2021 overview

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Massachusetts Water
Resources Authority
Environmental Quality
Department Report 2022-11 
2021 Outfall
Monitoring
Overview

Citation: 
Werme C, Wu D, Libby PS, Carroll SR, Codiga DL, Charlestra L, Ellis-Hibbett D, Goodwin C.
2022. 2021 outfall monitoring overview. Boston: Massachusetts Water Resources Authority.
Report 2022-11. 65 pages. 
Cover photos: 
Top: Humpback whale in Massachusetts Bay, courtesy David Silvia.
Bottom: Seafloor sampling in Boston Harbor, courtesy Eric Nestler, Normandeau Associates,
Inc.

2021
Outfall Monitoring Overview 
prepared by 
Christine Werme 
Independent Consultant
Oakland, CA 94612 
P. Scott Libby 
Battelle
72 Main Street
Topsham, ME 04086 
David Wu, Sally R. Carroll, Daniel L. Codiga, Lucner Charlestra,
Denise Ellis-Hibbett, and Chris Goodwin 
Massachusetts Water Resources Authority
Environmental Quality Department
100 First Avenue
Charlestown Navy Yard
Boston, MA 02129 
November 10, 2022

2021 Outfall Monitoring Panel and Committees 
Outfall Monitoring Science Advisory Panel (OMSAP) 
Judith Pederson, Massachusetts Institute of Technology Sea Grant (chair)
Robert Beardsley, Woods Hole Oceanographic Institution
Peter Burn, Suffolk University
Virginia P. Edgcomb, Woods Hole Oceanographic Institution
Loretta Fernandez, Northeastern University
Robert Kenney, University of Rhode Island
Mark Patterson, Northeastern University
Jeff Rosen, Corona Environmental Consulting
Juliet Simpson, Massachusetts Institute of Technology Sea Grant
Juanita Urban-Rich, University of Massachusetts, Boston 
Inter-Agency Advisory Committee (IAAC) 
Massachusetts Bays National Estuary Partnership
Massachusetts Coastal Zone Management
Massachusetts Department of Environmental Protection
Massachusetts Division of Marine Fisheries
NOAA Fisheries
Stellwagen Bank National Marine Sanctuary
US Army Corps of Engineers
US Environmental Protection Agency
US Geological Survey 
Public Interest Advisory Committee (PIAC) 
Association to Preserve Cape Cod
Boston Harbor Now
Cape Cod Commission
Center for Coastal Studies
Conservation Law Foundation
Massachusetts Audubon Society
Massachusetts Bays National Estuary Partnership
MWRA Advisory Board
MWRA Wastewater Advisory Committee
Safer Waters in Massachusetts
Save the Harbor/Save the Bay

i 
Executive Summary 
This 2021 Outfall Monitoring Overview
summarizes results from the Massachusetts Water
Resources Authority (MWRA) monitoring
program in Massachusetts Bay and presents
highlights from its companion monitoring program
in Boston Harbor. MWRA began to monitor the
harbor and the bay in 1991 and 1992, respectively,
when aging wastewater treatment plants were
discharging wastewater effluent to the harbor. In
September 2000, those effluent discharges were
diverted from the shallow harbor to the deeper and
more open waters of Massachusetts Bay.
A National Pollutant Discharge Elimination
System (NPDES) permit regulates the MWRA bay
discharge. The NPDES permit requires regular
monitoring of the effluent and the water column,
sea floor, and fish and shellfish in the bay to
ensure that any adverse effects will be detected,
should they occur. A Contingency Plan attached to
the permit mandates responses by MWRA and the
regulatory agencies in the event that monitoring
detects a potential environmental concern.
In 2021, MWRA marked its twenty-first year of treated wastewater discharge into
Massachusetts Bay, and its Deer Island Treatment Plant earned a National
Association of Clean Water Agencies Peak Performance award for no permit
violations over 15 consecutive years. Over the past more than two decades, there have
been appreciable improvements to the health of Boston Harbor, with no concurrent
adverse effects on Massachusetts Bay. Monitoring has shown no unanticipated or
meaningful effects on the water, the sea floor, or the fish and shellfish. 
The Boston Harbor Project began
in 1985, with the goal to clean up
the polluted harbor. As part of the
project, MWRA constructed
improved facilities, including a new
treatment plant. Today,
wastewater from more than 40
Greater Boston communities
receives secondary treatment at
Deer Island Treatment Plant.
MWRA also diverted the
wastewater effluent discharge
from Boston Harbor to
Massachusetts Bay, through a long
outfall tunnel and a diffuser
system. Monitoring has shown
that the harbor’s health has
greatly improved, with only small,
anticipated, and localized effects
on the bay.

ii 
Deer Island Treatment Plant produces clean effluent 
Producing high-quality wastewater effluent that meets the NPDES permit limits is
critical to protecting the health of Massachusetts Bay. Preventing pollutants from
entering the wastewater system is the first step of ensuring a clean effluent. MWRA
has championed projects to lessen household hazardous waste disposal and minimize
mercury discharges from hospitals and dentists. An industrial pretreatment/pollution
prevention program works to ensure that many toxic contaminants never reach the
treatment plant.
One of the most important measures of effluent quality is the suspended solids load,
the total amount of solid material discharged over a year. The 2021 solids load was
consistent with other recent years and far lower than loads before the discharge was
diverted from the harbor to the bay (Figure i). 
Figure i. Annual solids discharges, 1990–2021. Solids discharges decreased with each step of the
Boston Harbor Project and have remained low. 
One concern for any wastewater discharge is that high levels of nutrients could
promote excess algal growth, a condition called eutrophication, which could result in
lower dissolved oxygen levels. Total nitrogen load, a measure of nutrients in the
effluent, was well below levels of concern in 2021 (Figure ii). Modeling has
suggested that even greater discharges of nitrogen would have no effect on the
Massachusetts Bay environment.

iii 
Figure ii. Annual nitrogen discharges, 1996–2021. The warning threshold, 14,000 metric tons per
year, was set as the load anticipated for 2020; the caution threshold was set at 90% of the warning
threshold. Actual loads have remained lower than anticipated. 
Discharges have not changed algal growth or oxygen levels 
Ammonium, the nutrient that makes up the largest part of
the MWRA nitrogen discharge is a good effluent tracer.
As had been expected when the bay outfall began to
discharge, increased ammonium levels were frequently
detected at stations closest to the outfall (Figure iii).
Variability in ammonium measurements also increased,
with higher levels measured when sampling happened to
occur directly in the effluent plume, which moves with
the tides and currents. Intermittent increases are
sometimes also detected at greater distances.
Most importantly, increased nutrient levels have not increased the growth of
phytoplankton or reduced dissolved oxygen levels in Massachusetts Bay, partially
because the discharge is in deep water. During the summer months, warmer surface
waters keep the discharge plume below the depth where most phytoplankton grow. 
0
3000
6000
9000
12000
15000
1996 1999 2002 2005 2008 2011 2014 2017 2020 
Total Nitrogen Load (metric tons per year) 
Ammonium Nitrate/nitrite Other nitrogen species
Caution threshold Warning Threshold 
Concentrations of
ammonium have
increased near the outfall
but have not changed the
growth of phytoplankton,
the microscopic algae in
the water column, or
reduced dissolved oxygen
concentrations.

iv 
Figure iii. When the discharge was diverted from Boston Harbor to Massachusetts Bay,
ammonium concentrations increased near the outfall but decreased in the harbor. Appreciable
increases have been seen at Stations N21 and N18, very near the outfall, while levels at Station F23 at
the mouth of Boston Harbor have drastically decreased. The black line shows results from 2021. Red
lines and shading show data from 1992-2000, when effluent was discharged to Boston Harbor. Blue
lines and shading show data from September 2000, when the Massachusetts Bay outfall began to
discharge, through 2020. For the pre-2000 and the 2000–2020 data, lines are the 50 th percentile, dark
shading spans the 25 th to 75 th percentile, and light shading spans the range. 
Seafloor communities are not affected by the outfall 
MWRA’s study of the sea floor has also shown
little change related to the outfall. Bottom-
dwelling animal communities are influenced by
the coarseness of seafloor sediments and water
depth rather than by the discharge. Concerns
that the effluent might increase eutrophication,
smother bottom-dwelling life, or increase
sediment contaminants have been dispelled. The numbers of animals, numbers of
species, and the species makeup of the communities have remained relatively
constant, within the ranges of natural variability. 
Seafloor communities are
influenced by types of
sediments and water depth
rather than by the outfall
discharge.

v 
Fish and shellfish are healthy 
MWRA tests flounder (Figure iv), lobsters, and
mussels for toxic metals and pesticides, and flounder
for potential health effects. Levels of toxic
contaminants have declined in Boston Harbor and
remained low or even declined in fish and shellfish
sampled near the Massachusetts Bay outfall. Because
there has been no evidence of effects of the discharge,
the regulatory agencies have approved several
reductions in the timing and geographic extent of
monitoring.
MWRA examines flounder for physical abnormalities, such as fin disease, ulcers,
tumor precursors, and cancerous liver tumors. Flounder health has not declined but
has even improved near the Massachusetts Bay outfall and has greatly improved near
the former outfall in Boston Harbor. In the harbor, better flounder health correlates
well with the declines in total solids and organic material discharged. 
Figure iv. Abundant flounder catch near the Massachusetts Bay outfall site in 2021 . Photo credit
Michael Moore, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts. 
The great improvement
to flounder health is one
of the most notable
successes of the Boston
Harbor Project. Since
2004, no tumors have
been found in fish from
the harbor or the bay.
2004.

vi 
Boston Harbor is cleaner and still improving 
While monitoring in Massachusetts Bay has shown that the outfall does not degrade
the environment, Boston Harbor continues to improve since the effluent discharge
was diverted from the harbor to the bay. Monitoring stations that had been subject to
effluent discharge before September 2000 now exhibit healthy habitats, including
thriving eelgrass, a sign of good seafloor conditions (Figure v). 
Figure v. An eelgrass bed off Deer Island, where effluent was once discharged into Boston
Harbor, continued to thrive in 2021. Green dot on map shows Station R08, the location of the image.
The red markings on the photo edges are centimeters.

vii 
Table of Contents 
Executive Summary............................................................................................................. i 
1. Introduction ....................................................................................................................1 
2. Effluent ....................................................................................................................2 
2021 Effluent Characterization ................................................................................. 2 
Contingency Plan Effluent Thresholds ..................................................................... 9 
3. Water Column ...............................................................................................................10 
COVID-19 Pandemic Protocols .............................................................................. 12 
Physical Conditions ................................................................................................ 13 
Water Quality .......................................................................................................... 16 
Nutrients .............................................................................................................. 16 
Phytoplankton Biomass ...................................................................................... 19 
Dissolved Oxygen ............................................................................................... 21 
Phytoplankton Communities ................................................................................... 22 
Zooplankton Communities...................................................................................... 25 
Stellwagen Bank National Marine Sanctuary ......................................................... 28 
Boston Harbor Water Quality ................................................................................. 29 
Contingency Plan Water Column Thresholds......................................................... 30 
Oxygen Concentration and Saturation in Stellwagen Basin ............................... 31 
Alexandrium catenella Abundance ..................................................................... 32 
4. Sea Floor ..................................................................................................................34 
Sediment Characteristics and Tracers ..................................................................... 36 
Soft-bottom Communities ....................................................................................... 37 
Stellwagen Bank National Marine Sanctuary ......................................................... 42 
Boston Harbor Seafloor Monitoring ....................................................................... 42 
Contingency Plan Seafloor Thresholds ................................................................... 45 
5. Fish and Shellfish ..........................................................................................................46 
Flounder Health ...................................................................................................... 49 
Fish and Shellfish Tissue Chemistry....................................................................... 51 
Contingency Plan Fish and Shellfish Thresholds ................................................... 54 
6. Special Studies...............................................................................................................56 
COVID-19 Influent Monitoring .............................................................................. 56 
Contaminants of Emerging Concern ....................................................................... 57 
Dissolved Oxygen in Cape Cod Bay ...................................................................... 58 
Temperature Changes in the Gulf of Maine ........................................................... 60 
References ..................................................................................................................62 
List of Acronyms ...............................................................................................................65

viii 
List of Figures 
Figure i. Annual solids discharges, 1990–2021.................................................................. ii 
Figure ii. Annual nitrogen discharges, 1996–2021. .......................................................... iii 
Figure iii. Ammonium concentrations increased near the Massachusetts Bay outfall but
decreased in Boston Harbor...................................................................... iv 
Figure iv. Abundant flounder catch near the Massachusetts Bay outfall site in 2021. ..... vi
Figure v. An eelgrass bed off Deer Island, where effluent was once discharged into
Boston Harbor, continued to thrive in 2021. ............................................ vi
Figure 2-1. Annual and average rainfall in Boston, 1990–2021. ........................................2 
Figure 2-2. Annual full secondary-treated effluent flows and primary-blended flows,
1999–2021 ..................................................................................................3 
Figure 2-3. Monthly full secondary-treated and primary-blended flows and rainfall
during 2021.................................................................................................4 
Figure 2-4. Annual solids discharges, 1990–2021. ............................................................. 4 
Figure 2-5. Daily geometric mean of fecal coliform counts in Deer Island effluent in
2021. ...........................................................................................................5 
Figure 2-6. Annual nitrogen discharges, 1996–2021 ..........................................................6 
Figure 2-7. Annual metals discharges, 1990–2021. ............................................................7 
Figure 2-8. High- and low-molecular weight PAH discharges, 2006–2021 ....................... 8 
Figure 3-1. Water-column monitoring stations and instrumented buoys in Massachusetts
and Cape Cod Bays. .................................................................................11 
Figure 3-2. Humpback whale observed near the outfall in May 2021 ..............................12 
Figure 3-3. Flows of the Merrimack and Charles rivers....................................................13 
Figure 3-4. Surface- and bottom water temperature and salinity at Station N18 just to the
south of the outfall in 2021 compared to prior years................................14 
Figure 3-5. Wind speed and significant wave heights at the NDBC Buoy 44013, 1992–
2021 ..........................................................................................................15 
Figure 3-6. Station-average ammonium concentrations at selected stations in 2021
compared to prior years. ...........................................................................17 
Figure 3-7. (Left) Surface- and bottom-water ammonium on February 9, 2021 at the
monitoring stations during mixed (non-stratified) conditions. (Right)
Cross-sections of concentrations throughout the water column along
transects connecting selected stations ......................................................18

ix 
Figure 3-8. (Left) Surface- and bottom-water ammonium on August 25, 2021 at the
monitoring stations during stratified conditions. (Right) Cross-sections of
concentrations throughout the water column along transects connecting
selected stations ........................................................................................18 
Figure 3-9. Station average areal chlorophyll concentrations at selected stations in 2021
compared to prior years ............................................................................19 
Figure 3-10. Moderate-Resolution Imaging Spectroradiometer satellite imagery of
surface chlorophyll concentrations in 2021. .............................................20 
Figure 3-11. Near-bottom water dissolved oxygen concentrations (milligrams per liter) in
2021 compared to prior years ...................................................................21 
Figure 3-12. Total phytoplankton abundance (million cells per liter) at selected stations in
2021 compared to prior years ...................................................................22 
Figure 3-13. Phytoplankton species typical of Massachusetts Bay ...................................23 
Figure 3-14. Abundance of Karenia mikimotoi at the surface (Surf) and at the depth of
maximum chlorophyll for all MWRA samples, 2017–2021 ....................24 
Figure 3-15. Total zooplankton abundance (10,000 individuals per cubic meter) at
selected stations in 2021 compared to prior years ....................................26 
Figure 3-16. Total abundance of non-copepod zooplankton (10,000 organisms per cubic
meter) at selected stations in 2021. Radiolarians, which are usually found
offshore, dominated samples during July and November. Photo credit
Randolf Femmer, USGS, public domain image. ......................................27 
Figure 3-17. Dissolved oxygen concentrations at the NERACOOS Buoy A01 and at
deepwater Station F22 in Stellwagen Basin in 2021. ...............................29 
Figure 3-18. Bottom dissolved oxygen concentrations and percent saturation in the
nearfield and Stellwagen Basin, 2021. .....................................................31 
Figure 3-19. Maximum Alexandrium nearfield sample counts for 2021 surveys and
quartile distributions from all prior nearfield samples. ............................32 
Figure 4-1. Soft-bottom monitoring stations. ....................................................................35 
Figure 4-2. Concentrations of Clostridium perfringens spores in 2021. ...........................36 
Figure 4-3. Total organic carbon at selected stations, 1992–2021. ...................................37 
Figure 4-4. Total abundance of soft-bottom organisms by region, 1992–2021.. ..............38 
Figure 4-5. Polychaete worms dominate the soft-bottom habitats in Massachusetts Bay.39 
Figure 4-6. Ordination plot of 2021 Massachusetts Bay samples by location ..................40 
Figure 4-7. Percent fine sediments (top) and depth (bottom) superimposed on the
ordination plot of the 2021 samples .........................................................41 
Figure 4-8. Total abundance of soft-bottom animals (top) and species (bottom) per
sample in Boston Harbor samples, 1991–2021. .......................................43 
Figure 4-9. An eelgrass bed off Deer Island, where effluent was once discharged into
Boston Harbor, continued to thrive in 2021. ............................................44

x 
Figure 5-1. Fish-and-shellfish monitoring stations............................................................47 
Figure 5-2. Abundant flounder catch near the Massachusetts Bay outfall site in 2021 ....48 
Figure 5-3. A scientist examines a flounder at sea. ...........................................................49 
Figure 5-4. Annual prevalence of the tumor precursor centrotubular hydropic vacuolation
(CHV) in winter flounder, 1991–2021 .....................................................50 
Figure 5-5. Annual prevalence of neoplasia (liver tumors) in winter flounder, 1991–2021
..................................................................................................................51 
Figure 5-6. Total chlordanes in flounder fillets, 1993–2021. ............................................52 
Figure 5-7. DDT in lobster meat, 1994–2021 ...................................................................53 
Figure 5-8. Total PCBs in pre-deployment and deployed mussels, 2021.. .......................54 
Figure 6-1. Viral RNA in MWRA wastewater, March 2020 through September 2022. ...56 
Figure 6-2. Dissolved oxygen levels recorded on sensors deployed on lobster traps in
2021. .........................................................................................................59 
Figure 6-3. Average summer surface-water temperatures in Massachusetts Bay over four
six-year periods, 1998–2021. ...................................................................60 
List of Tables 
Table 2-1. Contingency Plan threshold values and 2021 results for effluent monitoring. ..9 
Table 3-1. Contingency Plan threshold values and 2021 results for water-column
monitoring. ...............................................................................................30 
Table 4-1. Contingency Plan threshold values and 2021 results for seafloor monitoring. 45 
Table 5-1. Contingency Plan threshold values and 2021 result for fish-and-shellfish
monitoring. ...............................................................................................55

1 
1. Introduction 
A generation ago, Boston Harbor was known as one of the dirtiest harbors in the
nation. Since 1984, the Massachusetts Water Resources Authority (MWRA) has
worked to reverse that reputation, minimizing adverse effects of municipal
wastewater discharges on the marine environment through a vigorous pretreatment
program, a carefully maintained treatment plant, and vigilant effluent and
environmental monitoring. One of the most important steps in MWRA’s Boston
Harbor Project came in September 2000, when the MWRA wastewater effluent
discharge was diverted from a shallow-water discharge in Boston Harbor to deeper,
more open waters in Massachusetts Bay. The outfall operates under a National
Pollutant Discharge Elimination System (NPDES) permit, jointly issued by the U.S.
Environmental Protection Agency (EPA) and the Massachusetts Department of
Environmental Protection (MassDEP). The independent Outfall Monitoring Science
Advisory Panel (OMSAP) assists EPA in addressing scientific questions about
potential environmental effects of the outfall on Massachusetts Bay.
The NPDES permit ensures that wastewater discharge does not degrade the
environment in Massachusetts Bay. It requires MWRA to measure effluent quality
before discharge and to monitor the water, sediments, and marine life that could be
affected in Massachusetts Bay. A Contingency Plan, which is attached to the permit,
requires comparing measured conditions against “caution” and “warning” thresholds.
If a caution threshold is exceeded, MWRA must investigate the issue, while a
warning threshold is a higher level of concern that could require responsive action.
Background information about the monitoring program (Werme et al. 2012), the most
current monitoring plan (MWRA 2021) and Contingency Plan (MWRA 2001), past
plans and overviews, and study-specific technical reports are available on MWRA’s
technical report list, http://www.mwra.state.ma.us/harbor/enquad/trlist.html.
This annual Outfall Monitoring Overview report fulfills a requirement of the NPDES
permit that MWRA produce an annual summary of monitoring results for
Massachusetts Bay. Annual overviews also report on special studies, conducted in
response to permit conditions and environmental concerns, often in cooperation with
other agencies. In 2021, MWRA documented changing water temperatures in the
Gulf of Maine and studied regional dissolved oxygen levels, conditions that are
important to understanding the complex harbor and bays system. In addition to
studies of possible outfall effects, MWRA continued to monitor the influent for the
virus that causes COVID-19 and posted daily results on its website.
This annual overview also reports on results relevant to the Stellwagen Bank National
Marine Sanctuary and presents some findings from MWRA’s in-house Boston Harbor
monitoring program. Harbor monitoring documents the success of the Boston Harbor
Project, while Massachusetts Bay monitoring ensures that no new harm occurs
offshore.

2 
2. Effluent 
Despite the continuing challenges of the COVID-19 pandemic, Deer Island Treatment
Plant continued to operate as designed through 2021, earning MWRA the National
Association of Clean Water Agencies (NACWA) Platinum 15 Peak Performance
Award. This NACWA award recognizes facilities with 100% compliance with
effluent permit limits over 15 consecutive years. 
2021 Effluent Characterization 
Wastewater influent to Deer Island Treatment Plant
includes not only municipal sewage but also
groundwater infiltration and stormwater inflow.
Consequently, rainfall is an important factor in
determining wastewater flows and contaminant
concentrations in the wastewater effluent. The Boston
area received 52 inches of rain in 2021, well above the
38 inches of rain in 2020 and also above the 1990–
2021 average (Figure 2-1). 
Figure 2-1. Annual and average rainfall in Boston, 1990–2021. Rain data are from the National
Weather Service rain gauge at Boston Logan International Airport. 
0
10
20
30
40
50
60
1990 1993 1996 1999 2002 2005 2008 2011 2014 2017 2020 
Rainfall (inches) 
Rainfall
Average 
MWRA’s pretreatment
program and secondary
sewage treatment minimize
contaminants, such as
pathogens, organic material,
and toxic compounds, that
are discharged into
Massachusetts Bay.

3
With high rainfall, effluent flow in 2021 was also higher than the flows in 2019 and
2020 (Figure 2-2). As in past years, almost all the flow in 2021 received full
secondary treatment, with only trace amounts of primary-treated effluent blended
with fully treated effluent prior to discharge (Figure 2-3). (Primary treatment is a
physical process, which involves removal of solid material through settling;
secondary treatment includes bacterial decomposition and removes many more
pollutants. All effluent is disinfected before discharge.)
Blending of primary-treated effluent occurs when inflow to the treatment plant
exceeds what the secondary treatment process is designed to handle. Excess flow is
diverted around the secondary process and blended back into full secondary-treated
effluent before disinfection and discharge. This process allows more wastewater to be
treated, preventing street flooding and sewage backups into homes and businesses,
while also relieving pressure on the secondary treatment system and preventing
washout of the beneficial bacteria that are part of that process. Blending occurs only
during heavy rain, and blended flows fully meet permit limits. Massachusetts state
regulations require MWRA to notify regulators and the public whenever blending
occurs. 
Figure 2-2. Annual full secondary-treated effluent flows and primary-blended flows, 1999–2021. 
1999 was the year in which all MWRA flow began to be treated at Deer Island. During large storms,
flow exceeding the secondary capacity of the plant is diverted around the secondary process; these
primary-treated flows are blended into fully treated flows before disinfection and discharge. Blended
flows meet all permit limits. 
0
50
100
150
200
250
300
350
400
450
1999 2002 2005 2008 2011 2014 2017 2020 
Flow (million gallons per day) 
Secondary Flows Primary-blended flows

4 
Figure 2-3. Monthly full secondary-treated and primary-blended flows and rainfall during 2021. 
During large storms, flow exceeding the secondary capacity of the plant is diverted around the
secondary process; these primary-treated flows are blended into fully treated flows before discharge. 
The total suspended solids load to Massachusetts Bay in 2021 was about 14.1 tons per
day, well below the levels discharged into Boston Harbor in the 1990s (Figure 2-4).
In recent years, the total solids load has averaged only about 10% of what had been
discharged to Boston Harbor in 1990–1991, and variability in the suspended solids
load has corresponded to variability in rainfall and, therefore, effluent flow. 
Figure 2-4. Annual solids discharges, 1990–2021. Solids discharges decreased with each
accomplishment of the Boston Harbor Project and have remained low. 
0
2
4
6
8
10
12
0
100
200
300
400
500
600
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 
Rainfall (inches)
Flow (million gallons per day) 
Secondary flows Primary-blended flows Rain

5
Biochemical oxygen demand (BOD), the amount of
oxygen consumed by microorganisms as they break down
organic matter, also remained well below levels that
would be expected to affect dissolved oxygen in the
environment. MWRA has consistently met its BOD
permit limit.
MWRA also monitors the effluent for fecal coliform, a
bacterial indicator for pathogens that can make shellfish
unhealthy for humans to eat. Levels of fecal coliform in
the effluent are well below permit limits (Figure 2-5).
MWRA also monitors fecal coliform in Massachusetts
Bay, and results at all locations, even those closest to the
outfall, meet the stringent shellfishing limits set by the
state. 
Figure 2-5. Daily geometric mean of fecal coliform counts in Deer Island effluent, 2021. Fecal
coliform counts in the effluent were well below the 14,000 colonies per 100 milliliter permit limit
throughout the year. The higher counts in the summer were likely due to the extremely high rainfall; at
higher flows, disinfection can be less effective. Note the y-axis log scale. 
Deer Island Treatment
Plant removes almost
all the solids from
sewage effluent and
more than 75% of the
biochemical oxygen
demand that would
deplete dissolved
oxygen.
Fecal coliform, a
bacterial sewage
indicator, remains well
below permit limits.

6
MWRA’s permit and monitoring plan include reporting requirements for nutrients
and some toxic metals and organic compounds. Nutrient measurements include
individual components of total nitrogen (ammonium, nitrate, and nitrite) and other
nutrients (for example, total phosphorus and phosphate). Metals include, for example,
lead and mercury, and organic compounds include selected pesticides,
polychlorinated biphenyls (PCBs), and polycyclic aromatic hydrocarbons (PAHs).
The total nitrogen load for 2021 was just under 11,000 metric tons, well below the
Contingency Plan caution threshold of 12,500 metric tons (Figure 2-6). The caution
threshold was set conservatively at about 90% of the warning threshold, 14,000
metric tons. The caution threshold was exceeded once, in 2019; however, scenario
simulations with the Bays Eutrophication Model suggest that even loads up to 24%
higher than the higher warning threshold would not have adverse effects (Deltares
2022). MWRA updates its report on potential nitrogen-removal strategies annually
(most recently in Ellis-Hibbett and Hunt 2022). 
Figure 2-6. Annual nitrogen discharges, 1996–2021. The warning threshold, 14,000 metric tons per
year, was set as the load anticipated for 2020; the caution threshold was set at 90% of the warning
threshold. Actual loads have remained lower than anticipated. 
0
3000
6000
9000
12000
15000
1996 1999 2002 2005 2008 2011 2014 2017 2020 
Total Nitrogen Load (metric tons per year) 
Ammonium Nitrate/nitrite Other nitrogen species
Caution threshold Warning Threshold

7
The portion of the effluent total nitrogen load composed of ammonium, a component
readily taken up by phytoplankton, steadily increased over many years of monitoring,
but has decreased since 2016. The ammonium load in 2021 was the lowest measured
since 2008. The increase had been a result of the treatment processes for both
biosolids and effluent; reasons for the recent decreases are not yet clear.
Metals loads remained low in 2021 (Figure 2-7). Zinc continued to be the most
abundant metal in the annual discharge, followed by copper. Both are present in water
pipes and fixtures. Other notable sources of zinc to wastewater include commercial
enterprises, such as beauty shops, automobile-repair shops, and hospitals; residential
household products, such as shampoos, ointments, and laundry detergent; and street
runoff (MWRA, unpublished data). 
Figure 2-7. Annual metals discharges, 1990–2021. Source reduction, industrial pretreatment, and
secondary treatment have dramatically decreased metals loads. 
Total loads of all metals remained small percentages of what had been anticipated
during planning for the Massachusetts Bay outfall. Except for copper, metals meet
water quality standards prior to discharge; on discharge, initial dilution further
reduces concentrations. Copper discharges meet the standard after initial dilution and
have declined over time, a result of drinking-water corrosion control, which decreases
leaching from water pipes, and other source-reduction efforts. Silver, once considered
a good effluent tracer, is now often at levels below detection limits, a result of the
decline in film-based photography, as well as secondary treatment. 
0
50
100
150
200
90 91 92 93 94 95 96 97 98 99 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 21 
Kilograms per day 
Zinc Copper Lead
Chromium Nickel Silver

8
Discharges of organic contaminants have varied slightly from year to year but have
been well below loads historically discharged into Boston Harbor. Annual PAH
loads, for example, remained lower than 100 kilograms, as they have for recent years
(Figure 2-8), a strong contrast with the 3,000 kilograms of PAHs that were estimated
to be discharged in sewage effluent into Boston Harbor in 1991 (Rex et al. 1992).
PAH concentrations now meet water quality standards at discharge, and loads in 2021
were the lowest measured of any monitoring year. For some other organic
compounds, such as 4,4’-DDE, one of the most prevalent breakdown products of the
pesticide DDT, the effluent data show evidence of the very slow declines anticipated
after it was banned along with other persistent substances. 
Figure 2-8. High- and low-molecular weight PAH discharges, 2006–2021. (A different analytical
method was used before 2006, so those data are not directly comparable to the 2006–2021 results.)
High molecular weight PAHs originate primarily from petroleum sources; low molecular weight PAHs
are formed during combustion. Discharges have remained lower than those that would cause
environmental concern, and loads in 2021 were the lowest measured in any monitoring year. 
0
50
100
150
200
250
2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 
PAH load (kilograms/year) 
HMW PAH LMW PAH

9 
Contingency Plan Effluent Thresholds 
There were no effluent Contingency Plan exceedances in 2021 (Table 2-1).
Exceedances of effluent permit conditions have been rare, and none have occurred
over the past 15 years. The total nitrogen caution level, which is not a permit
condition but set in the Contingency Plan, was exceeded in 2019, but the 2021 load
was among the lowest ever measured. 
Table 2-1. Contingency Plan threshold values and 2021 results for effluent monitoring. 
Parameter Baseline Caution Level Warning Level 2021 Results 
Permit Condition and Contingency Plan Thresholds 
pH NA None <6 or >9 Not exceeded
Fecal coliform NA None >14,000 fecal
coliforms/100 mL Not exceeded
Chlorine, residual NA None >631 μg/L daily,
>456 μg/L monthly Not exceeded
Suspended solids NA None >45 mg/L weekly
>30 mg/L monthly Not exceeded
cBOD NA None >40 mg/L weekly,
>25 mg/L monthly Not exceeded
Acute toxicity NA None LC50 <50% Not exceeded
Chronic toxicity NA None NOEC <1.5%
effluent Not exceeded
PCBs NA Aroclor>0.045 ng/L None Not exceeded
Plant performance NA 5 violations/year Compliance <95%
of the time 100% compliance
Flow NA None >436 MGD
average dry days Not exceeded
Oil and grease NA None >15 mg/L weekly Not exceeded 
Contingency Plan Thresholds 
Total nitrogen load NA >12,500
mtons/year
>14,000
mtons/year 10.995 mtons 
NA = not applicable
cBOD = carbonaceous biological oxygen demand
LC50 = 50% mortality concentration
NOEC = no observable effect concentration
PCB = polychlorinated biphenyl
mtons – metric tons (1,000 kilograms)
Plant performance = compliance with permit conditions

10 
3. Water Column 
Water-column monitoring evaluates physical oceanographic processes (freshwater
inflow, temperature, salinity, winds, and ocean currents), water quality (nutrients,
phytoplankton biomass, and dissolved oxygen), and phytoplankton and zooplankton
communities at stations in Massachusetts Bay, at the mouth of Boston Harbor, and in
Cape Cod Bay (Figure 3-1). Ship-based field surveys are augmented by
measurements from instrumented buoys and satellite imagery.
Water-column monitoring is primarily designed to protect Massachusetts Bay from
eutrophication, a potential result of excess nutrients. Monitoring has focused on
nutrients and potential eutrophication, because the effluent loads of other pollutants,
such as organic material, pathogens, and toxic contaminants, are too low to expect
any potential effects. Eutrophication occurs when phytoplankton growth is
overstimulated, which could lead to lower levels of dissolved oxygen or stimulate
nuisance or toxic algal blooms. One nuisance phytoplankton species, Phaeocystis
pouchetii , was a focus in past years but has been shown to vary in response to
physical conditions rather than the outfall and is no longer considered a concern.
Other potentially toxic species, particularly Alexandrium catenella and Pseudo-
nitzschia spp., continue to be evaluated.
Nine surveys are conducted from February through October of each year. Five
stations are in the nearfield (a 12- by 10-kilometer area centered on the outfall, where
some effects of the effluent were expected and have been observed), and nine are in
the more distant farfield, including the mouth of Boston Harbor, Cape Cod Bay, and
near Stellwagen Bank National Marine Sanctuary. Additional surveys may be
triggered by elevated abundance of the potentially toxic dinoflagellate Alexandrium
catenella . These Alexandrium Rapid-Response Study surveys (Libby et al. 2013)
provide in situ hydrographic data and water samples for measuring nutrients and 
Alexandrium abundance at up to 19 stations.
The water-column monitoring program benefits from collaboration with the Center
for Coastal Studies in Provincetown, Massachusetts, which samples the three water-
column stations in Cape Cod Bay and near Stellwagen Bank National Marine
Sanctuary. Regulators have set a target that, whenever possible, sampling in Cape
Cod Bay should occur within 48 hours of the Massachusetts Bay sampling.

11 
Figure 3-1. Water-column monitoring stations and instrumented buoys in Massachusetts and
Cape Cod Bays. Data are obtained from surveys, the NERACOOS A01 and NDBC 44013 buoys, and
satellite imagery. Also shown are the outfall and the Stellwagen Bank National Marine Sanctuary.

12
The surveys are supplemented by measurements on two instrumented buoys: the
Northeastern Regional Association of Coastal and Ocean Observing Systems
(NERACOOS) Buoy A01 off Cape Ann, and the National Oceanic and Atmospheric
Administration’s National Data Buoy Center (NDBC) Buoy 44013 in central
Massachusetts Bay. The National Aeronautics and Space Administration provides
Moderate Resolution Imaging Spectroradiometer satellite imagery of chlorophyll
fluorescence, a measure of phytoplankton biomass. 
COVID-19 Pandemic Protocols 
As the COVID-19 pandemic continued in 2021, field teams were reduced from six to
four during the February, March, and April surveys. These reductions meant that
there was no dedicated marine mammal observer, and some nutrient measurements
could not be completed. A marine mammal observer was allowed on board the
monitoring vessel in May (Figure 3-2), and beginning in June, a full complement of
scientists was able to complete all planned sampling and shipboard analyses. None of
the reductions affected calculation of Contingency Plan threshold parameters. 
Figure 3-2. Humpback whale observed near the outfall in May 2021 . Relaxing of COVID-19
protocols allowed for the return of a dedicated marine mammal observer on the monitoring vessel. This
whale was first observed from Station N21 at the outfall and again while underway to Station F22 near
the Stellwagen Bank National Marine Sanctuary. Photo credit David Silvia, Plymouth, Massachusetts.

13 
Physical Conditions 
Monitoring has shown that the water quality in the
vicinity of the outfall and throughout Massachusetts
and Cape Cod Bays is heavily influenced by weather,
river inflows, and other physical factors throughout
the region. Information about physical conditions has
proven key to interpreting the annual water-column
monitoring data.
After a dry 2020, which continued into early 2021, the summer of 2021 was rainy
(see Figure 2-1, page 2), with the highest summer river flows measured in the past 30
years (Figure 3-3; Libby et al. 2022). Year-to-year variability in rainfall and the
influx of freshwater in river discharges can exert large effects on conditions in the
bay. 
Figure 3-3. Flows of the Merrimack (top) and Charles (bottom) rivers. The Charles River flows
into Boston Harbor. The larger Merrimack River flows influence Massachusetts Bay after flowing into
the Gulf of Maine just south of the New Hampshire border. Red lines are 2021 data. Results from
1992–2020 are in light blue. The quarterly percentiles represent the 2021 flows in comparison to the
entire record. 
Average annual air temperature was somewhat cooler than in recent years, but
surface- and bottom-water temperatures were warm during most survey months, for
example, at Station N18 just south of the outfall (Figure 3-4, top two panels). Surface
temperatures at Station F13 off the coast of Boston’s South Shore reached 23.3
degrees C, about a half a degree warmer than any past temperature measurement
made throughout the monitoring program. 
Physical properties of the
water column in
Massachusetts Bay, such as
temperature and salinity, are
driven by river flow and the
larger patterns of currents in
the Gulf of Maine.

14
Surface- and bottom-salinity at Station N18 were high during the first half of the
survey season, but dropped to below-average levels in July (Figure 3-4, bottom
panels). These drops in salinity were directly related to the high summertime river
flows, a result of the rainy summer months. 
Figure 3-4. Surface- and bottom water temperature and salinity at Station N18 just to the south
of the outfall in 2021 compared to prior years. The black points and lines are results from 2021; the
blue lines and shading are results from 1992–2020: the line is the 50th percentile, dark shading spans
the 25–75th percentiles, and the light shading spans the range. PSU = practical salinity units or parts
per thousand.

15
Wind speeds and directions, which can exert large effects on bay conditions, were
largely typical through 2021, with the notable exception of a large storm with winds
from the northeast in late October, when significant wave heights reached almost nine
meters (Figure 3-5). Several storms in 2021 had winds from the northeast, though not
all were what New Englanders often call “Nor’easters.” Instead, these storms were
the western-edge remnants of tropical storms. An early September 2021 storm, for
example, was a remnant of Hurricane Ida. 
Figure 3-5. Wind speed and significant wave heights at the NDBC Buoy 44013, 1992–2021. Note
the large storm in late October 2021, with high wind speeds and wave heights of almost 9 meters. The
early September storm was a remnant of Hurricane Ida. 
The wind speeds and directions in June promoted upwelling (deep, colder waters
rising to the surface), which cools both surface and bottom waters. During July,
however, the stormy wind conditions were unusually favorable to downwelling,
forcing warmer surface waters deeper. These July downwelling-favorable conditions
contributed to the higher-than-average water temperatures observed during the
summer. High surface-water temperatures and low surface-water salinities during the
summer produced particularly strong water-column stratification. Strong stratification
effectively cuts off bottom waters from the surface and can lead to low levels of
oxygen at depth.

16 
Water Quality 
Water quality measurements include quantification of nutrients, phytoplankton
biomass, and dissolved oxygen. Results for 2021 continued to confirm predictions of
measurable outfall influence on some parameters at stations near the outfall. There
were no unexpected or environmentally adverse findings (Libby et al. 2022). 
Nutrients 
Dissolved inorganic nutrient concentrations in the nearfield stayed mostly within the
ranges measured in previous years, with many measurements at the historic medians.
Concentrations of nitrate, phosphate, and silicate continued to show the typical
seasonal patterns that were present before the offshore outfall began to discharge.
Nutrient levels naturally vary with phytoplankton uptake, exchange with the Gulf of
Maine, and inputs from river discharge.
Nitrogen, including the dissolved forms nitrate and ammonium, is the most important
nutrient for phytoplankton growth in marine waters. Ammonium is also the largest
fraction of the total nitrogen in wastewater (see Figure 2-6, page 6), making it a good
effluent tracer. Since the discharge was relocated from the harbor to the bay in late
2000, variable and elevated levels of ammonium have been detected at stations near
the outfall, (Figure 3-6). Higher ammonium concentrations at stations closest to the
outfall are sometimes a result of a sample being taken directly in the effluent plume,
which moves with tides and currents, while particularly low concentrations likely
reflect the sample completely missing the plume. Nitrogen concentrations measured
at Station F23 at the mouth of the harbor and in MWRA’s Boston Harbor monitoring
program have greatly declined since the discharge to the harbor ended in 2000.

17 
Figure 3-6. Station-average ammonium concentrations at selected stations in 2021 compared to
prior years. Black points and line are results from individual surveys in 2021. Red lines and shading
show data from 1992-2000, when effluent was discharged to Boston Harbor. Blue lines and shading
show data from September 2000, when the Massachusetts Bay began to discharge, through 2020. Red
and blue lines are the 50 th percentile, dark shading spans the 25 th to 75 th percentile, and light shading
spans the range. 
As is typical, the effluent plume’s ammonium signature was evident in surface waters
at stations closest to the outfall during the winter surveys, when the water column was
relatively well-mixed (Figure 3-7). During the August survey, when the water column
was stratified, the ammonium signature was detected at greater distance from the
outfall, farther than in the February unstratified survey and farther than in most past
years (Figure 3-8). However, as in all past years, the plume was confined beneath the
pycnocline, below depths where maximum phytoplankton growth occurs.

18 
Figure 3-7. (Left) Surface- and bottom-water ammonium on February 9, 2021 at the monitoring
stations during mixed (non-stratified) conditions. (Right) Cross-sections of concentrations
throughout the water column along transects connecting selected stations . Station N21 is directly
over the outfall. 
Figure 3-8. (Left) Surface- and bottom-water ammonium on August 25, 2021 at the monitoring
stations during stratified conditions. (Right) Cross-sections of concentrations throughout the
water column along transects connecting selected stations . The yellow line denotes the pycnocline.

19 
Phytoplankton Biomass 
The localized ammonium concentration increases have not fueled phytoplankton
growth or resulted in increased phytoplankton biomass at any station, even those
closest to the outfall (Figure 3-9). Survey phytoplankton biomass is reported as
vertically summed (areal) chlorophyll from measurements collected throughout the
water column from the surface to the sea floor. Seasonal peaks often occur in the
winter or spring and again in the fall, although timing and magnitude varies from year
to year. During the 2021 survey season, areal chlorophyll levels peaked during June
and July as well as the spring and fall at several stations. None of the 2021 peaks
were high compared to observations from previous years. 
Figure 3-9. Station average areal chlorophyll concentrations at selected stations in 2021
compared to prior years. For some stations, historic data (shaded areas) extend later in the year than
the current survey schedule. 
Satellite imagery, which helps fill in the gaps between survey dates, showed moderate
chlorophyll in January and early February, prior to the start of the survey season
(Figure 3-10). Imagery also showed elevated chlorophyll levels in May, variable
levels in the summer, and elevated levels in the fall. These patterns are typical of past
observations.

20 
Figure 3-10. Moderate-Resolution Imaging Spectroradiometer satellite imagery of surface chlorophyll
concentrations in 2021 . The dates (marked in each frame) are highly weather-dependent and do not represent
consistent intervals of time. The numbers 1–9 show the timing of the routine MWRA surveys; the imagery
helps fill the temporal gaps between the surveys. In 2021, a moderate bloom began in January, before the start
of the survey season and a fall bloom persisted after its end in early November.

21 
Dissolved Oxygen 
Typically, bottom-water dissolved oxygen levels (concentration and percent
saturation) begin the year relatively high and steadily decline throughout the summer,
while the water column is stratified. Stratification prevents exchange between the
atmosphere and bottom waters, so dissolved oxygen levels naturally decline, a result
of biological processes.
Massachusetts Bay bottom-water dissolved oxygen concentrations began the year
close to historic medians during the February survey (Figure 3-11). Concentrations
decreased throughout the region in the spring, at some stations reaching the lowest
levels measured for any May survey. Mixing resulting from storms in June and July
temporarily disrupted stratification and re-aerated the bottom waters at many stations.
However, an influx of river flow from those storms led to low salinity in surface
waters, which, coupled with warm surface waters, created particularly strong
stratification in July and August. Bottom-water dissolved oxygen concentrations
declined throughout the region, reaching the lowest annual minimum concentrations
measured during the monitoring program at several stations. The low percent
saturation of dissolved oxygen in Stellwagen Basin failed to meet Contingency Plan
thresholds in September and November. The Contingency Plan threshold for low
dissolved oxygen concentration in Stellwagen Basin was also not met in November.
Those exceedances are discussed on page 31. 
Figure 3-11. Near-bottom water dissolved oxygen concentrations (milligrams per liter) in 2021
compared to prior years. For some stations, historic data (shaded ranges) extend later in the year than
the current survey schedule.

22
Low dissolved oxygen also occurred in Cape Cod Bay. Bottom-water dissolved
oxygen at Station F01 in Cape Cod Bay was at historically low levels during May
through July. A Massachusetts Division of Marine Fisheries (DMF) study of
shallower, more inshore, areas not surveyed by MWRA recorded concentrations
lower than 3 milligrams per liter in mid-August (see Figure 3-15 on page 26 and
Section 6, Special Studies). Although hypoxia (dissolved oxygen concentrations
lower than two milligrams per liter) occurred in these inshore areas in 2019 and 2020,
mixing prevented a recurrence in 2021. 
Phytoplankton Communities 
Total phytoplankton abundances remained relatively low in Massachusetts Bay in
2021, comparable to recent years (Figure 3-12, Libby et al. 2022). The nearfield
annual abundance was 691,169 cells per cubic meter, only 52% of the long-term
mean and ranking 27 th out of 30 years of monitoring. 
Figure 3-12. Total phytoplankton abundance (million cells per liter) at selected stations in 2021
compared to prior years . For some stations, historic data (shaded ranges) extend later in the year than
the current survey schedule.

23
Species composition was typical of past years (Figure 3-13). The low overall
abundances were largely due to the lack of a spring bloom of the sometimes-common
nuisance species Phaeocystis pouchetii and continuing low abundance of both centric
and pennate diatoms, the two major types of silica-rich species common in marine
waters.
Pennate diatoms were present at only 17% of the long-term mean, ranking 29 th of 30
years, partially due to low abundances of the potentially toxic species group Pseudo-
nitzschia . At higher abundances, Pseudo-nitzschia spp. can produce domoic acid, a
neurotoxin that causes amnesic shellfish poisoning (ASP), a life-threatening illness in
animals that consume contaminated shellfish. Historically, ASP has not caused
shellfish closures in Massachusetts or Cape Cod Bays, and there were no closures in
2021. Other often-common diatoms, such as Thalassiosira spp., Thalassionema spp.,
and Asterionellopsis glacialis were also present in lower-than-average numbers. 
Figure 3-13. Phytoplankton species typical of Massachusetts Bay. Photo credits David Borkman,
University of Rhode Island, Narragansett, Rhode Island. 
Phaeocystis
Pseudo-nitzschia Asterionellopsis 
Thalassionema

24
Annual dinoflagellate abundance was somewhat closer to average than other
phytoplankton groups, with nearfield abundance at 75% of the long-term mean,
ranking 21 st of 30 years. Throughout the monitoring program, dinoflagellate
abundance has been cyclic, increasing and decreasing on approximately 11-year
natural cycles. The spring and early summer 2021 communities were dominated by
small species, such as Prorocentrum minimum. This species has been known to
produce toxins but has not been considered a nuisance species in Massachusetts Bay.
August and September were especially dominated by Prorocentrum spp. and Karenia
mikimotoi . 
Karenia mikimotoi was present for a fifth consecutive
year, but at lower abundance than in 2019 and 2020
(Figure 3-14). Maximum abundance was 36,215 cells
per liter, far lower than the 879,087 cells per liter
recorded in 2020. Karenia has, for the past two years,
been present almost year-round. In other geographic
locations, it is known for maximizing growth in areas
with strong vertical gradients, such as pycnoclines (Li
et al. 2019). Targeted sampling in Cape Cod Bay in August 2021 by the Center for
Coastal Studies, an MWRA monitoring partner, found more than 1 million Karenia
mikimotoi cells per liter at the pycnocline. The process of accumulation, senescence,
and decay of Karenia mikimotoi cells in the bottom waters below the pycnocline
appears to be a major factor in the low-oxygen conditions measured in shallow
inshore Cape Cod Bay over the past several years. 
Figure 3-14. Abundance of Karenia mikimotoi at the surface (Surf) and at the depth of maximum
chlorophyll (Cmax) for all MWRA samples, 2017–2021. Cmax is typically 10–15 meters depth.
Cells first appeared in 2017 and have been present for increasingly longer portions of the year. Each
dot represents one sample. Note log scale. Figure does not include data from the Center for Coastal
Studies. Photo credit David Borkman, University of Rhode Island, Narragansett, Rhode Island. 
Decay of Karenia mikimotoi 
cells in the waters below the
pycnocline appears to be a
major factor in the low-oxygen
conditions measured in
shallow inshore Cape Cod Bay
in 2019 and 2020.

25
Abundance of the potentially toxic dinoflagellate Alexandrium catenella (informally
known in New England as a “red tide” species) was low during February–May, but its
toxin, which causes paralytic shellfish poisoning (PSP), was detected in mussels on
June 28 by DMF, and MWRA’s routine survey, also on June 28, found elevated 
Alexandrium cell counts. The highest counts, 7,386 cells per liter, were found at
Station N01 located to the north of the outfall, but counts exceeding the 100 cells per
liter Contingency Plan threshold were also found at Station N18 near the outfall and
along the South Shore. Abundance was sufficient to exceed the Contingency Plan
caution threshold and trigger rapid-response surveys, which characterize Alexandrium
catenella blooms on a weekly basis. Three special surveys were completed in July,
and by July 21, Alexandrium abundances had subsided. By the July 27 routine survey,
the bloom had ended. Additional information on the Contingency Plan exceedance is
presented on page 32.
Although cell counts were high in Massachusetts Bay and in Boston Harbor
throughout the bloom, PSP toxicity was not. Toxicity was detected in New
Hampshire on July 5, and DMF measured levels of PSP toxin greater than 200
micrograms per 100 grams to the north of Cape Ann on July 12 (the DMF action level
is 80 micrograms per 100 grams). Toxicity remained below action levels within
Massachusetts Bay, but shellfishing beds were closed from July 12 until July 30. The
disconnect between high cell counts and low toxicity may be related to wind patterns
and currents, which continue to be analyzed. 
Zooplankton Communities 
Total zooplankton abundance and seasonal patterns were mostly typical in 2021
(Figure 3-15, Libby et al. 2021). As in past years, copepod adults and younger life
stages dominated in every survey. The small species Oithona similis continued to
dominate the zooplankton community.

26 
Figure 3-15. Total zooplankton abundance (10,000 individuals per cubic meter) at selected
stations in 2021 compared to prior years. For some stations, historic data (shaded regions) extend
later in the year than the current survey schedule. The high historic values that extend beyond the
y-axis occurred in July 2015, when larval bivalves were present in very large numbers. 
The July and November samples included an unprecedented number of radiolarians,
single-celled protozoans that build ornate silica exoskeletons (Figure 3-16).
Radiolarians were similarly abundant in August and September 2020, but had not
been observed in prior years of the monitoring program. Radiolarians are more
typically found in offshore waters, and their presence appears to reflect an influx of
water masses from the offshore. Changes in regional water movements have also
influenced water temperature trends; these shifts are discussed further in Section 6,
Special Studies.

27 
Figure 3-16. Total abundance of non-copepod zooplankton (10,000 organisms per cubic meter) at
selected stations in 2021 . Radiolarians, which are usually found offshore, dominated samples during
July and November. Photo credit Randolf Femmer, USGS, public domain image.

28 
Stellwagen Bank National Marine Sanctuary 
The NPDES permit to discharge from Deer Island Treatment Plant into
Massachusetts Bay requires annual reporting on results relevant to Stellwagen Bank
National Marine Sanctuary. Water column Station F22 is just north of Stellwagen
Basin, to the west of the sanctuary, and is considered to be representative of offshore
conditions. The instrumented NERACOOS Buoy is located within the sanctuary.
Ammonium levels have remained low at Station F22 since the outfall began to
discharge (see Figure 3-6, page 17). Sampling at Station F22, data from the
NERACOOS Buoy, and satellite imagery detected no unusual chlorophyll levels in
offshore regions in 2021. No effects on chlorophyll levels in the offshore areas of
Massachusetts Bay, including the sanctuary, were predicted as a result of moving the
discharge from Boston Harbor to the bay, and none have been measured.
Dissolved oxygen concentrations and percent saturation at Station F22 in Stellwagen
Basin did reach low levels in the fall, failing to meet the Contingency Plan warning
thresholds. These exceedances have not been attributed to the outfall and are
discussed further on page 31, below. Data from the NERACOOS Buoy (which are
not used to calculate Contingency Plan threshold parameters) showed the decline
during the stratified season and also documented the rapid return to oxygenated
conditions following fall mixing events (Figure 3-17).

29 
Figure 3-17. Dissolved oxygen concentrations at the NERACOOS Buoy A01 (lines) and at nearby
deepwater MWRA survey Station F22 (symbols) in 2021 . Note the rapid increase in dissolved
oxygen concentration captured by the buoy sensors following the late fall and early winter mixing
events, after the final MWRA survey of the year. 
Boston Harbor Water Quality 
Water quality in Boston Harbor has greatly improved during the decades of the
Boston Harbor Project, and those improvements were sustained in 2021.
Perhaps the most dramatic improvement in Boston Harbor was the immediate
decrease in ammonium levels. Ammonium concentrations in the harbor dropped
precipitously in 2000, when the effluent discharge was diverted from the harbor to the
bay, and have remained low. The decreases in nutrient inputs have been accompanied
by decreases in primary production and phytoplankton biomass, an abatement of the
harbor’s historic high level of eutrophication (Werme et al. 2018, Taylor et al. 2020).

30 
Contingency Plan Water Column Thresholds 
There were four exceedances of three water-column thresholds in 2021: oxygen
concentration in Stellwagen Basin in November, oxygen percent saturation in
Stellwagen Basin in September and November, and abundance of the nuisance algal
species Alexandrium catenella in June (Table 3-1). 
Table 3-1. Contingency Plan threshold values and 2021 results for water-column monitoring. 
Parameter Baseline Caution
Level
Warning
Level 2021 Results 
Dissolved oxygen* 
Nearfield
concentration 6.05 mg/L <6.5 mg/L <6.0 mg/L 6.36 mg/L
Nearfield percent
saturation 65.3% <80% <75% 71.3%
Stellwagen
concentration 6.23 mg/L <6.5 mg/L <6.0 mg/L 5.89 mg/L
Stellwagen
percent saturation 67.2% <80% <75% 65.9 %
Nearfield
depletion rate 0.024 mg/L/d >0.037 mg/L/d >0.049 mg/L/d 0.012 mg/L/d 
Chlorophyll 
Annual 72 mg/m 2 >108 mg/m 2 >144 mg/m 2 49 mg/m 2 
Winter/spring 50 mg/m 2 >199 mg/m 2 None 62 mg/m 2 
Summer 51 mg/m 2 >89 mg/m 2 None 43 mg/m 2 
Autumn 90 mg/m 2 >239 mg/m 2 None 42 mg/m 2 
Nuisance algae nearfield Pseudo-nitzschia 
Winter/spring 6,735 cells/L >17,900 cells/L None 130 cells/L
Summer 14,635 cells/L >43,100 cells/L None 3,110 cells/L
Autumn 10,500 cells/L >27,500 cells/L None 94 cells/L 
Nuisance algae nearfield Alexandrium catenella 
Any nearfield
sample
Baseline
maximum
163 cells/L
>100 cells/L None 7,386 cells/L
PSP toxin extent NA New incidence None No new
incidence 
*Dissolved oxygen caution and warning levels represent numerical criteria, with the caveat “unless
background conditions are lower.” Exceedances are highlighted in orange.
PSP = paralytic shellfish poisoning
NA = not applicable

31 
Oxygen Concentration and Saturation in Stellwagen Basin 
Dissolved oxygen parameters, including concentration, percent saturation, and the
rate of depletion throughout the summer months, are compared to baseline minima
rather than the specific caution and warning thresholds when the baseline levels were
already lower than the thresholds. No exceedances occurred in the nearfield in 2021,
but there were exceedances in Stellwagen Basin (Figure 3-18). Compared to a
background minimum of 67.2%, saturation at Station F22 was 66.3% during the
September survey and 65.9% during the November survey (originally scheduled for
October). The oxygen concentration at Stations F22 was 5.89 milligrams per liter on
November 2, compared to a background minimum of 6.23 milligrams per liter. 
Figure 3-18. Bottom dissolved oxygen concentrations (top) and percent saturation (bottom) in
the nearfield and Stellwagen Basin, 2021 .

32
These exceedances have not been attributed to the outfall, but instead appear to be the
result of broader, regional physical conditions. There is no evidence that changes in
nutrient levels have fueled algal blooms that could result in lower dissolved oxygen
measurements. The depth-averaged ammonium concentrations at Station F22 have
not changed from baseline levels. One likely driver of lower oxygen levels is the
warming temperatures that are being observed throughout the Gulf of Maine.
Increased temperatures in the region are discussed further in Section 6, Special
Studies. Alexandrium catenella Abundance 
The phytoplankton species Alexandrium catenella occurs regularly in Massachusetts
Bay, most typically peaking in May and June. Alexandrium blooms have been noted
in Massachusetts Bay since the early 1970s and were particularly common in the
1970s and 1980s, followed by a lull in the 1990s and early 2000s. When the water-
sample threshold for Alexandrium abundance was set at 100 cells per liter, OMSAP
recognized that blooms were patchy and unpredictable and therefore also endorsed an
alternative threshold based on PSP toxin in shellfish. The water-sample cell count
caution threshold (there is no warning threshold) was not exceeded in the first five
years after the outfall began to discharge to Massachusetts Bay, but it has been
exceeded nine times since 2005, including in 2021 (Figure 3-19). The threshold for
new incidence of PSP toxin, has never been exceeded. 
Figure 3-19. Maximum Alexandrium nearfield sample counts for 2021 surveys and quartile
distributions from all prior nearfield samples. Note log scale. Photo credit Don Anderson, Woods
Hole Oceanographic Institution, Woods Hole, Massachusetts.

33
In the past, Massachusetts Bay blooms originated from cyst beds to the north of
Massachusetts Bay, along the coast of Maine (Anderson et al. 2013). However, a
large bloom in 2019 may have resulted in the establishment of a more local cyst bed.
Cysts have been detected in Massachusetts Bay, so the possibility exists that blooms
may originate from a more local source. This hypothesis is being investigated.

34 
4. Sea Floor 
Seafloor monitoring assures continued health of soft- and hard-bottom habitats. Soft-
bottom surveys are conducted annually, while photographic and video assessments of
hard-bottom habitats occur at three-year intervals, most recently in 2020. A separate
seafloor monitoring program, including sediment-profile imagery, is conducted in
Boston Harbor.
The initial concerns for the sea floor, such as smothering by discharged solids, low
oxygen levels, or accumulation of toxic contaminants in the sediments, have been
contradicted by years of monitoring. The good results have allowed some monitoring
to be scaled back. Visual analyses by sediment-profile imaging and chemical analyses
of sediments are no longer part of the Massachusetts Bay monitoring program.
Measurements of sediment characteristics, sewage tracers, and community structures
continue.
Massachusetts Bay soft-bottom sediment sampling was completed in August 2021,
with samples analyzed for grain-size distribution, the effluent tracer Clostridium
perfringens spores, total organic carbon, infauna abundance, and species composition.
Samples were collected at 14 Massachusetts Bay stations (Figure 4-1). The stations
included four nearfield stations located within two kilometers of the outfall; six
nearfield stations in western Massachusetts Bay farther from the outfall; one station in
the “transition” area between Boston Harbor and the nearfield; and three farfield
reference stations in Massachusetts and Cape Cod Bays. For the purposes of threshold
testing, “nearfield” includes both nearfield groups and the transition station, for a total
of eleven stations.

35 
Figure 4-1. Soft-bottom monitoring stations. The inset shows the three farfield stations. Also shown
are the instrumented buoys, the MWRA outfall diffuser, and Stellwagen Bank National Marine
Sanctuary.

36 
Sediment Characteristics and Tracers 
As in past years, sediment grain-size distributions in 2021 varied broadly among
stations, ranging from silt and clay at some stations (particularly Station FF04 within
Stellwagen Basin in the farfield) to almost entirely sand at others (Nestler et al. 2022).
Within individual stations, sediment textures have remained generally stable over the
years of the monitoring program, with occasional changes following large storms. 
Clostridium perfringens are anaerobic bacteria found in the digestive tracts of humans
and other mammals and that form persistent resting spores if they reach oxygen-rich
conditions such as those found at the bottom of Massachusetts Bay. These bacteria
spores provide a sensitive tracer of sewage effluent. Spore counts are normalized by
the percent of the sediments made up of silt and clay (“percent fines”). As in other
years since the offshore outfall began to discharge, it was possible to detect elevated
levels of Clostridium spores at some stations located closest to the outfall in 2021
(Figure 4-2). In most years, Clostridium spore concentrations have been elevated at
stations located within two kilometers of the outfall. Concentrations at those nearfield
stations were lower or about the same in 2021 as in 2020. Across all stations, 2021 
Clostridium spore concentrations were among the lowest measured throughout the
monitoring program. 
Figure 4-2. Concentrations of Clostridium perfringens spores in 2021. Concentrations represent
spore counts (cfu, colony forming units) normalized to percent fines. As anticipated during outfall
planning, Clostridium spores are found in greater concentrations at stations closest to the outfall.
These spores are considered a tracer of sewage effluent.

37 
Percent total organic carbon content analyses were consistent with past results, with
no increased organic carbon at stations near the outfall or in any other area (Figure
4-3). In general, stations with finer sediments, such as Station FF04 within
Stellwagen Basin, have higher mean total organic carbon concentrations, while
stations with coarser sediments, such as Station NF17 just to the south of the outfall
have lower concentrations. Total organic carbon data continue to show no signs of
organic enrichment from the outfall, consistent with predictions made before the
outfall began to discharge and also consistent with a detailed special study of
sediment metabolism, which was completed in 2010 (Tucker et al. 2010, Tucker et al.
2014). 
Figure 4-3. Total organic carbon at selected stations, 1992–2021. Station FF01A is the northern
reference station; FF04 is within Stellwagen Basin; NF12 is >2km northwest of the outfall; and NF17
is in close proximity and southwest of the outfall, where the effects of the discharge might be expected
but have not been found. No effects of the discharge have been observed at any station. 
Soft-bottom Communities 
The 14 soft-bottom samples collected and analyzed in 2021 yielded 25,086
organisms, classified into 182 species and 20 other discrete taxonomic groups
(Nestler et al. 2022). Total abundance of organisms was slightly higher in 2021 than
in 2020 in both nearfield station groups and at the one transition station between
Boston Harbor and the nearfield (Figure 4-4). Diversity measures were slightly higher
than in 2020, but all measurements remained within the ranges measured throughout
the monitoring program.

38 
Figure 4-4. Total abundance of soft-bottom organisms by region, 1992–2021 . Regions include the
nearfield within two kilometers of the outfall, the nearfield farther than two kilometers from the
outfall, the transition area between Boston Harbor and the outfall, and the farfield. 
Polychaete worms (for example, Figure 4-5), continued to dominate at most stations.
These segmented worms are among the most common marine organisms. The spionid
polychaete Prionospio steenstrupi was slightly less abundant in 2021 than in 2020 but
remained the numerically dominant species at nearfield stations. Such minor species
changes from year to year are typical of the region. Other common polychaetes,
including Aricidea catherinae and Mediomastus californiensis , were present in
numbers comparable to those of other recent years. 
0
500
1000
1500
2000
2500
3000
3500
4000
4500
5000 Outfall Startup
1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011 2013 2015 2017 2019 2021
NF <2km
NF >2km
Tran
FF

39 
Figure 4-5. Polychaete worms dominate the soft-bottom habitats in Massachusetts Bay. This
species, Kirkegaardia baptistae , is frequently found in fine-grained, offshore sediments, and MWRA
samples were used in its original description. Photo credits James A. Blake, Museum of Comparative
Zoology, Harvard University, Cambridge, Massachusetts.

40
Community analyses continued to show no effects of the outfall on relative
abundance of animals or community composition. A series of multivariate analyses
assessed spatial and temporal patterns in the soft-bottom communities and found no
particular species or type of community specifically associated with the outfall.
One type of community analysis, cluster analysis, which groups stations by similarity
in species composition and abundance, continued to identify two main infauna
assemblage groups and one outlier group. Group I, including two subgroups, was
dominated by crustaceans and polychaete worms. Group II, including three
subgroups, comprised a greater abundance of polychaetes and also mollusks. The
outlier Group III included only the offshore station located within Stellwagen Basin,
which has consistently supported a unique polychaete community.
Ordination analysis, an additional analysis determining how closely related the
bottom communities within stations are to each other, continued to show no
indication of any relation of species composition to proximity to the outfall (Figure
4-6). Groups I and II included stations from both nearfield areas and from the farfield. 
Figure 4-6. Ordination plot of 2021 Massachusetts Bay samples by location. Each point on the plot
represents one of 14 stations, and varying colors and shapes depict locations in the nearfield, farfield,
and transition area between Boston Harbor and Massachusetts Bay. Placement of the points indicates
similarity of the communities—the nearer two points are to each other, the more similar their seafloor
communities. (2D Stress noted in the upper right is a measure of good confidence in the analysis.)

41
As in past years, further assessment of the ordination analysis demonstrated that
variations in species distributions largely followed differences in sediment grain size
and depth (Figure 4-7). That is, seafloor communities from stations with similar
sediment textures or water depths tended to be more closely related, as shown by
closer proximity on the ordination plots. These results and past monitoring have
confirmed that the Massachusetts Bay sea floor is dominated by physical factors. The
strong physical forces, as well as the continued high quality of the effluent discharge,
are the principal reasons that soft-bottom habitat quality has remained high. 
Figure 4-7. Percent fine sediments (top) and depth (bottom) superimposed on the ordination plot
of the 2021 samples. Data are shown as in Figure 4-6, with the size of each station marker indicating
the percentage of fine sediments (top) or water depth (bottom). Stations with similar sediment textures
and/or depths tended to be represented in the same groups. (2D Stress noted in the upper right is a
measure of good confidence in the analysis.)

42 
Stellwagen Bank National Marine Sanctuary 
The NPDES permit to discharge from Deer Island Treatment Plant into
Massachusetts Bay requires annual reporting on results relevant to Stellwagen Bank
National Marine Sanctuary. MWRA’s deep-water reference Station FF04 lies within
the depositional part of the sanctuary, Stellwagen Basin, where long-term
accumulation of pollutants and their effects would be expected if they were to occur.
Station FF04 is typical of the deep waters offshore from the outfall, representative of
a larger group of stations that were monitored in earlier years of the program, and it
continues to support a soft-bottom community typical of what had been found at the
larger suite of deep-water stations. Communities at those stations have always shown
distinct differences from those found at shallower stations, probably due to their
distance from shore, as well as their depth and their fine-grained sediments.
Superimposing percent grain size and depth on the ordination plot for 2021 samples
continued to show these natural differences (Figure 4-7). 
Boston Harbor Seafloor Monitoring 
While the chemistry and biology of the Massachusetts Bay sea floor have not been
adversely affected by the relocated outfall, conditions are much better and continue to
improve in Boston Harbor. MWRA has conducted ongoing seafloor monitoring in
Boston Harbor since 1991. Annual sediment samples are taken from nine stations,
and sediment-profile imaging is carried out at 61 stations throughout the harbor.
Sediment textures within the harbor have been generally stable over time, ranging
from mostly sand at some stations to silt and clay at others. Concentrations of total
organic carbon in harbor sediments have declined over time, reflecting the lowered
inputs of organic carbon associated with each milestone throughout the Boston
Harbor Project.
Over the past decade, the total abundance of organisms and species per sample have
stabilized (Figure 4-8), responses to continued and sustained improvement in seafloor
habitat conditions. In 2021, 18 samples yielded 31,349 specimens, classified into 132
species and 17 other discrete taxonomic groups. As in past years, the communities
varied along an outer- to inner-harbor gradient, reflecting the greater tidal flushing at
the outer harbor stations. Sediment-profile imaging has also confirmed an outer- to
inner-harbor gradient and clearly documented improvements to habitat conditions
throughout the duration of the Boston Harbor Project.

43 
Figure 4-8. Total abundance of soft-bottom animals (top) and species (bottom) per sample in
Boston Harbor samples, 1991–2021. Data are from eight harbor stations that have been consistently
monitored. 
Sediment-profile images depicted the continuing good conditions in 2021. One
primary indicator of habitat quality, the organism-sediment index, was higher in 2021
than in 2020, continuing to show improvements to seafloor habitat. Eelgrass
continues to be present at Station R08 in Deer Island Flats in 2021 (Figure 4-9).

44 
Figure 4-9. An eelgrass bed off Deer Island, where effluent was once discharged into Boston
Harbor, continued to thrive in 2021. Green dot on map shows Station R08, the location of the image.
The red markings on the photo edges are centimeters. 
2020

45 
Contingency Plan Seafloor Thresholds 
There were no threshold exceedances for the seafloor Contingency Plan parameters in
2021 (Table 4-1). All seafloor threshold values are calculated for the nearfield; for the
purposes of threshold testing, “nearfield” includes all nearfield stations (both nearer
and farther than two kilometers from the outfall) and the station in the transition area
between Boston Harbor and the Massachusetts Bay outfall.
Number of species per sample and the diversity and evenness indices remained higher
than Contingency Plan limits, while the percent opportunistic species remained far
below any level of concern, less than 1% compared to a caution level of 10%. All
threshold parameters continued to confirm that Massachusetts Bay maintains
persistently healthy seafloor habitats, unaffected by the outfall discharge. 
Table 4-1. Contingency Plan threshold values and 2021 results for seafloor monitoring. 
Parameter Baseline Caution
Level
Warning
Level 2021 Results 
Species per
sample NA <42.99 None 64.9
Fisher’s log-series
alpha NA <9.42 None 13.2
Shannon diversity NA <3.37 None 4.11
Pielou’s evenness NA <0.57 None 0.68
% opportunists NA >10% >25% 0.53% 
NA = not applicable There were no exceedances in 2021.

46 
5. Fish and Shellfish 
Fish and shellfish monitoring preserves healthy stocks
and safe seafood. Fish and shellfish can be good
indicators of overall environmental health, and
monitoring protects the public health of seafood
consumers. This monitoring includes external and
internal assessments of winter flounder health and
analysis of toxic contaminant levels in winter flounder,
lobsters, and cage-deployed blue mussels.
MWRA monitors winter flounder health each year and conducts chemical
contaminant analyses of flounder, lobster, and cage-deployed mussel tissues every
three years, including 2021. Sampling and deployment sites vary by species (Figure
5-1). Annual flounder monitoring focuses on external condition and the presence of
liver disease, precancerous conditions, and tumors. Contaminant monitoring focuses
on toxic metals and organic pollutants.
In April 2021, flounder were collected from the Massachusetts Bay outfall site, Deer
Island Flats (near the former Boston Harbor outfall), and eastern Cape Cod Bay, a
clean, coastal reference area. Monitoring of the eastern Cape Cod Bay site was to
have been discontinued after 2020, as contaminant levels have been consistently low,
but the location was sampled as part of a separate pilot project. Only health
assessments were made of those fish.
A full complement of 50 fish were collected from the outfall site and eastern Cape
Cod Bay (Figure 5-2). However, despite three hours of trawling, the time limit
designated in the work plan, only 33 fish were taken from Deer Island Flats. Catches
have been relatively low throughout the region for the past three years. Southern New
England winter flounder populations have declined since the 1980s, possibly a result
of overfishing (for example, Frisk et al. 2018). MWRA survey trawls have also been
compromised by abandoned lobstering gear and benthic algal growth clogging the
trawl net, and both those conditions hampered the 2021 Deer Island Flats catches. 
Flounder and lobster, which
feed on the sea floor, and
mussels, which filter large
volumes of seawater, have
potential exposure to
contaminated particles
suspended in water or
settled on the ocean floor.

47 
Figure 5-1. Fish-and-shellfish monitoring stations. IH = Inner Harbor; DIF = Deer Island Flats; DIL
= Deer Island Light; OS = Outfall Site; OS-M = Outfall Site, Mussels; LNB = Large Navigation Buoy
(buoy south of the outfall); ECCB = Eastern Cape Cod Bay. Also shown are the outfall, the
instrumented buoys, and the Stellwagen Bank Marine Sanctuary.

48 
Figure 5-2. Abundant flounder catch near the Massachusetts Bay outfall site in 2021 . However,
over the past three years, catches at Deer Island Flats have been low, as abandoned lobster gear
interferes with trawling. Photo credit Michael Moore, Woods Hole Oceanographic Institution, Woods
Hole, Massachusetts. 
Lobsters were collected by commercial fishermen from the same locations as the
flounder: the Massachusetts Bay outfall site, near Deer Island, and eastern Cape Cod
Bay. All lobster collections were completed during a one-week period in July.
Researchers acquired mussels from the Northeastern Massachusetts Aquaculture
Center, located at Cat Cove Marine Laboratory, a part of Salem State College in
Salem, Massachusetts. Caged mussels were placed at three locations for 30- and 60-
day deployments: near the diffusers at the Massachusetts Bay outfall, within Boston
Inner Harbor, and at Deer Island Light. Survival of the deployed mussels was high,
almost 100%.

49 
Flounder Health 
While at sea, scientists complete external health assessments and preserve livers for
laboratory analysis (Moore et al. 2022; Figure 5-3). Across all sites, mean age of fish
ranged from 4.8 to 5.5 years, and standard length (length from the tip of the head to
the base of the tail fin) ranged from 333 to 377 millimeters, somewhat older and
longer than the 2020 catches, but within the ranges observed in recent years. As in
past years and as is common throughout northeast coastal populations (Moore et al.
2016), the catches were dominated by females, with the highest proportion of females
taken from eastern Cape Cod Bay. 
Figure 5-3. A scientist examines a flounder at sea. 
Photo credit Eric Rydbeck, Normandeau Associates, Bedford, New Hampshire.

50
Measures of external condition, such as bent fin rays and occurrence and severity of
fin erosion, continued to suggest improved conditions since the 1980s and 1990s.
Incidence of fin erosion at Deer Island Flats was the lowest ever measured in fish
from near the former Boston Harbor outfall site. Blind-side ulcers, which remain
poorly understood but are observed in some years, were not present in 2021.
The incidence of centrotubular hydropic vacuolation (CHV), a tumor precursor and
mild liver condition associated with exposure to contaminants, remained lower than
the baseline observations at all sites (Figure 5-4). CHV incidence was the lowest
measured in any year at the outfall site and at Deer Island Flats. Total CHV incidence
at Deer Island Flats decreased from more than 75% in 1988 to 20% or less in recent
years and only 9% in 2021. CHV incidence has been lower across all age groups in
both the harbor and the bay, alleviating any concerns for increased liver disease in
Massachusetts Bay. 
Figure 5-4. Annual prevalence of the tumor precursor centrotubular hydropic vacuolation
(CHV) in winter flounder, 1991–2021. DIF = Deer Island Flats, ECCB = Eastern Cape Cod Bay, NB
= Nantasket Beach (sampled until 2020), OS = Outfall Site 
Liver tumors (neoplasia), which were present in up to 10% of fish in the 1980s, have
not been observed by the monitoring program since 2004 and have never been found
in fish taken from the Massachusetts Bay outfall site (Figure 5-5; see also Moore et
al. 2018).

51 
Figure 5-5. Annual prevalence of neoplasia (liver tumors) in winter flounder, 1991–2021. DIF =
Deer Island Flats, ECCB = Eastern Cape Cod Bay, NB = Nantasket Beach (sampled until 2020), OS =
Outfall Site. 
Fish and Shellfish Tissue Chemistry 
Samples for chemical analyses were taken from
the same winter flounder collections made for
health assessments at the Massachusetts Bay
outfall and Deer Island Flats. Samples of winter
flounder fillet were analyzed for PCBs,
pesticides, and mercury. Liver samples from the
same fish were analyzed for PCBs, pesticides,
PAHs, and selected metals.
Samples of lobster meat collected in July from those same two locations plus eastern
Cape Cod Bay were analyzed for PCBs, pesticides, and mercury. Digestive gland (the
hepatopancreas, often called tomalley) samples from the same animals were analyzed
for PCBs, pesticides, PAHs, and selected metals.
Mussels, deployed in cages in Boston Inner Harbor, Deer Island Flats, and near the
outfall, were analyzed for PCBs, pesticides, PAHs, lipids, mercury, and lead.
Concentrations following the 30- and 60-day deployments were compared to
concentrations in the reference mussels prior to deployment. 
Contaminants in flounder,
lobster, and mussels have
not increased since the
Massachusetts Bay discharge
began in 2000. Levels of
many contaminants have
declined, particularly near the
former Deer Island outfall in
Boston Harbor.

52
Overall, concentrations of metals and banned organochlorine pesticides and PCBs
remained low in flounder, lobster and mussel tissues, with the highest concentrations
measured in flounder and lobster tissues from near Deer Island and lowest in samples
from Cape Cod Bay. Slow declines in banned pesticides and PCBs from the 1990s to
present continued across all flounder and lobster tissue types and locations and were
particularly evident in samples from the fish caught near Deer Island.
For example, slow declines in concentrations of the banned pesticide chlordane in
flounder fillets (Figure 5-6) have persisted throughout the monitoring program.
Similarly, long-term declines in concentrations of the banned pesticide DDT and its
breakdown products have been observed in lobster meat, even in lobsters from the
relatively pristine sampling area in eastern Cape Cod Bay (Figure 5-7). 
Figure 5-6. Total chlordanes in flounder fillets, 1993–2021. Since 2003, sampling has occurred at
three-year intervals. Flounder were also collected from eastern Cape Cod Bay but not analyzed for
chemical contaminants.

53 
Figure 5-7. DDT in lobster meat, 1994–2021. (Since 2003, sampling has occurred at three-year
intervals.) 
Pesticide concentrations in deployed mussels have also declined over time, a result
not only of pesticide bans, but also due to improved treatment at Deer Island
Treatment Plant and the outfall relocation. Results from 2021 demonstrated that
contamination remains greatest in Boston Inner Harbor which has a legacy of inputs
other than wastewater discharges. For example, consistent with past years, total PCB
accumulation was greatest in mussels deployed in Boston Inner Harbor, intermediate
in mussels near Deer Island, and lowest in mussels at the Massachusetts Bay outfall
(Figure 5-8). Concentrations of PCBs in mussels deployed at the outfall were
indistinguishable from the pre-deployment reference mussels from the Northeastern
Massachusetts Aquaculture Center. Other contaminants showed similar patterns.

54 
Figure 5-8. Total PCBs in pre-deployment and deployed mussels, 2021. PCB levels show a clear
gradient of highest concentrations in the Inner Harbor and lowest at the Massachusetts Bay outfall. 
Mussels placed at the outfall are indistinguishable from mussels tested for PCBs prior to deployment. 
Contingency Plan Fish and Shellfish
Thresholds 
There were no fish or shellfish Contingency Plan threshold exceedances in 2021
(Table 5-1). Flounder liver disease levels (measured as CHV) were less than 10% of
the caution threshold and also well below baseline measurements. Except for mercury
in mussel tissue, contaminant levels also remained below the baseline, and those
mussel mercury levels were only 3–4% of the caution and warning thresholds. 
0
100
200
300
400
500
600
700
Pre-deployment Outfall Deer Island Inner Harbor
Total PCBs ng/gdw

55 
Table 5-1. Contingency Plan threshold values and 2021 result for fish-and-shellfish monitoring.* 
Parameter Baseline Caution Level Warning Level 2021 Results 
Flounder disease 
Liver disease
(CHV) 24.4% 44.9% None 4% 
Flounder fillet 
PCB 0.033 ppm 1 ppm
wet weight
1.6 ppm
wet weight 0.009 ppm
Mercury 0.074 ppm 0.5 ppm
wet weight
0.8 ppm
wet weight 0.083 ppm 
Flounder fillet, lipid normalized 
Chlordane 242 ppb 484 ppb None 16 ppb
Dieldrin 63.7 ppb 127 ppb None 0 ppb
DDT 775.9 ppb 1552 ppb None 89.7 ppb 
Lobster meat 
PCB 0.015 ppm 1 ppm
wet weight
1.6 ppm
wet weight 0.005 ppm
Mercury 0.148 ppm 0.5 ppm
wet weight
0.8 ppm
wet weight 0.128 ppm 
Lobster meat, lipid normalized 
Chlordane 75 ppb 150 ppb None 2 ppb
Dieldrin 161 ppb 322 ppb None 12 ppb
DDT 341.3 ppb 683 ppb None 37 ppb 
Mussel tissue 
PCB 0.011 ppm 1 ppm
wet weight
1.6 ppm
wet weight 0.007 ppm
Lead 0.415 ppm 2 ppm
wet weight
3 ppm
wet weight 0.139 ppm
Mercury 0.019 ppm 0.5 ppm
wet weight
0.8 ppm
wet weight 0.022 ppm 
Mussel tissue, lipid normalized 
Chlordane 102.3 ppb 205 ppb None 31.7 ppb
Dieldrin 25 ppb 50 ppb None 0 ppb
DDT 241.7 ppb 483 ppb None 30.7 ppb
PAH 1080 ppb 2160 ppb None 992 ppb 
* Exceedances are all values greater than caution or warning thresholds. There were no exceedances in 2021
CHV = centrotubular hydropic vacuolation

56 
6. Special Studies 
Besides monitoring the effluent and the water column, sea floor, and fish and
shellfish in Massachusetts Bay, MWRA conducts special studies in response to
specific permit requirements, scientific questions, and public concerns. This year’s
report on special studies focuses on COVID-19 monitoring in MWRA influent,
OMSAP evaluations of contaminants of emerging concern, dissolved oxygen
investigations in Cape Cod Bay, and changing temperatures in the Gulf of Maine. 
COVID-19 Influent Monitoring 
MWRA was one of the first wastewater agencies
to monitor the viral RNA in SARS-CoV-2, the
virus that causes COVID-19, in its wastewater
influent before treatment. Measurements began as
a pilot project for MWRA’s Department of
Laboratory Services, with Biobot Analytics.
MWRA routinely posts these data at
www.mwra.com (Figure 6-1) and also provides
data to the state COVID-19 Command Center. 
Figure 6-1. Viral RNA in MWRA untreated wastewater influent, March 2020 through November
9, 2022. 
There have been no known
cases of a person contracting
COVID-19 from untreated or
treated wastewater, and its
presence in MWRA influent is
not considered a risk to public
health or the environment.

57
Monitoring the virus in wastewater is proving invaluable around the world, and
wastewater monitoring is becoming a key tool for tracking other diseases as well. The
Centers for Disease Control and Prevention has recognized the value of wastewater
monitoring during the COVID-19 pandemic by launching the National Wastewater
Surveillance System to coordinate wastewater tracking on a national level.
Wastewater monitoring allows for the detection of a disease across the broad
population, regardless of whether a person has symptoms or has received a diagnostic
test. It can provide early indications of surges and declines and can track new variants
as they emerge.
There have been no known cases of a person contracting COVID-19 from untreated
or treated wastewater, and its presence in MWRA influent is not considered a risk to
public health or the environment. 
Contaminants of Emerging Concern 
In the summer of 2022, the advisory group that oversees the monitoring program,
OMSAP, issued a general framework for approaching questions about monitoring
contaminants of emerging concern in Massachusetts Bay. The framework included
white papers focusing on three specific contaminant groups: pharmaceuticals and
personal care products; per- and poly-fluoroalkyl substances (PFAS); and
microplastics (OMSAP 2022).
MWRA is participating in a number of projects to assess the presence of these
contaminants in both the effluent and in Massachusetts Bay. For each of the
contaminant groups, a number of compounds are widespread in the environment.
Public health concerns are not well known, and there are no regulations, limits, or
monitoring requirements, with the exception of PFAS, which is now being added to
NPDES permits. Projects receiving MWRA support are: 
 A pilot study sponsored by EPA detected low levels of some pharmaceutical
and personal care products and PFAS in MWRA effluent and in
Massachusetts Bay. MWRA provided effluent samples and technical
assistance to this pilot study. 
 Scientists from the Woods Hole Oceanographic Institution are measuring
microplastics at Deer Island Treatment Plant, in Massachusetts Bay, and in
Buzzards Bay, with MWRA providing ship time on consultant and MWRA
vessels. Their preliminary results found more particles and a greater diversity
of plastics in Buzzards Bay than in Massachusetts Bay.

58 
 MWRA is participating in two Water Research Foundation projects. One
examines PFAS occurrence in wastewater treatment facilities in the United
States, and the other, the potential release of PFAS from biosolids. Biosolids
are produced from sludge, those solids removed during the treatment process
that are often used as fertilizer. Search for Projects 5031 and 5042 at
https://www.waterrf.org/search?type=project for more details. 
Dissolved Oxygen in Cape Cod Bay 
In recent years, low dissolved oxygen conditions have been detected in the shallow
nearshore waters of Cape Cod Bay in the late summer, low enough that fish and
lobster mortalities were reported in 2019. These hypoxic conditions were not caused
or aggravated by nutrient inputs from the Massachusetts Bay outfall. However, since
the hypoxia in 2019, MWRA, its monitoring team members from the Center for
Coastal Studies and Woods Hole Oceanographic Institution, and other researchers
have participated in research to understand the causes of hypoxia (for example, Scully
et al. 2022) and better protect the fish and lobster resources.
In collaboration with DMF, the Massachusetts Lobster Foundation has sponsored a
group of local lobstermen to aid in these studies, the Cape Cod Bay Study Fleet. In
2021, DMF provided oxygen probes to local lobstermen for placement on the gear
they deploy on the sea floor. The probes provide near real-time measurements of
bottom-water dissolved oxygen conditions.
In August 2021, the Cape Cod Bay Study Fleet probes detected declining dissolved
oxygen concentrations at numerous sites. Dissolved oxygen levels reached as low as
2.3 milligrams per liter in one lobster trap in eastern Cape Cod Bay (Figure 6-2), well
below the state standard of 6 milligrams per liter. An advisory notified lobstermen to
check their traps regularly and consider moving some gear; both precautions could
prevent trapping lobsters in hypoxic conditions for extended periods of time.
Fortunately, conditions did not further decline, as a late August storm mixed and re-
aerated the bottom waters. No fish or shellfish mortalities were recorded in 2021.

59 
Figure 6-2. Dissolved oxygen levels recorded on sensors deployed on lobster traps in 2021. 
The lowest value, 2.3 milligrams per liter, was recorded in eastern Cape Cod Bay in mid-August. The
state water quality standard is 6 milligrams per liter. 
Occurrence of hypoxia in Cape Cod Bay appears to be exacerbated by the presence of 
Karenia mikimotoi , the dinoflagellate that first appeared in the region in 2017 (see
Section 3, Water Column and Scully et al. 2022). Karenia mikimotoi is well-suited to
exploit shallow waters with sharp and relatively deep pycnoclines, conditions found
in the Cape Cod Bay lobstering grounds.

60 
Temperature Changes in the Gulf of Maine 
Over the course of more than two decades of monitoring, MWRA has documented
increasing air and water temperatures. Water temperatures (Figure 6-3) have
increased at a faster rate than air temperatures, suggesting that they result from a
change in regional water circulation. Some 2020 and 2021 zooplankton samples were
dominated by radiolarians, possible further evidence of regional changes in water
flows, because radiolarians were previously observed only offshore in the Gulf of
Maine. 
Figure 6-3. Average summer surface-water temperatures in Massachusetts Bay over four six-
year periods, 1998–2021. Water temperatures have risen more quickly than air temperatures at the
NDBC Buoy 44013 (location shown on Figure 3-1 on page 11). 
High water temperatures can lead to lower levels of dissolved oxygen, and in 2021,
there were Contingency Plan exceedances for some Stellwagen Basin dissolved
oxygen parameters (see Section 3, Water Column). While the outfall discharge was
not a factor in these exceedances, MWRA monitoring observations show the general
trends of warming waters and declining dissolved oxygen levels in Massachusetts
Bay.
Changing wind patterns may also be a factor in higher temperatures. In recent years,
winds have come less frequently from the south and southwest (Scully et al. 2022).
This shift has reduced upwelling, which brings cool bottom waters to the surface. 
16
17
18
19
20 
1998-2003 2004-2009 2010-2015 2016-2021
Temperature (°C)

61
The MWRA measurements showing increasing water temperatures mesh with
findings from other groups in the broader region. For example, publications from
researchers at the Gulf of Maine Research Institute (GMRI) in Portland, Maine, show
that Gulf of Maine waters warmed faster than 99% of the world’s oceans from 2004
to 2013 (Pershing et al. 2015). The GMRI website suggests that the increases in the
past decade could be tied to “marine heat waves,” periods when five or more
consecutive days reach temperatures in the 90 th percentile compared to the average.
Scientists studying right whale populations see these temperature shifts as a driver to
pushing the North Atlantic right whale towards extinction. Their hypothesis is that a
physical shift has occurred, bringing warmer waters into the region. Beginning in
2010, scientists noted depressed calving success in the Gulf of Maine. By mid-
decade, right whales had moved their summer and fall foraging grounds northward
from the Gulf of Maine to the Scotian Shelf and the Gulf of Saint Lawrence. Since
2017, there has been evidence that this shift is resulting in greater mortality in
Canadian waters, both by entanglement in fishing gear and other marine hardware
and by ship strikes in the Gulf of Saint Lawrence (for example, Meyer-Gutbrod et al.
2021).
During the permitting process for the MWRA outfall, concern for the right whale was
a primary driver of the permit conditions. Concerns included the possibility that
whales could be threatened by infectious bacteria, viruses, or protozoans in the
effluent; that toxic metals or PCBs could affect whale health; or that increased
nutrient inputs might alter the types of available food (Rex et al. 1997). MWRA
scientists firmly believed during the planning for the outfall that those concerns
would not be realized, and the more than 20 years of data since the Massachusetts
Bay outfall began to discharge have supported their view. Because of its long data set,
the MWRA monitoring team is documenting changes that are unrelated to the outfall
but which may have much greater effects on this highly endangered species and on
the condition of the wider regional environment.

62 
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65 
List of Acronyms 
ASP Amnesic shellfish poisoning
cBOD Carbonaceous biochemical oxygen demand
CHV Centrotubular hydropic vacuolation
DDT Dichlorodiphenyltrichloroethane
DIF Deer Island Flats
DMF Massachusetts Division of Marine Fisheries
ECCB Eastern Cape Cod Bay
EPA U.S. Environmental Protection Agency
GMRA Gulf of Maine Research Institute
IAAC Inter-Agency Advisory Committee
LC50 50% mortality concentration
MassDEP Massachusetts Department of Environmental Protection
MGD Million gallons per day
MWRA Massachusetts Water Resources Authority
NA Not analyzed/not applicable
NACWA National Association of Clean Water Agencies
NB Nantasket Beach
NDBC National Data Buoy Center
NERACOOS Northeastern Regional Association of Coastal and Ocean Observing Systems
NOEC No observed effects concentration
NPDES National Pollutant Discharge Elimination System
OMSAP Outfall Monitoring Science Advisory Panel
OS Outfall site
PAH Polycyclic aromatic hydrocarbon
PCB Polychlorinated biphenyl
PFAS Per- and polyfluoroalkyl substance
PIAC Public Interest Advisory Committee
PSP Paralytic shellfish poisoning
PSU Practical salinity units
RNA Ribonucleic acid

Massachusetts Water Resources Authority
100 First Avenue • Boston, MA 02129 
www.mwra.com 
617-242-6000