2013 overview

Massachusetts Water Resources Authority · from the MWRA · 72 pages · 3.2 MB
open the file ↗ · original at the source ↗

2013 Outfall monitoring o verview 
1 
Massachusetts Water Resources Authority 
Environmental Quality Department 
Report 2014-15

Citation : 
Werme C, Keay KE, Coughlin K, Hall MP, Taylor DI, Libby, PS. 2014. 2013 outfall
monitoring overview . Boston: Massachusetts Water Resources Authority. Report
2014-15. 59 p.

2013 
Outfall Monitoring Overview 
prepared by 
Christine Werme 
Independent Consultant 
Berkeley, CA 94705 
and 
Kenneth E. Keay, Kelly Coughlin, Maurice P. Hall, David I. Taylor 
Massachusetts Water Resources Authority 
Environmental Quality Department 
100 First Avenue 
Charlestown Navy Yard 
Boston, MA 02129 
and 
P. Scott Libby 
Battelle 
153b Park Row 
Brunswick, ME 04011 
October 22, 2014

2013 Outfall Monitoring Panel and Committees 
Outfall Monitoring Science Advisory Panel (OMSAP) 
Andrew Solow (chair), Woods Hole Oceanographic Institution 
Robert Beardsley, Woods Hole Oceanographic Institution 
Norbert Jaworski, retired (Environmental Protection Agency) 
Robert Kenney, University of Rhode Island 
Judy Pederson, Massachusetts Institute of Technology Sea Grant 
Michael Shiaris, University of Massachusetts, Boston 
James Shine, Harvard School of Public Health 
Juanita Urban-Rich, University of Massachusetts, Boston 
Inter-Agency Advisory Committee (IAAC) 
US Geological Survey: Michael Bothner 
Massachusetts Coastal Zone Management: Todd Callaghan, Jan Smith 
US Army Corps of Engineers: Steve Wolf 
Stellwagen Bank National Marine Sanctuary: Benjamin Cowie-Haskell 
US Environmental Protection Agency: Matthew Liebman 
Massachusetts Division of Marine Fisheries: Jack Schwartz 
Massachusetts Department of Environmental Protection: Catherine
Vakalopoulos 
Public Interest Advisory Committee (PIAC) 
Save the Harbor/Save the Bay: Patty Foley (chair), Bruce Berman 
MWRA Wastewater Advisory Committee: Andreae Downs 
Conservation Law Foundation: Priscilla Brooks 
Massachusetts Audubon Society: Robert Buchsbaum 
MWRA Advisory Board: Joseph Favaloro 
Association to Preserve Cape Cod: Tara Nye 
Safer Waters in Massachusetts: Sal Genovese 
The Boston Harbor Association: Vivien Li

i 
Table of Contents 
Summary ....................................................................................................................... v 
1. Introduction ............................................................................................................... 1 
2. Effluent ..................................................................................................................... 2 
2013 Characterization ............................................................................................... 2 
Solids Processing and Energy Production ................................................................ 8 
Contingency Plan Thresholds ................................................................................... 9 
3. Water Column ......................................................................................................... 10 
Physical Conditions ................................................................................................ 11 
Water Quality .......................................................................................................... 13 
Phytoplankton Communities ................................................................................... 22 
Zooplankton Communities...................................................................................... 25 
Stellwagen Bank National Marine Sanctuary ......................................................... 27 
Contingency Plan Thresholds ................................................................................. 29 
4. Sea Floor ................................................................................................................. 30 
Sediment Characteristics and Tracers ..................................................................... 32 
Soft-bottom Communities ....................................................................................... 34 
Sediment-profile Imaging ....................................................................................... 36 
Stellwagen Bank National Marine Sanctuary ......................................................... 37 
Contingency Plan Thresholds ................................................................................. 38 
5. Fish and Shellfish .................................................................................................... 41 
Flounder Health ...................................................................................................... 42 
Contingency Plan Thresholds ................................................................................. 43 
6. Special Studies ........................................................................................................ 44 
Boston Harbor Beaches........................................................................................... 44 
Boston Harbor Water Column ................................................................................ 47 
Boston Harbor Sea Floor ........................................................................................ 50 
Boston Harbor Fish and Shellfish ........................................................................... 53 
Cape Cod Bay Studies ............................................................................................ 55 
References ................................................................................................................... 57 
List of Acronyms ........................................................................................................ 59

ii 
List of Figures 
Figure 2-1. Annual rainfall in Boston, 1950–2013.. ..................................................... 2 
Figure 2-2. Annual primary-blended and full secondary effluent flows, 1999–2013 .. 3 
Figure 2-3. Monthly primary-blended and full secondary effluent flows during 2013 3 
Figure 2-4. Annual solids discharges, 1990–2013 ........................................................ 4 
Figure 2-5. Annual biochemical oxygen demand, 1999–2013 ..................................... 5 
Figure 2-6. Annual nitrogen discharges, 1999–2013 .................................................... 6 
Figure 2-7. Annual metals discharges, 1999–2013 ....................................................... 7 
Figure 2-8. Annual mercury discharges, 1999–2013 .................................................... 7 
Figure 3-1. Water-column monitoring stations ........................................................... 10 
Figure 3-2. Flows of the Merrimack and Charles rivers ............................................. 12 
Figure 3-3. Nearfield surface- and bottom-water temperatures .................................. 13 
Figure 3-4. Mean depth-averaged nutrient concentrations at nearfield station N18 in
2013, compared to prior years .................................................................................... 14 
Figure 3-5. Depth-averaged ammonium concentrations by station in Massachusetts
and Cape Cod bays...................................................................................................... 15 
Figure 3-6. (Top) Surface- and bottom-water ammonium concentrations on February
6, 2013, showing monitoring stations during mixed conditions. (Bottom) Cross-
sections of concentrations along transects connecting selected stations. ................... 16 
Figure 3-7. (Top) Surface- and bottom-water ammonium concentrations on July 24,
2013 at the monitoring stations during stratified conditions. (Bottom) Cross-sections
of concentrations along transects connecting selected stations .................................. 17 
Figure 3-8. Average chlorophyll fluorescence by station in Massachusetts and Cape
Cod bays...................................................................................................................... 18 
Figure 3-9. Moderate Resolution Imaging Spectroradiometer satellite imagery of
surface chlorophyll concentrations in 2013 ................................................................ 19 
Figure 3-10. Nearfield surface and bottom water dissolved oxygen concentrations .. 20 
Figure 3-11. Bottom-water dissolved oxygen concentration at stations in
Massachusetts and Cape Cod bays during the nine surveys conducted in 2013 ........ 21 
Figure 3-12. Total phytoplankton abundance in 2013. ............................................... 22 
Figure 3-13. Mean nearfield abundance Phaeocystis pouchetii, 1992–2013 ............. 23 
Figure 3-14. Long-term seasonally adjusted average abundance of centric diatoms
and Phaeocystis pouchetii . .......................................................................................... 24 
Figure 3-15. Nearfield abundance of Alexandrium fundyense, 1992–2013................ 25 
Figure 3-16. Total zooplankton abundance in 2013 ................................................... 26 
Figure 3-17. Average surface-layer ammonium at representative stations ................. 27 
Figure 3-18. Bottom water dissolved oxygen concentrations in Stellwagen Basin in
2013 compared to the previous years of monitoring .................................................. 28 
Figure 4-1. Soft-bottom monitoring stations .............................................................. 30 
Figure 4-2. Sediment-profile imaging stations ........................................................... 31 
Figure 4-3. Concentrations of Clostridium perfringens spores, corrected for sediment
grain size, in 2013 ....................................................................................................... 33

iii 
Figure 4-4. Mean concentrations of Clostridium perfringens spores during the
baseline and outfall-discharge years ........................................................................... 33 
Figure 4-5. Mean infaunal abundance per sample in four areas of Massachusetts Bay,
1992–2013l ................................................................................................................. 34 
Figure 4-6. Mean total abundance per sample and abundance of five dominant species
at nearfield stations, 1992–2013 ................................................................................. 35 
Figure 4-7. Annual apparent color RPD depth for data from nearfield stations ......... 36 
Figure 4-8. Percent fine sediments superimposed on a non-metric multidimensional
scaling ordination plot of the 2013 infauna samples. ................................................. 37 
Figure 4-9. Annual community parameters with nearfield Contingency Plan
thresholds .................................................................................................................... 39 
Figure 4-10. Mean Schwartz Dominance Index per sample at nearfield stations in
Massachusetts Bay during the baseline and early post-diversion, 2010– 2012, and
2013............................................................................................................................. 40 
Figure 5-2. Annual prevalence of centrotubular hydropic vacuolation, corrected for
age ............................................................................................................................... 43 
Figure 6-1. Map of Boston Harbor beaches and bacteria-sampling sites ................... 44 
Figure 6-2. Percentage of days that South Boston beaches failed swimming standards
before and after the CSO storage tunnel came on line in 2011 .................................. 46 
Figure 6-3. Water-column sampling locations in Boston Harbor ............................... 47 
Figure 6-4. Water quality measurements in Boston Harbor, 1995–2013 ................... 48 
Figure 6-5. Annual average ammonium concentrations in four geographic regions of
Boston Harbor ............................................................................................................. 49 
Figure 6-6. Soft-bottom sampling stations in Boston Harbor ..................................... 50 
Figure 6-7. Clostridium perfringens spores and total organic carbon in Boston Harbor
sediments during four time periods marking changes in sewage loadings ................. 51 
Figure 6-8. Number of species per sample and log-series alpha in Boston Harbor
infauna samples during four time periods marking changes in sewage loadings. ..... 52 
Figure 6-9. Incidence of liver tumor precursors and liver tumors in winter flounder
from Deer Island Flats in Boston Harbor, 1987–2013 ................................................ 53 
Figure 6-10. High molecular weight PAHs in mussels deployed in Boston Harbor and
Massachusetts Bay, 1991–2012 .................................................................................. 54 
Figure 6-11. The Center for Coastal Studies monitors its own eight stations and three
MWRA stations (F01, F02, and F29) in and near Cape Cod Bay .............................. 55 
Figure 6-12. Right whale sightings in Cape Cod Bay, 1998–2013. ........................... 56

iv 
List of Tables 
Table i. Contingency Plan threshold values and 2013 results for effluent monitoring.
...................................................................................................................................... vi 
Table ii. Contingency Plan threshold values and 2013 results for water-column
monitoring. .................................................................................................................. vii 
Table iii. Contingency Plan threshold values and 2013 results for sea-floor
monitoring. ................................................................................................................. viii 
Table iv. Contingency Plan threshold values and 2013 result for fish-and-shellfish
monitoring. ................................................................................................................. viii 
Table 2-1. Contingency Plan threshold values and 2013 results for effluent
monitoring. .................................................................................................................... 9 
Table 3-1. Contingency Plan threshold values and 2013 results for water-column
monitoring. .................................................................................................................. 29 
Table 4-1. Contingency Plan threshold values and 2013 results for sea-floor
monitoring. .................................................................................................................. 38 
Table 5-1. Contingency Plan threshold values and 2013 results for fish-and-shellfish
monitoring. .................................................................................................................. 43 
Table 6-1. Compliance with swimming standards at Boston Harbor beaches in 2013.
..................................................................................................................................... 45

v 
Summary 
Each year, the Massachusetts Water Resources Authority (MWRA) prepares this
overview of environmental monitoring related to the discharge of municipal effluent
from Deer Island Treatment Plant through an offshore outfall tunnel into Massachusetts
Bay. The report presents monitoring results and information relevant to the MWRA’s
permit-required Contingency Plan, including threshold exceedances and permit
violations, responses, and corrective actions. The overview also includes monitoring
results relevant to the Stellwagen Bank National Marine Sanctuary and information on
special studies conducted in response to specific permit requirements, scientific
questions, or public concerns. 
The 2013 report marks almost nine years of baseline monitoring and more than thirteen
years of “outfall-discharge” monitoring, covering the years since September 2000, when
MWRA ceased discharge of sewage effluent to the relatively confined waters of Boston
Harbor and began to discharge into deeper water in Massachusetts Bay. It includes
results of effluent analyses; water-column, sea-floor, and fish-and-shellfish monitoring
in the outfall nearfield and at reference stations; and special studies. This year’s report
on special studies focuses on improvements in Boston Harbor following the transfer of
discharges to offshore waters and on ongoing Cape Cod Bay studies. 
Operations at the Deer Island Treatment Plant continued to be exceptional in 2013,
earning MWRA a National Association of Clean Water Agencies (NACWA) Platinum 7
Peak Performance Award. This NACWA award recognizes facilities with 100% permit
compliance for seven consecutive years. 
Nearfield and reference-station monitoring results from 2013 were consistent with
predictions made more than 20 years ago and past results, showing no unanticipated
effects of the discharge (Tables i through iv). No Contingency Plan “warning level”
exceedances were observed in 2013. There were “caution level” Contingency Plan
exceedances * for two soft-bottom benthic community parameters, Shannon-Wiener
diversity and Pielou’s evenness. These exceedances, which occurred for a fourth
consecutive year, were indications of a somewhat more diverse community, resulting
from normal cycles of relative abundance in the animal populations. Increased diversity
is not considered to be environmentally adverse, and the changes are not thought to be
related to the outfall. 
* MWRA’s NPDES permit includes Contingency Plan threshold indicators that may indicate a need for action. The
thresholds are based on permit limits, state water quality standards, and expert judgment. “Caution level” thresholds
generally indicate a need for a closer look at the data to determine the reason for an observed change. “Warning level”
thresholds are a higher level of concern, and the permit requires a series of steps to evaluate whether adverse impacts
occurred and if so, whether they were related to the discharge. If caused by the discharge, MWRA may need to
implement corrective action. 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.

vi 
Table i. Contingency Plan threshold values and 2013 results for effluent monitoring. 
Parameter Baseline Caution Level Warning Level 201 3 Results 
pH NA None <6 or >9 Not exceeded 
Fecal coliform NA None 14,000 fecal 
coliforms/100 m L Not exceeded 
Chlorine, residual NA None 631 μ g/L daily, 
456 μ g/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 Noncompliance 
>5% 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

vii 
Table ii. Contingency Plan threshold values and 2013 results for water-column monitoring . 
Parameter Baseline Caution Level Warning Level 201 3 Results 
Dissolved oxygen * 
Nearfield 
concentration 6.05 mg/L 6.5 mg/L 6.0 mg/L 6. 71 mg/L 
Nearfield percent 
saturation 65.3 % 80% 75% 73.6 % 
Stellwagen 
concentration 6.2 3 mg/L 6.5 mg/L 6.0 mg/L 6.97 
mg/L 
Stellwagen percent 
saturation 67.2 % 80 75% 75.3 % 
Nearfield depletion 
rate 0.024 mg/L/d 0.037 mg/L/d 0.049 mg/L/d 0.02 1 mg/L/d 
Chlorophyll 
Annual 72 mg/m 2 1 0 8 mg/m 2 1 44 mg/m 2 61 mg/m 2 
Winter/spring 50 mg/m 2 199 mg/m 2 None 53 mg/m 2 
Summer 51 mg/m 2 89 mg/m 2 None 65 mg/m 2 
Autumn 90 mg/m 2 2 39 mg/m 2 None 6 4 mg/m 2 
Nuisance algae Phaeocystis pouchetii 
Winter/spring 622,000 cells/L 2, 86 0,000 cells/L None 5,160 cells/L 
Summer 72 cells/L 357 cells/L None Absent 
Autumn 370 cells/L 2, 96 0 cells/L None Absent 
Nuisance algae nearfield Pseudo - nitzschia 
Winter/spring 6,735 cells/L 17,9 00 cells/L None Absent 
Summer 14,635 cells/L 43,100 cells/L None 667 cells/L 
Autumn 10,050 cells/L 2 7,5 00 cells/L None 490 cells/L 
Nuisance algae nearfield Alexandrium fundyense 
Any nearfield 
sample 
Baseline maximum 
163 cells/L 100 cells/L None 23 cells/L 
PSP toxin extent N A 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

viii 
Table iii. Contingency Plan threshold values and 2013 results for sea-floor monitoring. 
Parameter Baseline Caution Level Warning Level 201 3 Results 
Sediment parameters 
RPD depth NA < 1.18 cm None 3.76 cm 
Benthic community parameters 
Species per 
sample NA < 42.99 or >81.85 None 55.55 
Fisher’s log - series 
alpha NA <9.42 or >1 5.8 None 1 3.14 
Shannon diversity NA <3.37 or > 3.99 None 4.08 , caution level 
exceedance 
Pielou’s evenness NA < 0.57 or >0.6 7 None 0.71 , caution level 
exceedance 
% opportunists NA >10% >25% 0.47 % 
NA = not applicable 
RPD = Redox potential discontinuity 
Table iv. Contingency Plan threshold values and 2013 result for fish-and-shellfish monitoring. 
Parameter Baseline Caution Level Warning Level 201 3 Results 
Liver disease CHV 24.4% 44.9% None 18 % 
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
wastewater discharge on the marine environment. The mission of what became
known as MWRA’s Boston Harbor Project included reducing inflow of contaminants
into the waste stream, ending biosolids discharge, improving wastewater treatment
facilities, and providing better dilution of the sewage effluent discharge. Throughout
MWRA’s early years, scientists conducted environmental monitoring in Boston
Harbor and also in Massachusetts Bay, at the (then future) location of a relocated
sewage-effluent discharge. 
By the end of 2000, most of the Boston Harbor Project had been completed, including
the relocated outfall, which diverted sewage effluent from Boston Harbor to the
deeper, less confined waters of Massachusetts Bay. The outfall operates under a
National Pollutant Discharge Elimination System (NPDES) permit for the Deer Island
Treatment Plant (DITP) constructed as part of 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 sewage
effluent and for ambient monitoring of the receiving waters. Monitoring assesses
compliance with specific permit conditions and additional conditions specified by a
permit-required Contingency Plan. Background information on the monitoring
program can be found in Werme et al. (2012). 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 also include
information relevant to the Stellwagen Bank National Marine Sanctuary. 
This outfall monitoring overview presents results from 2013, marking the twenty-
second year of MWRA’s monitoring program, including more than thirteen years of
outfall-discharge monitoring. Measurements include effluent, water-column, sea-
floor, and fish-and-shellfish parameters, as well as special studies conducted in
response to permit conditions and environmental concerns. Data specifically related
to the Stellwagen Bank National Marine Sanctuary are included in the overview’s
water-column and sea-floor sections.

2 
2. Effluent 
2013 Characterization 
As in past years, DITP continued to operate as designed through 2013, earning
MWRA the National Association of Clean Water Agencies (NACWA) Platinum 7
Peak Performance Award. This NACWA award recognizes facilities with 100%
permit compliance over seven consecutive years. 
The Boston area received about 40 inches of rain in 2013, almost 4 inches more than
in 2012, but less than the long-term average (Figure 2-1). These two dry years
contrast with mostly wetter years since the outfall came on line in 2000.
Consequently, total effluent flow in 2013 was also lower than average, second only to
2012 in low flows (Figure 2-2). Virtually all the flow, 99.2%, received full primary
and secondary treatment. Flows were lower than average in every month except
June, and autumn flows were especially low, with no storm-related discharges of
primary-only effluent blended with effluent receiving full secondary treatment prior
to discharge (Figure 2-3). 
Figure 2-1. Annual rainfall in Boston, 1950–2013. Most years since the Massachusetts Bay outfall
came on line have been wet, but rainfalls in 2012 and 2013 were below the long-term average (shown
as the red line). 0
10
20
30
40
50
60
70 
Inches

3 
Figure 2-2. Annual primary-blended and full secondary effluent flows, 1999–2013. In 2013,
99.2% of effluent received full secondary treatment. (During large storms, flow exceeding the
secondary capacity of the plant is diverted around the secondary process to prevent washing out the
essential microbes that carry out secondary treatment. These primary-blended flows are combined with
full secondary flows before disinfection and discharge. All discharges meet permit limits.) 
Figure 2-3. Monthly primary-blended and full secondary effluent flows during 2013. Total flow
was below average in every month except June, and there were only small amounts of primary-blended
flow in any month. 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 
Million gallons per day 
Primary-blended f lows
Secondary f lows 0
50
100
150 
200 
250
300
350
400 
450 
500
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 
Million gallons per day 
Primary-blended f lows
Secondary f lows

4 
The total suspended solids load to Massachusetts Bay was 13.5 tons per day, well
below the loads discharged to Boston Harbor before the outfall came on line in 2000
and also below the average for recent years (Figure 2-4). Carbonaceous biochemical
oxygen demand (BOD) was also low, remaining well below levels that might be
expected to affect ambient waters at the discharge site (Figure 2-5). Nitrogenous
BOD (also shown in Figure 2-5), which is a result of the biological processes in
secondary treatment and not a permit limit or Contingency Plan parameter, was
lower, except for 2012, than any level measured since 2001. 
Figure 2-4. Annual solids discharges, 1990–2013 . Solids discharges remained low in 2013, 13.5 tons
per day. 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 
Tons per day 
Sludge
Nut Island
Deer Island

5 
Figure 2-5. Annual biochemical oxygen demand, 1999–2013. MWRA’s permit limits carbonaceous
BOD. Nitrogenous BOD is the result of microbiological breakdown that occurs as a result of secondary
treatment and is not regulated by the permit. 
The total nitrogen load also remained below its threshold in 2013 (Figure 2-6). The
portion of the load made up of ammonium continued to be higher than in earlier years
of the Boston Harbor Project. About 10% of the ammonium in the sewage influent is
removed by secondary treatment, but the biological treatment process converts some
organic forms of nitrogen to ammonium. Also, ammonium-rich liquids from the
biosolids pelletizing (fertilizer) plant, built as part of the Boston Harbor Project, are
reintroduced to DITP for treatment, adding to the ammonium load. As required by its
permit, MWRA continually evaluates nitrogen-removal technologies, so that removal
could be quickly implemented, should a need arise (Smolow et al. 2013). Because
nitrogen loads have remained below the Contingency Plan caution threshold, and
there have not been nitrogen-related adverse environmental effects, nitrogen removal
has not been required or implemented. 0
5 
10 
15
20
25
30
35
1998 2000 2002 2004 2006 2008 2010 2012 2014 
Tons per day 
Carbonaceous BOD
Nitrogenous BOD

6 
Figure 2-6. Annual nitrogen discharges, 1999–2013. Most of the nitrogen in the effluent is in the
form of ammonium. 
Metals loads remained low in 2013, with zinc and copper comprising most of the
annual discharge (Figure 2-7). Metals discharges are now only a small fraction of
what they were before the Boston Harbor Project, 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, a result of removal efficiencies and the change
from film to digital photography. 
Mercury loads were also low, with only 3.7 pounds per year discharged in 2012 and
2013, compared to more than 50 pounds per year in 1999 and less than one percent of
the amount anticipated during the planning process for the outfall (Figure 2-8).
Although sensitive methods have been adopted for mercury analysis, mercury is now
only rarely detected in effluent samples, the consequence of efforts on the part of
MWRA and the New England states and New York to reduce mercury use, handle
workplace spills, and discourage disposal practices that introduce mercury into the
sewer system. Most mercury entering New England waters is in atmospheric
deposition. 0
3000
6000
9000
12000
15000
99 00 01 02 03 04 05 06 07 08 09 10 11 12 13 
Metric tons per year 
Caution Threshold Other Nitrogen Species
Nitrite/Nitrate Ammonium

7 
Figure 2-7. Annual metals discharges, 1999–2013. Total metals discharges remained low in 2013,
with removal efficiencies greater than 90% for lead, copper, and zinc. Except for copper, the metals
meet receiving water quality criteria in the effluent, even without the dilution provided by the outfall. 
Figure 2-8. Annual mercury discharges, 1999–2013. Mercury discharges are only about 1% of the
loads that had been predicted during the outfall-siting process. 0
50
100
150
200
250
99 00 01 02 03 04 05 06 07 08 09 10 11 12 13 
Average pounds per day 
Silver 
Nickel
Chromium
Lead
Copper
Zinc 0
10
20
30
40
50
60
99 00 01 02 03 04 05 06 07 08 09 10 11 12 13 
Pounds per year

8 
Polychlorinated biphenyl (PCB) and pesticide loads decreased to record lows in 2013.
About one pound of PCBs and fewer than two pounds of chlorinated pesticides were
discharged. All contaminant loads remained well below those that had been
anticipated during the planning process for the relocated outfall. Those predictions
were that more than 10 pounds of the chlorinated pesticide DDT and its breakdown
products and more than 100 pounds of PCBs would be discharged each year. 
Solids Processing and Energy Production 
On average, DITP removes more than 94% of solids and organic material present in
wastewater influent before discharging effluent into Massachusetts Bay, resulting in
an average of almost 250 dry tons of biosolids per day. Anaerobic digestion at DITP
further removes about 62% of the volatile solids from those biosolids, more than the
industry-wide average of 45–50% removal. Almost 190,000 standard cubic feet per
hour of digester gas is produced by the process and burned on site, enough to provide
97% of DITP’s heating needs, as well as 27 million kilowatt-hours of energy each
year. Overall, the digester gas provides 62% of the energy needs at DITP. In 2013,
production and burning of digester gas resulted in $27-million of avoided costs to the
operation of the treatment plant. 
After digestion, the remaining 106 dry tons of biosolids per day are pumped to
MWRA’s pelletizing plant, where they are dewatered, dried, and compressed into
small, granular pellets suitable for beneficial re-use, mostly as slow-release organic
fertilizers. The fertilizer pellets contain approximately 60% organic matter and have
more nutrients than compost. Typical uses include turf farms, parks, and golf
courses.

9 
Contingency Plan Thresholds 
DITP had no permit violations, and there were no exceedances of the Contingency
Plan effluent thresholds in 2013 (Table 2-1). 
Table 2-1. Contingency Plan threshold values and 2013 results for effluent monitoring. 
Parameter Caution Level Warning Level 201 3 Results 
pH None <6 or >9 Not exceeded 
Fecal coliform None 14,000 fecal coliforms/100 m L Not exceeded 
Chlorine, residual None 631 μ g/L daily, 
456 μ g/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% for shrimp and fish Not exceeded 
Chronic toxicity None 
NOEC for fish survival and growth 
and sea urchin fertilization <1.5% 
effluent 
Not exceeded 
PCBs Aroclor=0.045 ng/L None Not exceeded 
Plant performance 5 violations/year Noncompliance >5% of the time Not exceeded 
Flow None >436 MGD for annual average of 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 
cBOD = carbonaceous biological oxygen demand 
LC50 = 50% mortality concentration 
NOEC = no observable effect concentration 
PCB = polychlorinated biphenyl

10 
3. Water Column 
The water-column monitoring program measures relevant physical-oceanographic
processes and water quality and evaluates 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 annual surveys at fourteen stations in 2013 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 (see Boston Harbor
Water Quality in Section 6, Special Studies, for some additional results from that
program). In some years, special surveys are conducted in response to Alexandrium
fundyense red tide blooms, but no additional surveys were necessary in 2013. 
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 the annual outfall monitoring overview. In 2013, all
Cape Cod Bay sampling was completed within the required time frame. (See Cape
Cod Bay Monitoring in Section 6, Special Studies, for additional results from that
program.) 
The field monitoring program was augmented by measurements on two instrumented
buoys, the Northeastern Regional Association of Coastal and Ocean Observing
Systems (NERACOOS) Buoy A01 and the National Oceanic and Atmospheric
Administration’s National Data Buoy Center (NDBC) Buoy 44013. The National
Aeronautics and Space Administration provided Moderate Resolution Imaging
Spectroradiometer (MODIS-Aqua) satellite imagery. 
Physical Conditions 
Monitoring has shown that the water column in the vicinity of the outfall and
throughout Massachusetts and Cape Cod bays is heavily influenced by river inflows,
weather, and other physical factors. Information about physical conditions has
proven key to interpreting the annual monitoring data. 
The year 2013 was slightly drier than other recent years, although not as dry as 2012
(See Figure 2-1 in Section 2, Effluent). It was warmer than average in the winter and
spring, with storms in February and March, which produced large waves. The
strongest of these winter storms, nicknamed “Nemo,” produced 10-meter waves
within Massachusetts Bay, sufficient to reach the sea floor and resuspend deposited
sediments. Resuspended sediment was evident in satellite imagery from February 10,
the day after the storm.

12 
For a second consecutive year, the relatively dry conditions resulted in slightly lower-
than-average river discharges in both the Merrimack and Charles rivers (Libby et al.
2014). Flows from both rivers were below average in every season except July
through September, when low flows are typical (Figure 3-2). 
Figure 3-2. Flows of the Merrimack (top) and Charles (bottom) rivers. Flows from both rivers
were below average, less than the 50 th percentile throughout much of the year, but higher in summer,
when low flows are typical. 
Warm air temperatures in the late winter and spring led to higher-than-average
nearfield surface- and bottom-water temperatures at the onset of spring stratification
of the water column. Surface-water temperatures reached a record high for the
monitoring program in July (Figure 3-3). For the first half of the year, bottom-water
temperatures followed a similar trajectory, but were about average for the monitoring
program in August through October. 30 th 25 th 
percentile 84 th 7 th 
43 rd 39 th 
percentile 70 th 11 th

13 
Figure 3-3. Nearfield surface- and bottom-water temperatures. Surface-water temperatures were
warmer than average during the early part of the year and reached record high for the monitoring
program in July. 
Surface- and bottom-water salinities began the year at higher-than-normal levels, due
to the dry conditions in 2012. A surge in flow from the Charles River caused a large
drop in surface salinity in June. No similar drop was observed in bottom waters,
which are affected more by flow from the Merrimack River. High bottom-water
salinities persisted throughout the duration of field sampling for the year. 
Wind conditions promoted strong downwelling in February and March, a result of the
strong winter storms. A downwelling event also occurred in July, and strong
upwelling was not observed until August. Summer stratification intensity, estimated
by the difference in densities of surface and bottom waters, was among the strongest
measured by the monitoring program. Destratification, the re-mixing of the water
column that occurs as waters cool in the autumn, occurred later than in most years.
Downwelling conditions in November ended summertime stratification. 
Water Quality 
Water quality measurements for 2013 included quantification of nutrients,
phytoplankton biomass (measured as chlorophyll), 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. 2014).

14 
Nitrate, silicate, and phosphate concentrations averaged through the water column
were lower during February, the first survey of the year, than most years (Figure 3-4),
possibly due to continual phytoplankton production over the warm winter or to an
early phytoplankton bloom that occurred prior to the start of the sampling season.
For the rest of the year, concentrations of the major nutrients important to
phytoplankton growth fell into the ranges observed throughout the monitoring
program. 
Figure 3-4. Mean depth-averaged nutrient concentrations at nearfield station N18 in 2013,
compared to prior years. Spring 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.) 
Elevated ammonium levels were apparent at the outfall for most surveys (Figure 3-5),
consistent with the results from prior years. As has been typical since the offshore
outfall began to discharge, the plume was found in surface waters during the winter
and spring (Figure 3-6), but was confined beneath the pycnocline during the summer,
stratified season (Figure 3-7). This ammonium signature could be detected within
10–20 kilometers of the outfall in both well-mixed and stratified seasons. Jan Mar May Jul Sep Nov Jan
0
5
10
15 
 M 
NH4 Jan Mar May Jul Sep Nov Jan
0
0.5
1
1.5 
 M 
PO4 Jan Mar May Jul Sep Nov Jan
0
5
10
15 
 M 
NO3PLUSNO2 Jan Mar May Jul Sep Nov Jan
0
5
10
15 
 M 
SIO4 
Nitrate Ammonium 
Silicate Phosphate

15 
Figure 3-5. Depth-averaged ammonium concentrations 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. 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Feb 06 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Mar 21 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Apr 10 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
May 17 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Jun 18 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Jul 24 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Aug 20 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Sep 04 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Oct 22 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Mar 21 μM

16 
Figure 3-6. (Top) Surface- and bottom-water ammonium concentrations on February 6, 2013,
showing monitoring stations during mixed conditions. (Bottom) Cross-sections of concentrations
along transects connecting selected stations. The plume reached surface waters during the winter.

17 
Figure 3-7. (Top) Surface- and bottom-water ammonium concentrations on July 24, 2013 at the
monitoring stations during stratified conditions. (Bottom) Cross-sections of concentrations along
transects connecting selected stations. The plume remained beneath the pycnocline during the
summer.

18 
At many stations, particularly in Boston Harbor and nearby shallow-water stations,
peak chlorophyll levels occurred in July (Figure 3-8). Over much of the year,
chlorophyll levels were low, often at historic minima for the monitoring program.
Satellite imagery (Figure 3-9) suggested that chlorophyll levels were somewhat
elevated in January and February, relatively low from late February until July,
increasing in later July, and higher throughout the fall. 
Figure 3-8. Average chlorophyll fluorescence by station in Massachusetts and Cape Cod bays. . 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Feb 06 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Mar 21 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Apr 10 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
May 17 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Jun 18 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Jul 24 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Aug 20 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Sep 04 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Oct 22 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 2 4 6 8 10 
Feb 06 μg/L

19 
Figure 3-9. Moderate Resolution Imaging Spectroradiometer satellite imagery of surface
chlorophyll concentrations in 2013. These images are heavily weather dependent and do not
represent consistent intervals of time. The stars show the timing of the nine MWRA surveys. 
Highlights: 
1 st row – early elevated chlorophyll levels January – February 
2 nd & 3 rd rows – relatively low from late February into July 
4 th row – late summer chlorophyll increase, September bloom 
5 th row – elevated chlorophyll levels into early November 1/5 1/18 1/27 2/10 2/18
4/28 5/5 6/15 7/15 7/30
2/26 3/26 4/4 4/8 4/17
8/6 8/24 9/4 9/18 10/1
10/20 11/5 11/16 11/28 12/18

20 
Nearfield bottom-water dissolved oxygen concentrations were relatively low during
the first surveys of the year, a result of warm temperatures and high salinity (Figure
3-10). Levels declined at rates typically observed throughout the summer and fall.
The fall oxygen minima were moderate in comparison to other years and higher than
observed in 2012. With low levels at the onset of the season and strong stratified
conditions persisting in October, it was surprising that the minima were not lower
than observed. Data from the NERACOOS buoy indicated that levels in the deep
bottom waters of Massachusetts Bay remained above 6.5 mg/L throughout the season. 
Figure 3-10. Nearfield surface and bottom water dissolved oxygen concentrations. .Dissolved
oxygen concentrations were low relative to other years of the monitoring program. Even lower values
would be expected based on the warmer than average bottom temperatures and higher than average
bottom salinity measurements. 
The lowest dissolved oxygen concentrations measured in 2013 were at Station F02 in
eastern Cape Cod Bay, where levels fell below 5 mg/L during the October survey
(Figure 3-11) . During the same survey, bottom-water dissolved oxygen levels in
western Cape Cod Bay had increased to more than 8 mg/L, indicating that remixing
occurred earlier in that area. High-nutrient, low-oxygen spots have occurred in Cape
Cod Bay in some other years, likely a result of southward coastal flow, long residence
time, and strong stratification (Jiang et al. 2007).

21 
Figure 3-11. Bottom-water dissolved oxygen concentration (mg/L) at stations in Massachusetts
and Cape Cod bays during the nine surveys conducted in 2013. The lowest concentration measured
in 2013 was at Station F02 in eastern Cape Cod Bay. Levels lower than 5 mg/L have been only rarely
measured by the monitoring program. (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.) 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
4 5 6 7 8 9 
Feb 06 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
4 5 6 7 8 9 
Mar 21 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
4 5 6 7 8 9 
Apr 10 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
4 5 6 7 8 9 
May 17 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
4 5 6 7 8 9 
Jun 18 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
4 5 6 7 8 9 
Jul 24 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
4 5 6 7 8 9 
Aug 20 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
4 5 6 7 8 9 
Sep 04 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
4 5 6 7 8 9 
Oct 22 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
4 5 6 7 8 9 
Feb 06 mg/L

22 
Phytoplankton Communities 
Total abundance of phytoplankton was low in 2013, ranking 21 st of 22 years of
monitoring (Libby et al. 2014). The sampling program detected no winter/spring
bloom, although there was a detectable summer bloom, particularly in Boston Harbor
and the nearfield (Figure 3-12). Abundances were typical through the fall. 
Figure 3-12. Total phytoplankton abundance in 2013 . Annual abundance was low, approximately
one third the long-term mean. 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 1 2 3 4 5
x 10 6 
Feb 06 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 1 2 3 4 5
x 10 6 
Mar 21 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 1 2 3 4 5
x 10 6 
Apr 10 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 1 2 3 4 5
x 10 6 
May 17 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 1 2 3 4 5
x 10 6 
Jun 18 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 1 2 3 4 5
x 10 6 
Jul 24 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 1 2 3 4 5
x 10 6 
Aug 20 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 1 2 3 4 5
x 10 6 
Sep 04 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 1 2 3 4 5
x 10 6 
Oct 22 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 1 2 3 4 5
x 10 6 
Feb 06 Million cells L -1

23 
The lack of an observed winter/spring bloom partially explains the overall low
phytoplankton abundances in 2013. Annual abundances of Chaetoceros spp., 
Skeletonema spp., and Thalassiosira spp., which are usually dominant diatom species
in spring blooms, all declined. There were also declines in abundances of the small,
often numerous, microflagellates and cryptophytes. 
Some species increased in abundance in 2013. Summer blooms of the centric diatom 
Dactyliosolen fragilissimus occurred in Boston Harbor and the nearfield.
Abundances of the large flagellates Ceratium spp. were elevated, with total
abundance for the year ranking 2 nd of the 22 years. Ceratium are large dinoflagellates
with cyclical abundance patterns. 
Most noteworthy in 2013, there was no significant bloom of the nuisance species 
Phaeocystis pouchetii (Figure 3-13). The 2013 mean average Phaeocystis abundance
was only 2,020 cells/L, compared to a long-term average of 272,258 cells/L.
Abundances were lower than in any year since annual blooms began to occur
regularly just before the outfall came on line in 2000. 
Figure 3-13. Mean nearfield abundance Phaeocystis pouchetii, 1992–2013 . (Top) Winter/spring.
(Bottom) Summer. 0
1 
2 
3
4
5 
Winter-spring Phaeocystis 
(million cells/l) 
baseline outfall discharge caution threshold 1 
10
100
1000
10000 
100000 
1000000 
Summer Phaeocystis 
(cells/l + 1) 
baseline outfall discharge caution threshold

24 
Long-term-trend analyses suggest that abundance of Phaeocystis pouchetii is
inversely correlated with diatom abundance in Massachusetts Bay (Figure 3-14). In
2013, while Phaeocystis abundance was low, diatoms abundance was approximately
at the long-term mean. Monitoring and modeling have suggested that reduced nitrate
levels, such as were observed during the early winter/spring period in 2013, may
prevent development of large Phaeocystis blooms in Massachusetts Bay (Jiang et al.
2014). The simultaneous low levels of silicate at the beginning of the monitoring
season may have prevented diatom growth during the monitoring-program season as
well. 
Figure 3-14. Long-term seasonally adjusted average abundance of centric diatoms and 
Phaeocystis pouchetii . Diatom abundance in 2013 was near the long-term mean, while Phaeocystis 
abundance was low. 0
100,000
200,000
300,000
400,000
500,000
600,000
700,000
800,000
1990 1995 2000 2005 2010 2015
Year
Abundance trend (cells L -1 )
Diatoms
Phaeocystis

25 
Abundance of the toxic dinoflagellate Alexandrium fundyense was lower than it had
been in recent years, with only a small bloom (Figure 3-15). The Woods Hole
Oceanographic Institution predicted a larger, moderate bloom, but that did not occur
anywhere in the Gulf of Maine. Modeling suggests that low winter/spring nutrient
levels throughout the region may have contributed to the lack of a larger bloom. 
Figure 3-15. Nearfield abundance of Alexandrium fundyense, 1992–2013. 
Zooplankton Communities 
The 2013 zooplankton abundances (Figure 3-16), species composition, and seasonal
progressions of the communities fell within the general patterns of past years,
although there were atypically high abundances of some species (Libby et al. 2014).
Abundances of total zooplankton, total copepod adults and copepodites, Oithona
similis , Calanus finmarchicus , and Pseudocalanus spp. were generally higher than in
most previous years and, except for C. finmarchicus , the highest levels observed since
the outfall began to discharge. Several pulses of meroplankton occurred, including
barnacle nauplii in March and April and bivalve veligers in July and August. 
The relatively high abundances of zooplankton in 2013 may have been influenced by
the warm, saline conditions. High abundances were somewhat unexpected in the face
of the low winter/spring chlorophyll levels and low total phytoplankton abundances.
However, links between phytoplankton and zooplankton abundances can be difficult
to discern. In Massachusetts Bay, the dominant zooplankton species Oithona similis 
feeds on small microorganisms rather than on phytoplankton, and there are no
abundance data for those microzooplankton species. 
Increases in zooplankton abundance have been noted by the monitoring program over
the past several years, following declines in abundance in the early 2000s. The
reasons for long-term changes are not well understood, but appear to occur on large
regional scales. There has been no indication of any effect of the outfall discharge on
the zooplankton communities in Massachusetts Bay. 1 
10 
100 
1000
10000
100000
92 93 94 95 96 97 98 99 00 01 02 03 04 05 06 07 08 09 10 11 12 13 
Alexandrium per sample (cells/l +1 ) 
baseline outfall discharge caution threshold

26 
Figure 3-16. Total zooplankton abundance in 2013. Abundance patterns were typical, increasing
from the winter through the spring, peaking in the summer, and declining in the fall. 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 3 6 9 12 15
x 10 4 
Feb 06 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 3 6 9 12 15
x 10 4 
Mar 21 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 3 6 9 12 15
x 10 4 
Apr 10 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 3 6 9 12 15
x 10 4 
May 17 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 3 6 9 12 15
x 10 4 
Jun 18 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 3 6 9 12 15
x 10 4 
Jul 24 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 3 6 9 12 15
x 10 4 
Aug 20 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 3 6 9 12 15
x 10 4 
Sep 04 71 o W 48' 36' 24' 12' 70 o W
42 o N 
10'
20'
30'
40' 
0 3 6 9 12 15
x 10 4 
Oct 22 Individuals m -3

27 
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. Station F22 is in Stellwagen Basin to the northwest of the sanctuary and is
considered to be representative of northern, offshore conditions. Surface-water
ammonium levels have not changed, remaining low, at Station F22 since the outfall
began to discharge (Figure 3-17). Levels have also remained low at Station F06.
located to the south and offshore. Increased ammonium levels can be detected at
Station N18 in the nearfield, while dramatic decreases have been detected at
representative harbor and coastal stations. 
Figure 3-17. Average surface-layer ammonium at representative stations. Black line is 2013, red
lines are the baseline (1992–August 2000, and light blue lines are other discharge years (September
2000–2012). Surface-water ammonium levels at Station F22 in Stellwagen Basin (Northern Offshore)
have remained low throughout the duration of the monitoring program. See Figure 3-1 for precise
locations of all stations. J F M A M J J A S O N D
0
5
10
15 
 M 
NH4 J F M A M J J A S O N D
0
5
10
15 
 M 
NH4 J F M A M J J A S O N D
0
5
10
15 
 M 
NH4 J F M A M J J A S O N D
0
5
10
15 
 M 
NH4 Harbor
(F23)
Coastal
(F13)
Northern 
Offshore
(F22) 
Nearfield
(N18)
Southern
Offshore
(F06) J F M A M J J A S O N D
0
5
10
15 
 M 
NH4

28 
Bottom-water dissolved oxygen concentrations at Station F22 were relatively low
throughout 2013 (Figure 3-18). These levels reflected the warm, saline conditions
found throughout the region. Data from the NERACOOS Buoy A01, located within
the sanctuary, documented the return to oxygenated conditions with fall mixing. 
Figure 3-18. Bottom water dissolved oxygen concentrations in Stellwagen Basin in 2013
compared to the previous years of monitoring. Data from the NERACOOS Buoy A01 are shown in
red. DO = dissolved oxygen

29 
Contingency Plan Thresholds 
All water-quality parameters were within normal ranges throughout 2013, and there
were no exceedances of Contingency Plan thresholds (Table 3-1). 
Table 3-1. Contingency Plan threshold values and 2013 results for water-column
monitoring . 
Parameter Baseline Caution Level Warning Level 201 3 Results 
Dissolved oxygen * 
Nearfield 
concentration 6.05 mg/L 6.5 mg/L 6.0 mg/L 6. 71 mg/L 
Nearfield percent 
saturation 65.3 % 80% 75% 73.6 % 
Stellwagen 
concentration 6.2 3 mg/L 6.5 mg/L 6.0 mg/L 6.97 
mg/L 
Stellwagen percent 
saturation 67.2 % 80 75% 75.3 % 
Nearfield depletion 
rate 0.024 mg/L/d 0.037 mg/L/d 0.049 mg/L/d 0.02 1 mg/L/d 
Chlorophyll 
Annual 72 mg/m 2 1 0 8 mg/m 2 1 44 mg/m 2 61 mg/m 2 
Winter/spring 50 mg/m 2 199 mg/m 2 None 53 mg/m 2 
Summer 51 mg/m 2 89 mg/m 2 None 65 mg/m 2 
Autumn 90 mg/m 2 2 39 mg/m 2 None 6 4 mg/m 2 
Nuisance algae Phaeocystis pouchetii 
Winter/spring 622,000 cells/L 2, 86 0,000 cells/L None 5,160 cells/L 
Summer 72 cells/L 357 cells/L None Absent 
Autumn 370 cells/L 2, 96 0 cells/L None Absent 
Nuisance algae nearfield Pseudo - nitzschia spp. 
Winter/spring 6,735 cells/L 17,9 00 cells/L None Absent 
Summer 14,635 cells/L 43,100 cells/L None 667 cells/L 
Autumn 10,050 cells/L 2 7,5 00 cells/L None 490 cells/L 
Nuisance algae nearfield Alexandrium fundyense 
Any nearfield 
sample 
Baseline maximum 
163 cells/L 100 cells/L None 23 cells/L 
PSP toxin extent N A 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 the
caution and warning levels. 
NA = not applicable

30 
4. Sea Floor 
Sea-floor monitoring in 2013 included sampling for soft-bottom sediment conditions
and infauna at 14 stations and sediment-profile imaging at 23 stations (Figures 4-1
and 4-2). 
Figure 4-1. Soft-bottom monitoring stations. Fourteen stations were sampled for benthic community
parameters and sediment characteristics. Also shown are the instrumented buoys, the MWRA outfall
diffuser, and the Stellwagen Bank National Marine Sanctuary.

31 
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.

32 
Sampling for grain-size distribution, total organic carbon, the effluent tracer 
Clostridium perfringens spores, and benthic infauna was completed during August.
Sediment and infauna sampling included one station in the “transition” area, located
between Boston Harbor and the nearfield stations (FF12); four nearfield stations
located within two kilometers of the outfall (NF13, NF14, NF17, NF24); six nearfield
stations located within Massachusetts Bay but farther than two kilometers from the
outfall (NF04, NF10, NF12, NF20, NF21, NF22); and three farfield reference stations
located in Massachusetts Bay and Cape Cod Bay (FF01A, FF04, and FF09). For the
purposes of threshold testing, “nearfield” includes the transition station, as well as
both groups of nearfield stations, for a total of eleven stations. 
Sediment-profile imaging was also completed in August. The images were used to
measure the apparent reduction-oxidation (redox) potential discontinuity (RPD)
depth, apparent successional stage of the community, and an organism sediment
index which is derived from the RPD depth and the successional stage. 
Sediment Characteristics and Tracers 
Sediment grain-size distributions in 2013 ranged from silt and clay at some stations to
mostly sand at others (Nestler et al. 2014). 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 2013. For example,
sediments at Station NF12, just to the northwest of the outfall, became siltier, while
those at Station FF01, a sandy station off Cape Ann, were the coarsest ever measured
during the monitoring program. These changes are thought to have resulted from
sediment transport during the February and March storms. (See Section 3, Water
Column; the strongest of these storms produced wave heights of 10 m within
Massachusetts Bay.) 
Percent organic carbon content 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. 
As in past years since the outfall came on line (except 2006), it was possible to detect
elevated levels of the effluent tracer, Clostridium perfringens spores, at the stations
located closest to the outfall (Figures 4-3 and 4-4). Concentrations of Clostridium
perfringens spores have declined or remained comparable to the baseline in all other
locations.

33 
Figure 4-3. Concentrations of Clostridium perfringens spores, corrected for sediment grain size,
in 2013. 
Figure 4-4. Mean concentrations of Clostridium perfringens spores during the baseline and
outfall-discharge years. ( Tran = transition area, stations located between Boston Harbor and the
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 Outfall Startup 
1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011 2013 
Tran
NF <2km
NF >2km
FF

34 
Soft-bottom Communities 
The 14 soft-bottom samples collected and analyzed in 2013 yielded 14,522
organisms, classified into 183 species and 24 other discrete taxonomic groups
(Nestler et al. 2014). Infaunal abundance was within the range observed over the
monitoring program, but generally low, comparable to abundances in the 1993
baseline year (Figure 4-5). The low abundances in 2013 were observed in all areas
sampled. Relative abundances of the five dominant species in the samples, those
contributing at least 5% to total abundances, were low in 2013, as observed for
several years (Figure 4-6). In particular, the polychaete Prionospio steenstrupi ,
which was the numerically dominant species during much of the 1990s and 2000s,
was present in relatively low numbers. 
Figure 4-5. Mean infaunal abundance per sample in four areas of Massachusetts Bay, 1992–2013. 
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 Total Abundance
0
500
1000
1500
2000
2500
3000
3500
4000
4500 Outfall Startup 
1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011 2013 
Tran
NF <2km
NF >2km
FF

35 
Figure 4-6. Mean total abundance per sample and abundance of five dominant species at
nearfield stations, 1992–2013. Molgula manhattensis is a tunicate; the other four species are
polychaetes. 
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. (See Figure 4-8 in the section on
Stellwagen Bank National Marine Sanctuary, below.) Total abundance 
0
500
1000
1500
2000
2500
3000
3500
4000 Outfall Startup 
1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011 2013 
Mediomastus californiensis
Molgula manhattensis
Prionospio steenstrupi
Spio limicola
Tharyx acutus
Total abundance

36 
Sediment-profile Imaging 
Sediment-profile images continued to show no adverse effects of the outfall (Nestler
et al. 2014). Monitoring has shown that physical processes, such as storms and
storm-induced sediment transport, are the primary stressors on the sea floor. The
dominance of physical forces may be considered typical of outfalls that have been
located in high-energy areas that promote rapid dispersion of effluent. 
The 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 4-7). These deep RPD depths were measured despite a decline in
overall depth of penetration by the wedge-shaped prism onto which the sediment-
profile-image camera is mounted. In 2013, RPD depths at 13 of the 23 stations were
deeper than could be measured, so with better prism penetration, RPD measurements
for 2013 would have been even deeper. Prism penetration is typically hampered by
coarse-grained sediments and shell fragments, and even small changes in those
conditions can affect average RPD measurements. The environmental concern before
the outfall came on line was that the RPD depth would become shallower, so a deeper
RPD depth continues to indicate that there has been no adverse effect from the
discharge. 
Figure 4-7. Annual apparent color RPD depth for data from nearfield stations. The 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
Outf all Startup
Threshold

37 
The sediment-profile images also found no indications of organic carbon
accumulation and no adverse effects on the types of organisms inhabiting the
sediments. Even at stations located closest to the outfall, there was no evidence of
organic carbon accumulation, observations supported by organic carbon
measurements made at the stations shown in Figure 4-1. 
If organic carbon concentrations were increasing in the sediments, the images would
have shown increased darkening at the sediment surface, but instead, they continued
to show light-colored, oxygenated surface sediments. The generally light color of the
sediments suggested that the true RPD depths, if measured by electrode rather than
color discontinuity, would be deeper than the prism penetration at all stations. The
color shifts in the apparent RPD are likely indicative of shifts from oxic to suboxic
rather than to anoxic conditions. 
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 sanctuary, in Stellwagen
Basin, which is considered a long-term sediment sink. 
Multivariate analyses of soft-bottom data from 2013 (Figure 4-8) showed that, as in
previous years, fauna from Station FF04 were distinct, grouping separately from other
stations. The separate grouping reflects Station FF04’s deep water and silty sediment,
typical for Stellwagen Basin. 
Figure 4-8. Percent fine sediments superimposed on a non-metric multidimensional scaling
ordination plot of the 2013 infauna samples. Each point represents the sample from each of the 14
stations. The size of the dot corresponds to the percent fine sediments. The groupings represent the
similarity in faunal assemblages, as determined by a cluster analysis. As in previous years, Station
FF04, located within Stellwagen Basin, has a unique, deepwater faunal community.

38 
As in past years, the Stellwagen Basin community was dominated by polychaetes.
The most abundant species in 2013— Levinsenia gracilis, Chaetozone anasimus,
Cossura longocirrata, Anobothrus gracilis and Aricidea quadrilobata —have been
among the ten most abundant species since 2009, usually comprising the five most
abundant taxa. Monitoring during 1992–2010, which included more stations than are
currently sampled, showed the faunal community currently found at Station FF04 to
be widespread throughout deeper waters, with similar faunal assemblages occurring
at all stations with water depths greater than 50 meters. 
The decline in abundance of the once-dominant polychaete Prionospio steenstrupi ,
which has been noted in nearfield samples, has occurred at Station FF04 as well. 
Prionospio was not found in samples from FF04 in 2013. 
Contingency Plan Thresholds 
RPD depth was more than three times the caution-level depth. However, for a fourth
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 caution-level ranges
(Figure 4-9). Two other community threshold parameters, total number of species per
sample 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. 
Table 4-1. Contingency Plan threshold values and 2013 results for sea-floor monitoring. 
Parameter Caution Level Warning Level 201 3 Results 
Sediment parameters 
Nearfield RPD depth < 1.18 cm None 3.76 cm 
Nearfield benthic community parameters 
Species per sample < 42.99 or >81.85 None 55.55 
Fisher’s log - series alpha <9.42 or >1 5.8 None 1 3.14 
Shannon - Wiener diversity <3.37 or > 3.99 None 4.08 , caution level 
exceedance 
Pielou’s evenness < 0.57 or >0.6 7 None 0.71 , caution level 
exceedance 
% opportunists >10% >25% 0.47 %

39 
Figure 4-9. Annual community parameters with nearfield Contingency Plan thresholds. The
varied symbols represent differences in the stations sampled over the years of the program. Results
were tested against thresholds calculated for each sampling design, but only the current threshold
values are shown. Except for the percent opportunists threshold, which is based on levels in Boston
Harbor, thresholds have both upper and lower bounds to show potentially meaningful changes from the
baseline. SD = standard deviation 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 0.40
0.45 
0.50
0.55
0.60 
0.65
0.70
0.75 
0.80 
Evenness (J)
Baseline mean Thresholds
Mean +/-1SD Outfall startup

40 
Similar exceedances of the two indices were observed in 2010–2012, prompting
analysis of data from all four years of exceedances. The investigations focused on the
species that arithmetically contributed the most in the calculations of the higher
values and on possible geographic and temporal patterns that might suggest an effect
of the outfall discharge. 
The analyses showed that exceedances resulted from changes in the degree to which
samples are dominated by a few species (Nestler et al. 2014). The decreases in
populations of the formerly most dominant taxon, the polychaete Prionospio
steenstrupi , and other dominant polychaetes, such as Spio limicola and Mediomastus
californiensis , had the greatest mathematical effect on both the diversity measures. 
One analysis, the Schwartz Dominance Index, which represents the minimum number
of species it takes to comprise 75% of animals in a sample, demonstrated the changes
between the baseline and years since the outfall came on line (Figure 4-10). Both the
diversity measures that exceeded thresholds are affected by dominance, while the
other two diversity measures, total number of species and log-series alpha, which uses
different parameters in its calculation, are not. 
Figure 4-10. Mean Schwartz Dominance Index per sample at nearfield stations in Massachusetts
Bay during the baseline and early post-diversion, 2010– 2012, and 2013 . The Schwartz Dominance
Index is the minimum number of species it takes to make up 75% of the total abundance within a
sample. (Samples with a greater Schwartz Dominance Index values are more evenly distributed;
samples with low index values are dominated fewer species.) 
As in other years, the analyses 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. Schwartz Dominance Index
6.5
7.0
7.5
8.0
8.5
9.0
9.5
10.0
10.5
11.0
11.5
Baseline
(1992-2000)
Post-diversion
(2001-2009)
2010-2012 2013

41 
5. F ish 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 blue mussel tissue. Sampling in 2013 was
limited to winter flounder. 
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

42 
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 2013,
50 sexually mature flounder were collected from each site (Moore et al. 2013). 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
continued to interfere with catches, particularly in muddy depressions at the outfall
and at Deer Island Flats. 
Average ages, lengths, and weights of the winter flounder collected from near the
outfall in 2013 were greater than in 2012, but remained within historic ranges, as they
did at all sites. As has been common throughout the duration of the monitoring
program, the catches were dominated by females, ranging from 66% females at Deer
Island Flats to 98% in flounder from eastern Cape Cod Bay. Factors affecting
flounder sex ratios are complex and poorly understood, but there are no indications of
any effect of the Massachusetts Bay effluent discharge. The already high proportion
of the catches made up of females increased at all sites during the 1991–1999 baseline
period, and in the eight of thirteen years since the outfall came on line, catches from
eastern Cape Cod Bay, 75 km from the outfall, have had the highest proportion of
females. 
External condition measures also fell within historic ranges. Prevalence of fin
erosion, a condition that can be indicative of elevated concentrations of ammonium
and other pollutants, 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 absent in 2013. Elevated
occurrence of ulcers occurred in 2003–2006 and again 2011. Preliminary results
indicate that they were also rare in 2014. The pathology of the ulcers has been
studied but is not understood. 
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 Boston Harbor Fish and Shellfish in Section 6, Special Studies, for
more information). Neoplasia has never been observed in a fish taken from near the
outfall. 
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
higher at the outfall than in 2012 (Figure 5-2). During 2005–2010, there was a slow
increase in age-corrected CHV in fish from near the outfall, followed by declines in
2011 and 2012. CHV incidence in fish from Deer Island Flats remained well below
the relatively high baseline levels and about the same as was measured in 2011 and
2012. Average severity of CHV also remained lower than baseline levels.

43 
Over the course of the monitoring program, there has been no indication of adverse
effects near the outfall, while there have been major improvements in flounder health
in Boston Harbor. These improvements are further discussed in Section 6, Special
Studies. 
Figure 5-2. Annual prevalence of centrotubular hydropic vacuolation (CHV), corrected for age. 
Contingency Plan Thresholds 
There was no exceedance of the only Contingency Plan threshold for fish and
shellfish in 2013 (Table 5-1). Incidence of CHV, the most common indicator of liver
disease in the winter flounder of the region, was 18% in fish taken from the vicinity
of the outfall, lower than the caution threshold and the baseline average. CHV
incidence in flounder was the only threshold parameter calculated for 2013; chemistry
parameters in flounder, lobster, and mussels are measured every three years. 
Table 5-1. Contingency Plan threshold values and 2013 results for fish-and-shellfish monitoring. 
Parameter Baseline Caution Level Warning Level 201 3 Results 
Liver disease CHV 24.4% 44.9% None 18 % 
CHV = centrotubular hydropic vacuolation 0% 
2%
4% 
6% 
8%
10% 
12% 
14% 
1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011 2013 
CHV/mean age 
Deer Island 
Nantasket
Outfall
Cape Cod Bay

44 
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 outfall monitoring overview reports on ongoing monitoring in
Boston Harbor and Cape Cod Bay. 
Boston Harbor Beaches 
MWRA provides technical support to the Massachusetts Department of Conservation
and Recreation for its Boston Harbor beach-monitoring program, which allows daily
monitoring of beach water quality during the swimming season for urban beaches in
Boston Harbor and throughout the MWRA service area (Figure 6-1). Monitoring
results are used to post swimmers’ advisories throughout the swimming season.
Daily monitoring results are also used to assist beach managers in developing and
updating rainfall thresholds for precautionary beach postings following wet-weather
events. 
Figure 6-1. Map of Boston Harbor beaches and bacteria-sampling sites.

45 
Most harbor beaches generally comply with bacteria swimming standards, with most
beaches meeting the single-sample Enterococcus limit, 104 colony-forming units/100
mL, more than 90% of the time in 2013 (Table 6-1). Compliance was 100% at City
Point Beach in South Boston. Wollaston and Tenean beaches, within Boston Harbor,
and Kings Beach, outside the harbor in Lynn, were exceptions, with compliance rates
below 90%. 
The cleanest beaches in Boston Harbor in 2013 were posted with swimmers’
advisories due to elevated bacteria counts only one or two days or not at all, while
those with poorer water quality were posted more than 15 days out of a 79-day
season. (At beaches with multiple sampling locations, daily postings are triggered if
two or more locations on a beach exceed the Enterococcus limit, so the percent of
samples meeting standards does not necessarily correspond directly with the total
days posted.) 
Table 6-1. Compliance with swimming standards at Boston Harbor beaches in 2013. Percent
samples meeting the Enterococcus standard in 2013 and the five-year average and total 2013
swimmers’ advisory postings due to bacteria levels over a 79-day season. 
City or Town/ Harbor Beach 
Percent samples 
meeting standards in 
2013 
( 2009 – 2013 average) 
Total daily postings 
due to high bacteria 
South Boston Carson Beach 99% (92%) 2 days 
M St reet Beach 99% (97%) 1 day 
City Point Beach 100% (98%) 0 days 
Pleasure Bay Beach 96% (96%) 0 days 
Dorchester Tenean Beach 79% (84%) 16 days 
Quincy Wollaston Beach 88% (86%) 12 days 
East Boston Constitution Beach 97% (92%) 1 day 
Winthrop Winthrop Beach * 94% (97%) 1 day 
Short Beach * 94% (96%) 1 day 
Revere Revere Beach * 92% (96%) 1 day 
Lynn Kings Beach * 75% (61%) 17 days 
*Beaches located outside Boston Harbor .

46 
Wet-weather discharges due to urban runoff, stormwater, and combined sewer
overflows (CSOs) can present challenges to maintaining good water quality at
swimming beaches. In South Boston, the North Dorchester Bay CSO storage tunnel
came on line in May 2011, eliminating stormwater discharges in up to 5-year storms
and CSO discharges in up to 25-year storms. This project resulted in reductions in
bacteria levels following wet-weather events at South Boston beaches (Figure 6-2).
The discharges had been the primary causes of elevated bacteria levels at those
beaches. 
Figure 6-2. Percentage of days that South Boston beaches failed swimming standards before and
after the CSO storage tunnel came on line in 2011 . The blue line shows summer rainfall during
those same years. 21% 24% 
18% 
5% 4% 4% 
2
4
6
8 
10 
12 
14 
0%
5%
10%
15% 
20% 
25% 
30% 
2008 2009 2010 2011 2012 2013 
Swimming season rainfall (in.)
% of days bacteria failed standard 
% of days failing to meet swimming standard Rainfall total

47 
Boston Harbor Water Column 
In addition to bacterial water quality monitoring (which includes the beach
monitoring discussed above), MWRA tracks water quality in Boston Harbor for
nutrients, algal biomass (chlorophyll) and dissolved oxygen. Water-column
monitoring in Boston Harbor includes 13 stations throughout the harbor (Figure 6-3).
The program has documented harbor-wide changes in nutrient concentrations,
chlorophyll, and dissolved oxygen throughout each phase of the Boston Harbor
Project, including the diversion of sewage effluent offshore in September 2000
(Figure 6-4). 
Figure 6-3. Water-column sampling locations in Boston Harbor. Stations include MWRA internal
sites, as well as some sites that are also sampled as part of the harbor-and-outfall-monitoring (HOM)
program. Dotted red lines depict the regional divisions between the inner, northwest, central, and
southeast regions. R = river, WWTF = wastewater treatment facility 
Inner
Harbor 
Northwest 
Harbor 
Central Harbor 
Southwest 
Harbor

48 
Figure 6-4. Water quality measurements in Boston Harbor, 1995–2013. The green line and change
from black to red on the data lines show the diversion of effluent from the harbor to Massachusetts
Bay. N=nitrogen, TN=total nitrogen, DIN=dissolved inorganic nitrogen, P=phosphorus, TP=total
phosphorus, DIP=dissolved inorganic phosphorus, CHL-A=chlorophyll, DO=dissolved oxygen 1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013 
0.0
0.5
1.0
1.5
2.0
2.5 
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013 
0
10
20
30
40
50 
DIP
TP
DIN 
AVERAGE P CONC.
(  MOL L -1 ) 
POST-DIVERSION
TN 
AVERAGE N CONC.
(  MOL L -1 ) 1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013 
5
6
7
8
9
10 
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013 0
2
4
6
8
10 
State
std.
Bottom
DO 
MINIMUM MONTHLY DO
CONC. ( MG L -1 ) 
POST-DIVERSION
Summer
chl-a 
AVERAGE CHL-A CONC.
(  G L -1 ) 
Nitrogen 
(annual average) 
Phosphorus 
(annual average) 
Chlorophyll 
(summer average) 
Dissolved oxygen

49 
In 2013, concentrations of the nutrients total nitrogen and total phosphorus were the
lowest recorded by the monitoring program, marking continued recovery of the
harbor after years of eutrophic conditions. Summer chlorophyll levels were the
second highest recorded since the effluent diversion from the harbor, but remained
lower than those of the pre-diversion period. Concentrations of dissolved oxygen in
bottom waters were high, also reflecting the sustained recovery from eutrophication. 
In addition to monitoring harbor-wide trends in water quality, MWRA evaluates
changes in four geographic regions: the inner, northwest, central, and southwest
harbor. The large declines in ammonium concentrations, which were observed
immediately after the outfall diversion to Massachusetts Bay, continued in all regions
of the harbor (Figure 6-5). Ammonium comprises the largest portion of the nitrogen
in wastewater (see Section 2, Effluent). 
Figure 6-5. Annual average ammonium concentrations in four geographic regions of Boston
Harbor.

50 
Boston Harbor Sea Floor 
Prior to the Boston Harbor Project, the harbor sediments were polluted with toxic
metals, pesticides, oil, and other compounds, and in many places, no oxygen
penetrated the surface. The resulting seafloor was called black mayonnaise,” and
most scientists anticipated that recovery would be slow. MWRA has conducted
ongoing sea-floor monitoring in Boston Harbor since 1991. Annual sediment and
infauna samples are taken from nine stations (Figure 6-6). 
Figure 6-6. Soft-bottom sampling stations in Boston Harbor. Nine stations are sampled each year
for sediment characteristics and infauna analyses.

51 
Data from Boston Harbor are frequently presented according to four time periods:
Period I, when the harbor received effluent discharges to both the northern and
southern harbor, as well as biosolids (sludge) discharges, ending with the cessation of
biosolids discharge; Period II, marking the completion of a new primary treatment
plant at Deer Island and the beginning of upgrades to secondary treatment; Period III,
following the end of effluent discharges to the southern harbor; and Period IV,
following the end of all effluent discharge to the harbor. Benthic data analyses offset
the time periods by one year to allow for a lag in response. 
Annual average concentrations of the sewage tracer Clostridium perfringens spores
and total organic carbon (Figure 6-7) document the improvements in the harbor in
response to each step of the Boston Harbor Project (Pembroke et al. 2014).
Particulate organic carbon concentrations have steadily declined throughout the
course of facilities upgrades. Abundance of Clostridium perfringens spores
particularly responded to the upgrade to secondary treatment than occurred in periods
II and III, as well as the ending of sewage discharge to the southern harbor. 
Figure 6-7. Clostridium perfringens spores and total organic carbon in Boston Harbor sediments
during four time periods marking changes in sewage loadings. (Data are ± one standard error. Data
from 1991 were excluded as being variable and anomalously high in comparison with later years.) 
. 0
0.5
1
1.5
2
2.5
3
3.5 
0
50
100
150
200
250 
300 
350
400 
450 
500 
Period I Period II Period III Period IV 
Total Organic Carbon (%) 
Clostridium perfringens (CFU/g dry/%fines 
Clostridium 
Total Organic Carbon

52 
Benthic-community parameters have also changed in response to the changes in
sewage loadings to the harbor. Mean total abundance of organisms has not changed
greatly, trending downward in periods III and IV, but there have been steady
increases in the number of species per sample and diversity indices, such as log-series
alpha, throughout the four periods (Figure 6-8). The other diversity indices,
Shannon-Wiener diversity and Pielou’s evenness, have shown similar increases
throughout the course of monitoring. 
Figure 6-8. Number of species per sample and log-series alpha in Boston Harbor infauna samples
during four time periods marking changes in sewage loadings. (Data are ± one standard error.) 
The decreases in total abundance of organisms resulted from decreases in the
numbers of opportunistic species, such as the polychaete Capitella capitata , which is
a common indicator of disturbed habitats. Dominance patterns have varied through
the years, with some species, such as tube-building amphipods dominant in some
years, but not in others. In 2013, two species of oligochaetes and five polychaetes
dominated the samples. 
The changes in community-diversity parameters and the individual taxa found each
year all point to continued improving benthic conditions. The community analyses,
along with additional evidence from sediment-profile imagery, suggest that the harbor
is now more affected by physical stresses, such as storms, than by the organic
enrichment, eutrophication, and contaminant stress associated with sewage
discharges. 0
1
2
3
4
5
6
7
8
9
0
5
10
15
20
25
30
35
40
45
Period I Period II Period III Period IV 
Log-Series Alpha (mean/sample)
Species per Sample 
Number of Species
Log-Series Alpha

53 
Boston Harbor Fish and Shellfish 
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 from Nantasket
Beach, outside the harbor (see Section 5, Flounder Studies). 
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, 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 6-9). 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, centrotubular hydropic vacuolation (CHV, see
Section 5, Flounder Studies), has dropped by more than half. 
Figure 6-9. Incidence of liver tumor precursors and liver tumors in winter flounder from Deer
Island Flats in Boston Harbor, 1987–2013. Incidence of tumor precursors has fallen, 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

54 
Fish liver disease has been associated with organic contaminants, such as PCBs and
chlorinated pesticides, substances that have been banned since the 1970s and 1980s.
Slow declines in these persistent compounds, as well as the MWRA efforts to limit
their release in sewage effluent, have contributed to the improvements to flounder
health within Boston Harbor, without corresponding increases in liver disease in fish
taken from Massachusetts Bay. 
In conjunction with its Massachusetts Bay outfall-monitoring program, MWRA
measures contaminants in flounder and lobster taken from Boston Harbor, and in
mussels that are collected from clean, coastal sites and deployed in cages at Deer
Island Light near the former harbor outfall. MWRA has documented decreases since
the early 1990s in some contaminants in both flounder and lobster tissues (Hall et al.
2013). 
Since flounder and lobster can move between Boston Harbor and Massachusetts Bay
over the course of the year, mussels provide the best documentation of changes within
the harbor. For example, there have been substantial declines in concentrations of
high molecular weight polycyclic aromatic hydrocarbons (PAHs) in mussels
deployed for 60 days at Deer Island Light (Figure 6-10). At the same time, mussels
deployed with the mixing zone of the Massachusetts Bay outfall showed modest
increases in PAHs during the early years of the discharge (2001–2003). Since 2006,
levels at the outfall have been similar to those at a reference location (Buoy “B”)
located a kilometer away from the outfall. 
Figure 6-10. High molecular weight PAHs in mussels deployed in Boston Harbor and
Massachusetts Bay, 1991–2012. (Mass Bay outfall data are from mussels deployed within the mixing
zone; Buoy “B” data are from mussels deployed one kilometer from the Massachusetts Bay outfall.
Note change in study frequency from annual to every three years after 2003.) 0 
200
400 
600 
800
1,000 
1,200
1,400 
1,600
1,800
ng/g dry weight 
Deer Island Light 
Buoy "B" 
Mass Bay outfall

55 
High molecular weight PAHs are byproducts of hydrocarbon combustion, and many
are known carcinogens. They are targets of MWRA’s toxics-reduction program.
MWRA’s secondary sewage treatment removes about 80–90% of PAHs before
discharge. 
Cape Cod Bay Studies 
For many years, the Center for Coastal Studies has conducted a monitoring program
in Cape Cod Bay, and since 2011, MWRA has collaborated on a portion of the
program. The Center for Coastal Studies monitoring program includes MWRA
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 6-11). 
Figure 6-11. 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 zooplankton portion of the program focuses on larger species than the MWRA
sampling, specifically targeting species that may be prey for right whales. These
methods better characterize the abundance of larger species present in lower
abundances than many in MWRA’s sampling, such as the oil-rich copepod Calanus
finmarchicus , as well as Pseudocalanus spp. These species are favored whale prey.
In 2013, abundances of those species were higher than recorded in 2012, and right
whale sightings were high (Figure 6-12).

56 
Figure 6-12. Right whale sightings in Cape Cod Bay, 1998–2013 . (Figure from the Center for
Coastal Studies.) 0
1
2 
3
4 
5
6 
IPUE

57 
References 
Hall M, Lao Y, Moore M. 2013. 2012 fish and shellfish report. Boston:
Massachusetts Water Resources Authority. Report 2013-08. 47 p. 
Jiang MS, Borkman DG, Libby PS, Townsend DW, Zhou M. 2014. Nutrient input
and the competition between Phaeocystis pouchetii and diatoms in Massachusetts
spring bloom. Journal of Marine Systems 134:29–44. 
Jiang MS, Wallace GT, Zhou M, Libby S, Hunt CD. 2007. Summer formation of a
high-nutrient low-oxygen pool in Cape Cod Bay, USA. Journal of Geophysical
Research 112:C05006. 22 p. 
Libby PS, Borkman DG, Geyer WR, Turner JT, Costa AS. 2014. 2013 water column
monitoring results. Boston: Massachusetts Water Resources Authority. Report 2014-
17. 43 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. 2013. Flounder monitoring report: 2013
results. Boston: Massachusetts Water Resources Authority. Report 2013-17. 17 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.

58 
Nestler EC, Diaz RJ, Pembroke AE, Keay KE. 2014. Outfall benthic monitoring
report: 2013 results. Boston: Massachusetts Water Resources Authority. Report 2014-
10. 35 p. plus appendices. 
Pembroke AE, Diaz RJ, Nestler EC. 2014. Harbor benthic monitoring report: 2013
results. Boston: Massachusetts Water Resources Authority. Report 2014-12. 41 p. 
Smolow M, Wu D, Zhou Y. 2013. Technical survey of nitrogen removal alternatives
of the Deer Island Treatment Plant. Boston: Massachusetts Water Resources
Authority. Report 2013-18. 37 p. 
Werme C, Rex AC, Hunt, C. 2012. Outfall monitoring overview background: 2012
update. Boston: Massachusetts Water Resources Authority. Report 2012-02. 59 p.

59 
List of Acronyms 
BOD Biochemical oxygen demand 
cBOD Carbonaceous biochemical oxygen demand 
CHL-A Chlorophyll 
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 
EPA U.S. Environmental Protection Agency 
FF Farfield 
HOM Harbor and outfall monitoring program 
IAAC Inter-Agency Advisory Committee 
LC50 50% mortality concentration 
MADEP Massachusetts Department of Environmental Protection 
MODIS Moderate Resolution Imaging Spectroradiometer 
MWRA Massachusetts Water Resources Authority 
N Nitrogen 
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 
P Phosphorus 
PAH Polycyclic aromatic hydrocarbon 
PCB Polychlorinated biphenyl 
PIAC Public Interest Advisory Committee 
PSP Paralytic shellfish poisoning 
R River 
RPD Redox potential discontinuity 
TN Total nitrogen 
TP Total phosphorus 
WWTF Wastewater treatment facility

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