold parameter calculated for 2014; chemistry
parameters in flounder, lobster, and mussels are measured every three years and will
be reported next in 2015. 
Table 5-1. Contingency Plan threshold values and 2014 result for fish-and-shellfish monitoring. 
Parameter Baseline Caution Level Warning Level 2014 Results 
Liver disease CHV 24.4% 44.9% None 10% 
CHV = centrotubular hydropic vacuolation

59 
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. This year’s overview focuses on bacterial water quality in Boston Harbor;
water-quality modeling; and ongoing monitoring by the Center for Coastal Studies in
Cape Cod Bay. 
Boston Harbor Bacterial Water Quality 
Before the Boston Harbor Project, bacterial pollution from untreated combined sewer
overflows (CSOs), incompletely treated primary wastewater effluent, and daily
discharge of digested sewage sludge (biosolids) resulted in widespread beach closures
and violations of bacterial water-quality standards throughout the harbor. Degraded
water quality from bacterial pollution was one of the main drivers behind the creation
of MWRA and the court-ordered Boston Harbor Project. 
Before 1991, wet-weather exceedances of water-quality standards were common and
severe, with many parts of Boston Harbor exceeding the Enterococcus bacteria
swimming standard (35 colonies/100 ml), sometimes by a factor of five or more
(Figure 6-1, left). Since 2007, after the completion of DITP and most CSO projects,
water quality in most of Boston Harbor and its tributaries meets the Enterococcus 
standard, even in wet weather (Figure 6-1, right). Remaining wet-weather 
Enterococcus exceedances occur in smaller areas and are less severe. 
The improvements in Boston Harbor have not been accompanied by any degradation
to Massachusetts Bay. MWRA conducts bacterial monitoring in the vicinity of the
Massachusetts Bay outfall in support of the Massachusetts Division of Marine
Fisheries shellfish sanitation programs. Results from that monitoring since the
offshore outfall came on line in 2000 have shown that bacterial water quality meets
the most sensitive standards, even in wet weather. A report on those results is
currently in preparation.

60 
Figure 6-1. Bacterial water quality prior to the Boston Harbor Project and after completion of the
treatment plant and most CSO projects. 
Prior to Boston Harbor projects (1989-1991) Most Boston Harbor projects complete (post-2007)

61 
Massachusetts Bay Water-Quality Modeling 
MWRA uses the numerical Bays Eutrophication Model to simulate and predict the
physical and biological conditions in Massachusetts Bay. The model includes a
hydrodynamic (ocean circulation) and a water quality model. It has been
continuously updated to incorporate new research methods and to improve agreement
of model results with monitoring observations. 
The most recent modeling efforts included simulations to examine the sensitivity of
water quality to hypothetical changes in nutrient loads from the Massachusetts Bay
outfall (Zhou et al. 2015). One impetus for the model runs was that a new program
for co-digestion of engineered food wastes at DITP is under consideration. Initial
estimates suggest that the additional input could increase nutrient concentrations in
the effluent by up to 5%. Model runs used 2013 conditions and included hypothetical
10% and 100% nutrient increases, as well as a no-increase control. All other
conditions were kept the same. Projections for concentrations of nutrients,
chlorophyll, and dissolved oxygen were compared between model runs. 
Past modeling and data analyses had shown that the outfall has little effect on the
function of Massachusetts Bay, and the new simulations using 2013 conditions
largely confirmed those results (Figures 6-2, 6-3). With a 10% increase in nutrient
loads, concentrations of dissolved inorganic nitrogen increased only in the immediate
vicinity of the outfall, primarily near the sea floor. With a 100% nutrient increase,
dissolved inorganic nitrogen levels were substantially higher, about 53% near the
seafloor in the vicinity of the outfall. A 10% increase resulted in almost
imperceptible effects on chlorophyll and dissolved oxygen (not shown), while a 100%
increase resulted in model projections showing modest changes, up to a 7% increase
in chlorophyll concentrations and less than a 0.5% decrease in dissolved oxygen
levels. 
The 2013 nutrient loads used in the hypothetical runs were considered to be
representative of typical conditions, as interannual variation in nutrient loads has been
small throughout the duration of the program. Results suggested that even a 10%
increase, a level that would exceed the effluent Contingency Plan threshold for
nitrogen, would exert little effect on the ecological health of Massachusetts Bay.

62 
Figure 6-2. Modeled dissolved inorganic nitrogen concentrations in bottom waters at selected
stations. Model runs based on 2013 conditions. Black lines = control; red = 10% increase in nutrient
load; blue = 100% increase. Where the three traces overlie each other, only the blue trace appears;
where red and black traces overlie each other but differ from blue, only the red trace appears. 
Outfall 
Outfall 
N01 
N07 
F06 
F02 
N01 N07 
F06 F02 
Outfall nutrient load 
Observed/control 
10% increase 
100% increase

63 
Figure 6-3. Modeled dissolved inorganic nitrogen concentrations in surface waters at selected
stations. Model runs based on 2013 conditions. Black lines = control; red = 10% increase in nutrient
load; blue = 100% increase. Where the three traces overlie each other, only the blue trace appears;
where red and black traces overlie each other but differ from blue, only the red trace appears. 
Outfall 
Outfall 
N01 
N07 
F06 
F02 
N01 N07 
F06 F02 
Outfall nutrient load 
Observed/control 
10% increase 
100% increase

64 
Cape Cod Bay Studies 
The Center for Coastal Studies has conducted a monitoring program in Cape Cod Bay
for many years, and since 2011, MWRA has collaborated on a portion of the
program. The Center for Coastal Studies monitoring program includes MWRA
water-column station F29, on the southern boundary of Stellwagen Bank National
Marine Sanctuary, MWRA stations F01 and F02 in Cape Cod Bay, and eight
additional stations (Figure 6-4). 
Figure 6-4. 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) 
The Center for Coastal Studies also monitors North Atlantic right whales, with aerial
surveys flown along a series of east-west tracks over Cape Cod Bay. The surveys
record presence, dive times, and whale behaviors. Right whales typically occur in
Cape Cod Bay during January through May, entering when nutrients and chlorophyll
levels are high, temperatures are low, and food is abundant. Water quality and
plankton abundance followed typical patterns in 2014 (Figure 6-5). Whales typically
remain in Cape Cod Bay to feed until June, when summer stratification of the water
column begins and zooplankton populations diminish. In 2014, whales were present
from February through May.

65 
Figure 6-5. Water quality measurements and zooplankton and phytoplankton abundance in
Cape Cod Bay in 2014. Whales were present in Cape Cod Bay from February through May. (Figures
from the Center for Coastal Studies.) 
Early whale sightings, in February 2014, appeared to follow temperature patterns,
with most sightings occurring in waters with temperatures 0.2–2.2ºC. Whale
distribution within Cape Cod Bay in 2014 was also associated with zooplankton
abundance, particularly in April, when 500 whales were sighted during nine aerial
reconnaissance flights (Figure 6-6). 
0
5
10
15
20
25
0
1
2
3
4
5
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Dec 
Temperature (˚C)
Chlorophyll (μg/L) and NOx (μM) Chlorophyll
Nitrate+Nitrite
Temperature 
0
2
4
6
8
10
0
5000
10000
15000
20000
25000
30000
Feb Mar Apr May Jun Jul Aug Sep Oct 
Phytoplanton (million cells/L)
Zooplankton (individuals/m3) Zooplankton
Phytoplankton

66 
Figure 6-6. Zooplankton abundance (individuals per square meter, blue scale) and whale sightings (black
dots) in Cape Cod Bay, January – April 2014. Whale sightings, particularly in April, were associated with
zooplankton abundance. (Figures from the Center for Coastal Studies.) 
Aerial surveys in 2014 recorded the fourth highest abundance of total right whales
since 1998. The surveys sighted the second highest total of known, individual
whales, representing about half the total known right whales in the North Atlantic
population. Annual whale sightings have been relatively high in recent years,
compared to the late 1990s and early 2000s (Figure 6-7). The North Atlantic right
whale remains protected under the U.S. Endangered Species and Marine Mammal
Protection acts, with Massachusetts and Cape Cod bays considered to be key habitat
for the western North Atlantic population. 
January February
March April

67 
Figure 6-7. Right whale sightings in Cape Cod Bay, 1998–2014 . (Figure from the Center for Coastal
Studies.) IPUE = individuals per unit effort

68 
References 
Libby PS, Borkman DG, Geyer WR, Turner JT, Costa AS. 2015. 2014 water column
monitoring results. Boston: Massachusetts Water Resources Authority. Report 2014-
09. 42 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. 2014. Flounder monitoring report: 2014
results. Boston: Massachusetts Water Resources Authority. Report 2014-16. 18 p. 
Murchelano RA, Wolke RE. 1991. Neoplasms and nonneoplastic liver lesions in
winter flounder, Pseudopleuronectes americanus , from Boston Harbor,
Massachusetts. Environmental Health Perspectives 90:17–26. 
Nestler EC, Diaz RJ, Hecker B, Pembroke AE, Keay KE. 2015. Outfall benthic
monitoring report: 2014 results. Boston: Massachusetts Water Resources Authority.
Report 2015-08. 42 p. 
Smolow M. 2015. Technical survey of nitrogen removal alternatives of the Deer
Island Treatment Plant. Boston: Massachusetts Water Resources Authority. Report
2015-01. 37 p. 
Taylor DI. 2015. Boston Harbor water quality, 1994–2014. Boston: Massachusetts
Water Resources Authority. Report 2015-05. 11 p.

69 
Tucker J, Giblin AE, Hopkinson CS, Kelsey SW, Howes, BL. 2014. Response of
benthic metabolism and nutrient cycling to reductions in wastewater loading to
Boston Harbor, USA. Estuarine, Coastal and Shelf Science 151:54–68. 
Werme C, Rex AC, Hunt, C. 2012. Outfall monitoring overview background: 2012
update. Boston: Massachusetts Water Resources Authority. Report 2012-02. 59 p. 
Zhou L, Chen C, Beardsley RC, Codiga DL, Leo WS, Mickelson MJ. 2015. Modeling
2013 in Massachusetts Bay using the unstructured-grid Bays Eutrophication Model.
Boston: Massachusetts Water Resources Authority. Report 2015-03. 102 p.

70 
List of Acronyms 
BOD Biochemical oxygen demand 
cBOD Carbonaceous biochemical oxygen demand 
CHV Centrotubular hydropic vacuolation 
CSO Combined sewer overflow 
DDT Dichlorodiphenyltrichloroethane 
DIF Deer Island Flats 
DIN Dissolved inorganic nitrogen 
DITP Deer Island Treatment Plant 
DO Dissolved oxygen 
ECCB Eastern Cape Cod Bay 
EPA U.S. Environmental Protection Agency 
FF Farfield 
HMW High molecular weight 
IAAC Inter-Agency Advisory Committee 
IPUE Individuals per unit effort 
LC50 50% mortality concentration 
LMW Low molecular weight 
MADEP Massachusetts Department of Environmental Protection 
MODIS Moderate Resolution Imaging Spectroradiometer 
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 
PAH Polycyclic aromatic hydrocarbon 
PCB Polychlorinated biphenyl 
PIAC Public Interest Advisory Committee 
PSP Paralytic shellfish poisoning 
RPD Redox potential discontinuity 
SPI Sediment-profile imaging

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