2019 overview

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2019 Outfall
Monitoring
Overview 
Massachusetts Water
Resources Authority
Environmental Quality
Department Report 2020-11

Citation:
Werme C, Keay KE, Libby PS, Taylor D, Codiga DL, Charlestra L, Carroll SR. 2020.
2019 outfall monitoring overview. Boston: Massachusetts Water Resources Authority.
Report 2020-11. 5 8 pages.
Cover photo credits (top to bottom):
Deer Island Treatment Plant and Boston Harbor Islands 
Wayne Wurtsbaugh, LimnoVision 
Water Column Sampling in Massachusetts Bay, 2020 
Alex Whiffen-Mansfield, Battelle

2019
Outfall Monitoring Overview 
prepared by 
Christine Werme 
Independent Consultant
Oakland, CA 94612 
Kenneth E. Keay 
Massachusetts Water Resources Authority
Environmental Quality Department
100 First Avenue
Charlestown Navy Yard
Boston, MA 02129 
P. Scott Libby 
Battelle
72 Main Street
Topsham, ME 04086 
David Taylor, Daniel L. Codiga, Lucner Charlestra, Sally R. Carroll 
Massachusetts Water Resources Authority
Environmental Quality Department
100 First Avenue
Charlestown Navy Yard
Boston, MA 02129 
November 9, 2020

2019 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 Edgcomb, Woods Hole Oceanographic Institution
Loretta Fernandez, Northeastern University
Robert Kenney, University of Rhode Island
Mark Patterson, Northeastern University
Jeff Rosen, Corona Environmental
Juliet Simpson, Massachusetts Institute of Technology Sea Grant
Juanita Urban-Rich, University of Massachusetts, Boston 
Inter-Agency Advisory Committee (IAAC) 
U.S. Geological Survey
Massachusetts Coastal Zone Management
U.S. Army Corps of Engineers
Stellwagen Bank National Marine Sanctuary
U.S. Environmental Protection Agency
Massachusetts Division of Marine Fisheries
Massachusetts Department of Environmental Protection 
Public Interest Advisory Committee (PIAC) 
Save the Harbor/Save the Bay
MWRA Wastewater Advisory Committee
Conservation Law Foundation
Massachusetts Audubon Society
MWRA Advisory Board
Association to Preserve Cape Cod
Safer Waters in Massachusetts
Boston Harbor Now

i 
Table of Contents 
Executive Summary ...................................................................................................... v 
1. Introduction ............................................................................................................... 1 
2. Effluent ..................................................................................................................... 2 
2019 Effluent Characterization ................................................................................. 2 
Contingency Plan Thresholds ................................................................................... 7 
3. Water Column ........................................................................................................... 9 
Physical Conditions ................................................................................................ 10 
Water Quality .......................................................................................................... 14 
Nutrients .............................................................................................................. 14 
Phytoplankton Biomass ...................................................................................... 17 
Dissolved Oxygen ............................................................................................... 18 
Phytoplankton Communities ................................................................................... 19 
Zooplankton Communities...................................................................................... 24 
Stellwagen Bank National Marine Sanctuary ......................................................... 25 
Boston Harbor Water Quality ................................................................................. 26 
Contingency Plan Thresholds ................................................................................. 27 
4. Sea Floor ................................................................................................................. 28 
Sediment Characteristics and Tracers ..................................................................... 30 
Soft-bottom Communities....................................................................................... 32 
Sediment-profile Imaging ....................................................................................... 35 
Stellwagen Bank National Marine Sanctuary ......................................................... 36 
Boston Harbor Seafloor Monitoring ....................................................................... 37 
Contingency Plan Thresholds ................................................................................. 40 
5. Fish and Shellfish .................................................................................................... 41 
Flounder Health ...................................................................................................... 42 
Contingency Plan Thresholds ................................................................................. 44 
6. Special Studies ........................................................................................................ 45 
Nutrient Discharges into Massachusetts Bay .......................................................... 45 
Sediment-Habitat Structures ................................................................................... 47 
Hypoxia in Cape Cod Bay ...................................................................................... 49 
7. Monitoring Plan Revisions ..................................................................................... 51 
Sediment Contaminants .......................................................................................... 52 
Sediment-profile Imaging ....................................................................................... 53 
Winter Flounder Health .......................................................................................... 54 
References ................................................................................................................... 56 
List of Acronyms ........................................................................................................ 58

ii 
List of Figures 
Figure i. Annual solids discharges, 1990–2019. ........................................................... v 
Figure ii. Annual nitrogen discharges, 1996–2019, and estimated population of the
MWRA service area, 2006–2019. ................................................................................ vi 
Figure iii. Station average ammonium concentrations at selected stations in 2019
compared to prior years .............................................................................................. vii 
Figure iv. Alexandrium abundance in surface- and mid-depth samples during the 2019
bloom. ........................................................................................................................ viii 
Figure v. Storms and other climate-related factors continue to have the greatest
effects on the habitats and communities in Massachusetts Bay, as indicated by the
thickness of the arrows................................................................................................. ix 
Figure vi. Incidence of the tumor precursor centrotubular hydropic vacuolation in
flounder from Deer Island Flats and the Massachusetts Bay outfall over time. ........... x 
Figure 2-1. Annual and average rainfall in Boston, 1990–2019 ................................... 2 
Figure 2-2. Annual primary-blended and full secondary effluent flows and average
annual flow, 1999–2019................................................................................................ 3 
Figure 2-3. Monthly primary-blended and full secondary flows and rainfall during
2019............................................................................................................................... 3 
Figure 2-4. Annual solids discharges, 1990–2019 ........................................................ 4 
Figure 2-5. Annual metals discharges, 1990–2019....................................................... 5 
Figure 2-6. Annual discharges of organochlorine compounds, 2006–2019 ................. 6 
Figure 2-7. Annual nitrogen discharges, 1996–2019, and estimated population of the
MWRA service area, 2006–2019 .................................................................................. 8 
Figure 3-1. Water-column monitoring stations and instrumented buoys in
Massachusetts and Cape Cod bays ............................................................................... 9 
Figure 3-2. Flows of the Merrimack and Charles rivers. ............................................ 11 
Figure 3-3. Surface-water temperature at the NDBC Buoy in 2019 compared to prior
years e ......................................................................................................................... 12 
Figure 3-4. Annual average mid-June through mid-August air and surface-water
temperatures at the NDBC Buoy, 1992–2019. ........................................................... 12 
Figure 3-5. Stratification at selected stations 2019 compared to prior years .............. 13 
Figure 3-6. Station average ammonium concentrations at selected stations in 2019
compared to prior years. ............................................................................................. 15 
Figure 3-7. (Left) Surface- and bottom-water ammonium at selected stations on
March 20, 2019, during mixed conditions. (Right) Cross-sections of concentrations
throughout the water column along transects connecting selected stations. ............... 16 
Figure 3-8. (Left) Surface- and bottom-water ammonium at selected stations on July
17, 2019, during stratified conditions. (Right) Cross-sections of concentrations
throughout the water column along transects connecting selected stations ................ 16 
Figure 3-9. Station average areal chlorophyll concentrations at selected stations in
2019 compared to prior years. .................................................................................... 17

iii
Figure 3-10. Near-bottom water dissolved oxygen concentrations in 2019 compared
to prior years ............................................................................................................... 18 
Figure 3-11. Near-bottom water dissolved oxygen concentrations at Cape Cod Bay
stations in 2019 compared to prior years. ................................................................... 19 
Figure 3-12. Total phytoplankton abundance at selected stations in 2019 compared to
prior years ................................................................................................................... 20 
Figure 3-13. Total dinoflagellate abundance (100,000 cells per liter) at selected
stations in 2019 compared to prior years. ................................................................... 21 
Figure 3-14. Nearfield abundance of Alexandrium catenella , 1992–2019. Note log
scale............................................................................................................................. 22 
Figure 3-15. Alexandrium abundance in surface- and mid-depth samples during the
2019 bloom. ................................................................................................................ 23 
Figure 3-16. Total zooplankton abundance at selected stations in 2019 compared to
prior years. .................................................................................................................. 24 
Figure 3-17. Trends in abundance of total phytoplankton and total zooplankton in the
nearfield ...................................................................................................................... 25 
Figure 3-18. Deepwater dissolved oxygen at the NERACOOS Buoy A01 and Station
F22 in Stellwagen Basin ............................................................................................. 26 
Figure 4-1. Soft-bottom monitoring stations. ............................................................. 28 
Figure 4-2. Sediment-profile imaging stations ........................................................... 29 
Figure 4-3. Concentrations of Clostridium perfringens spores corrected for sediment
grain size, in 2019 ....................................................................................................... 31 
Figure 4-4. Total organic carbon at selected stations, 1992–2019 ............................. 31 
Figure 4-5. Total abundance by region, 1992–2019. .................................................. 32 
Figure 4-6. Ordination plot of 2019 Massachusetts Bay samples by location............ 33 
Figure 4-7. Percent fine sediments and depth superimposed on the ordination plot of
the 2019 infauna samples ............................................................................................ 34 
Figure 4-8. Annual apparent color RPD depth for nearfield stations. ........................ 35 
Figure 4-9. Trend in the Massachusetts Bay organism sediment index over time ..... 36 
Figure 4-10. Soft-bottom sampling stations in Boston Harbor ................................... 37 
Figure 4-11. Mean number of species per sample in Boston Harbor, 1991–2019 .... 38 
Figure 4-12. Organism sediment index at 61 sediment-profile stations in Boston
Harbor, 1992–2019 ..................................................................................................... 39 
Figure 5-1. Fish-and-shellfish monitoring stations ..................................................... 41 
Figure 5-2. Lobster gear in flounder net trawl ............................................................ 42 
Figure 5-3. Annual prevalence of centrotubular hydropic vacuolation, 1991–2018 .. 43 
Figure 6-1. Depth-averaged nitrogen concentrations and declines with distance from
the Massachusetts Bay outfall ..................................................................................... 46 
Figure 6-2. Depth-averaged chlorophyll concentrations and distance from the
Massachusetts Bay outfall........................................................................................... 46 
Figure 6-3. Reducing past sewage loadings, a result of the Boston Harbor Project, has
led to recovery of benthic habitat and communities in Boston Harbor ...................... 48 
Figure 6-4. Storms and other climate-related factors continue to have the greatest
effects on the habitats and communities in Massachusetts Bay ................................. 48

iv
Figure 6-5. The hypoxia and anoxia dissolved oxygen event in southern Cape Cod
Bay, 2019 .................................................................................................................... 49 
Figure 7-1. Average total PCB concentrations in nearfield sediments, 1992–2017 ... 52 
Figure 7-2. Sediment-profile image from Station NF17, just south of the outfall, with
healthy amphipod tubes in 2019 ................................................................................. 53 
Figure 7-3. Centrotubular hydropic vacuolation incidence at Deer Island Flats and the
Massachusetts Bay outfall over time .......................................................................... 54 
List of Tables 
Table 2-1. Projected and actual loads of metals in MWRA effluent. ........................... 5 
Table 2-2. Contingency Plan threshold values and 2019 results for effluent
monitoring. .................................................................................................................... 7 
Table 3-1. Contingency Plan threshold values and 2019 results for water-column
monitoring. .................................................................................................................. 27 
Table 4-1. Contingency Plan threshold values and 2019 results for sea-floor
monitoring. .................................................................................................................. 40 
Table 5-1. Contingency Plan threshold values and 2019 result for fish-and-shellfish
monitoring. .................................................................................................................. 44

v 
Executive Summary 
This outfall monitoring overview for 2019 marks the twenty-eighth year of the
Massachusetts Water Resources Authority (MWRA) Massachusetts Bay monitoring
program, including eight years of baseline studies. Twenty years ago, in September
2000, MWRA took an important step to clean up Boston Harbor, diverting the greater
Boston area municipal effluent discharge from the relatively shallow, confined waters
of Boston Harbor to the deeper, more open waters of Massachusetts Bay. Since then,
the MWRA monitoring program has worked to ensure that the discharge leads to no
environmental harm.
Through 2019, Deer Island Treatment Plant continued to operate as designed, earning
MWRA the National Association of Clean Water Agencies Platinum 13 Peak
Performance Award for facilities with 100% compliance with permit conditions over
13 consecutive years. Annual solids discharges, that portion of the MWRA effluent
that contains most of the persistent organic and inorganic contaminants, remained
low, only a small fraction of the biosolids (sludge) and effluent discharges to Boston
Harbor in the 1990s (Figure i).
. 
Figure i. Annual solids discharges, 1990–2019. Before December 1991, biosolids (sludge) removed
during treatment were disinfected and discharged into Boston Harbor. Ending biosolids disposal in
1991, ending effluent discharge to the southern portion of the harbor from Nut Island in 1998,
implementing secondary treatment, and ending all discharges to the harbor in September 2000 were
important steps in the Boston Harbor Project. Since 2006, variability in solids discharges to
Massachusetts Bay can mostly be attributed to variation in flow rather than to variations in treatment.

vi
Total nitrogen discharges in 2019 were 13,217 metric tons, exceeding MWRA’s
Contingency Plan caution level (12,500 metric tons per year), which is set at
approximately 90% of the warning level, 14,000 metric tons per year (Figure ii). The
warning level had represented the anticipated nitrogen load for the year 2020, so it was
not surprising that the caution level could be exceeded in 2019. In fact, nitrogen
removal at Deer Island Treatment plant has been more successful than had initially been
predicted, about 30% rather than 10–15%. Total nitrogen discharges track well with
population growth in the MWRA service area. Population growth has been about 8%
since 2010, while increases in nitrogen discharges have been about 7%. 
Figure ii. Annual nitrogen discharges, 1996–2019, and estimated population of the MWRA
service area, 2006–2019. During outfall planning, experts estimated that discharges would total
14,000 metric tons per year by 2020. The warning threshold was set at that level, and the caution level
was set at about 90% of that projected load. A water-quality model simulation using 120% of the 2016
discharge (green line) projected negligible environmental effect.
This caution-level exceedance is not considered an environmental concern for
Massachusetts Bay or the surrounding region. Water-quality monitoring has detected
no increases in nitrogen levels outside the immediate vicinity of the Massachusetts
Bay discharge, and there has been no indication of nutrient stimulation of
phytoplankton growth, even at stations nearest to the outfall. Water-quality modeling
has suggested that even large increases in discharges would not adversely affect the
marine environment.

vii
Despite the Contingency Plan caution exceedance for total nitrogen discharge, the
change to the nutrient regimes in Boston Harbor and Massachusetts Bay remains one
of the great successes of the outfall relocation. Concentrations of ammonium, the
form of nitrogen most readily taken up by phytoplankton, plummeted in Boston
Harbor immediately following the effluent discharge diversion from the harbor to
Massachusetts Bay (Figure iii). Elevated concentrations of ammonium have been
detected at stations closest to the outfall, as had been anticipated, but not at stations
further away. A recent review of results from the past nine years of data collection
has reconfirmed those findings. The deeper water outfall further protects the
environment by confining the summer discharge to beneath the pycnocline, below the
well-lit depths where most phytoplankton growth occurs. 
Figure iii. Station average ammonium concentrations at selected stations in 2019 compared to
prior years. Black points and lines are results from individual surveys in 2019. Red lines and shading
show data from Boston Harbor discharge years (1992–September 2000). Results from Massachusetts
Bay discharge years (September 2000–2018) are in blue. Line is the 50 th percentile, dark shading spans
the 25 th to 75 th percentile, and light shading spans the range.

viii
Massachusetts Bay remains susceptible to periodic spring blooms of the nuisance
dinoflagellate species Alexandrium catenella , which, at high densities, can cause
paralytic shellfish poisoning or PSP, a public health risk. These blooms occur when
strong spring winds from the northeast bring Alexandrium cells from coastal Gulf of
Maine waters into Massachusetts Bay. The 2019 Alexandrium bloom was relatively
large and prolonged, exceeding the Contingency Plan caution level, but it was
otherwise typical of past years, with cells first detected in northern samples (Figure
iv). Massachusetts Bay shellfish beds were closed from mid-June until mid-July,
when the bloom quickly ended. Neither the timing nor geographic progression of the
bloom suggested any influence of the Massachusetts Bay outfall. 
Figure iv. Alexandrium abundance in surface- and mid-depth samples during the 2019 bloom. 
The upper half of the symbols indicates abundance in surface waters; the lower half indicates
abundance at about 10 meters.

ix
Seafloor communities in Massachusetts Bay have remained unaffected by the
relocated outfall. The bacterial effluent tracer Clostridium perfringens spores can be
detected in sediment samples at stations closest to the outfall, but there has been no
evidence of increased organic carbon content. Total abundances, numbers of species,
and diversity measurements of the soft-bottom communities have remained within
expected ranges over the 28 years of baseline and post-discharge monitoring.
Community structures appear to be affected by sediment grain size and water depth
rather than by proximity to the outfall.
Sediment-habitat measures, such as the redox potential discontinuity depth, a measure
of how deeply oxygen penetrates into sediments, and a related organism sediment
index have documented improvements in nearfield conditions over time rather than
any adverse effects of the outfall.
Long-term analyses have now shown that weather and climate are the driving forces
that shape the seafloor habitats and probably the water column as well (Figure v).
Long-term trends in water temperatures and salinities may affect the species making
up the seafloor communities. Severe winter storms with winds strong enough to
resuspend and transport sediments can affect species compositions in the succeeding
years. Severe winter storms have been increasingly common during recent years of
the monitoring program, most likely a result of regional oscillations and long-term
trends. 
Figure v. Storms and other climate-related factors continue to have the greatest effects on the
habitats and communities in Massachusetts Bay, as indicated by the thickness of the arrows.

x
Winter flounder remained healthy, without the widespread tumors and precancerous
conditions that occurred in Boston Harbor in the 1980s and 1990s. MWRA
monitoring has never detected tumors in fish taken from near the Massachusetts Bay
outfall or tumors in fish from any location since 2004. Improvements in Boston
Harbor flounder health began in the first years of the Boston Harbor cleanup, and
incidence of cancer precursors has also declined at the Massachusetts Bay outfall site
(Figure vi). The improvements correlate well with declines in total solids and
organic-contaminant discharges. Improving winter flounder health in Boston Harbor
without degrading it in Massachusetts Bay has been one of the most notable successes
of MWRA’s improvements to sewage treatment and relocation of the discharge. 
Figure vi. Incidence of the tumor precursor centrotubular hydropic vacuolation in flounder from
Deer Island Flats and the Massachusetts Bay outfall over time . Incidence at the outfall has
remained well below the Contingency Plan caution-level threshold of 44.9%.
Looking ahead, MWRA has worked with its regulators to identify parts of the
monitoring program that, based on past results, could be reduced or ended. Some of
these changes will be implemented in 2020 and 2021. Possible new additional
monitoring questions addressing contaminants of emerging concern are also being
considered. Recommendations for approaches to address these new questions will be
issued in late 2020 or early 2021. 
0
10
20
30
40
50
60
70
80
90
1986 1988 1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 2018 2020
Centrotubular Hydropic Vacuolation (percent) Deer Island Flats Outfall
Threshold 44.9%,
(Outfall results only)

1 
1. Introduction 
For more than 35 years, the Massachusetts Water Resources Authority (MWRA) has
worked to minimize adverse effects of municipal discharges on the marine
environment. When MWRA was established in 1984, Boston Harbor was known as
one of the dirtiest in the nation, largely due to discharges of both biosolids (also
called sludge) and inadequately treated sewage effluent. MWRA’s mission, dubbed
the “Boston Harbor Project,” was to clean up the harbor without causing new
environmental harm. The project included reducing contaminants entering the
wastewater through better management practices and pretreatment; ending biosolids
discharges; rebuilding aged treatment facilities; and sending highly treated effluent
not to the shallow, confined harbor, but to the deeper, more open waters of
Massachusetts Bay.
During the 1990s, MWRA ended biosolids discharges, ended effluent discharges to
the southern part of the harbor, and upgraded Deer Island Treatment Plant. In
September 2000, the highly treated effluent discharge was diverted from the harbor to
Massachusetts Bay. The relocated 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). An independent Outfall Monitoring Science
Advisory Panel (OMSAP) provides technical review to the regulatory agencies.
The NPDES permit requires monitoring of the effluent before discharge and of the
Massachusetts Bay waters, sediments, and marine life that could be affected.
Monitoring assesses compliance with permit conditions and with a permit-required
Contingency Plan, which was specifically designed to protect the environmental
health of the bay. Background information about the monitoring program (Werme et
al. 2012), the monitoring plan (MWRA 2010), the Contingency Plan (MWRA 2001),
past plans and overviews, and study-specific technical reports are available at
http://www.mwra.state.ma.us/harbor/enquad/trlist.html.
MWRA’s long-term environmental monitoring in both Boston Harbor and
Massachusetts Bay has documented the cleanup of the harbor, while ensuring that no
environmental harm has come to the bay. This report, the annual outfall monitoring
overview, as required by the discharge permit, summarizes annual monitoring results.
This year’s overview presents results from 2019, marking the twenty-eighth year of
Massachusetts Bay monitoring and more than nineteen years of discharge from the
deep-water outfall. The report presents information relevant to permit and
Contingency Plan requirements in the effluent, water column, sea floor, and fish and
shellfish; special studies conducted in response to permit conditions and
environmental concerns; and recently approved changes to the monitoring plan.

2 
2. Effluent 
Deer Island Treatment Plant continued to operate as designed through 2019, earning
MWRA the National Association of Clean Water Agencies (NACWA) Platinum 13
Peak Performance Award. This NACWA award recognizes facilities with 100%
compliance with effluent permit limits over 13 consecutive years. 
2019 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 determining wastewater flows and contaminant
concentrations in the wastewater effluent. The Boston area received about 50 inches
of rain in 2019, marking a second consecutive year with higher than average rainfall
(Figure 2-1). 
Figure 2-1. Annual and average rainfall in Boston, 1990–2019. 
Despite the high rainfall, effluent flow in 2019 was slightly less than the 1998–2019
average, those years since all effluent flow was transferred to Deer Island (Figure 2-
2). Virtually all the flow received full primary and secondary treatment, with only
trace amounts of primary-treated effluent blended with fully treated effluent prior to
discharge in months with particularly strong rainstorms (Figure 2-3).

3 
Figure 2-2. Annual primary-blended and full secondary effluent flows and average annual flow,
1999–2019. During large storms, flow exceeding the secondary capacity of the plant is diverted around
the secondary process. Primary-treated flows are blended into secondary-treated flows before
discharge. 
Figure 2-3. Monthly primary-blended and full secondary flows and rainfall during 2019. 
0
50
100
150
200
250
300
350
400
450
500
99 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 
Million gallons per day
Secondary flows Primary ‐ blended flows Average Annual Flow

4
In 2019, the total suspended solids load to Massachusetts Bay, about 17 tons per day,
was similar to recent rainy years and well below the levels discharged into Boston
Harbor before the outfall diversion to Massachusetts Bay in 2000 (Figure 2-4). In
recent years, variability in the suspended solids load has corresponded to variability
in rainfall and effluent flow. Carbonaceous biochemical oxygen demand, a measure
of the amount of oxygen consumed by microorganisms, also remained low (not
shown), well below levels that would be expected to affect dissolved oxygen
concentrations at the discharge. 
Figure 2-4. Annual solids discharges, 1990–2019. Before December 1991, biosolids (sludge)
removed during treatment were disinfected and discharged into Boston Harbor. Ending biosolids
disposal, ending effluent discharge to the southern portion of the harbor from Nut Island, implementing
secondary treatment, and ending all discharges to the harbor in September 2000 were important steps
in the Boston Harbor Project. Since 2006, variability in solids discharges to Massachusetts Bay can
mostly be attributed to variation in flow.
Metals loads also remained low in 2019, with little evidence of increases associated
with higher flow (Figure 2-5). 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).

5 
Figure 2-5. Annual metals discharges, 1990–2019. 
Total loads of all metals remained small percentages of what had been anticipated
during planning for the Massachusetts Bay outfall (Table 2-1). Except for copper,
metals meet water quality standards prior to discharge, where 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. 
Table 2-1. Projected and actual loads of metals in MWRA effluent. Loads of metals and organic
contaminants are far below those projected during the planning and permitting process. 
Parameter SEIS Projected Load
(kg/year)
2019 Load
(kg/year)
Percent
Projected Load 
Chromium 3,517 310 8.8%
Copper 11,945 2,493 21%
Lead 4,961 267 5.4%
Mercury 216 2.0 9.3%
Nickel 8,926 775 8.6%
Silver 290 20 6.9% 
SEIS = Supplemental Environmental Impact Statement (EPA 1988)

6
Polycyclic aromatic hydrocarbon (PAH) and other organic contaminant loads were
also low and only a small fraction of what had been anticipated during planning for
the outfall, as they have been throughout the monitoring program. Discharges of
organic contaminants have varied slightly from year to year but have been well below
levels historically discharged into Boston Harbor. For some compounds, such as
4,4’-DDE, a breakdown product of the pesticide DDT, there is some evidence of the
very slow declines anticipated after those persistent substances were banned (Figure
2-6). 
Figure 2-6. Annual discharges of organochlorine compounds, 2006–2019. 
The total nitrogen load for 2019 was 13,217 metric tons, below the Contingency Plan 
warning-level threshold, 14,000 metric tons per year, but exceeding the caution-level
threshold of 12,500 metric tons, set at about 90% of the warning level.
See Figure 2-7 and further discussion, below.

7 
Contingency Plan Thresholds 
There were no permit violations in 2019, but the 2019 nitrogen load exceeded the
Contingency Plan caution-level threshold (Table 2-2). Effluent threshold
exceedances based on permit conditions have been rare, and none have occurred in
the past 13 years. The Deer Island NPDES permit does not include an effluent limit
for nitrogen, so that threshold exceedance did not represent a permit violation. 
Table 2-2. Contingency Plan threshold values and 2019 results for effluent monitoring. 
Parameter Baseline Caution Level Warning Level 2019 Results
Permit Conditions 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 Not exceeded
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
13,217 mtons/year
caution level
exceedance 
NA = not applicable
cBOD = carbonaceous biological oxygen demand
LC50 = 50% mortality concentration
NOEC = no observable effect concentration
PCB = polychlorinated biphenyl
Plant performance = compliance with permit conditions
MGD = million gallons per day
Total effluent nitrogen loads reflect variability in nitrogen levels in the influent
reaching Deer Island, with about 30% of the nitrogen removed during treatment
(compared to 10–15% removal predicted at the start of the Boston Harbor Project).
Total nitrogen loads have increased modestly since the Massachusetts Bay outfall
began to discharge, most likely due to population increases in the MWRA service
area (Figure 2-7). MWRA’s sewered population in 2019 was about 6% higher than
the population projections for 2020 that were used to develop the thresholds.

8 
Figure 2-7. Annual nitrogen discharges, 1996–2019, and estimated population of the MWRA
service area, 2006–2019. During outfall planning, experts estimated that discharges would total
14,000 metric tons per year by 2020. The warning threshold was set at that level, and the caution level
was set at about 90% of that projected load. A water-quality model simulation using 120% of the 2016
discharge (green line) projected negligible environmental effect.
Interestingly, much of the nitrogen increase in 2019 was due to an increase in what is
known as “other nitrogen species,” or organic nitrogen, rather than ammonium and
nitrate/nitrite, the forms of nitrogen most readily used by phytoplankton. Evaluation
of the 2019 results does not suggest any analytical error or change in treatment
processes that would explain the results.
The exceedance did not result in any observed unexpected or adverse environmental
effects due to nitrogen discharge into Massachusetts Bay, such as increased
phytoplankton biomass or decreased dissolved oxygen levels. Water-quality
modeling has suggested that even large increases to the nitrogen discharge would
have no adverse effect on the environment.
Each year, MWRA assesses alternatives for nitrogen-removal technologies, should
they be required in the future (see, for example Ellis-Hibbett 2020). About 13 acres
of land on Deer Island have been identified as potentially available for possible
nitrogen-removal facilities, although alternatives to treatment at Deer Island could be
employed, such as treating the return flow from the pelletizing plant where biosolids
are converted to fertilizer. These returns account for only about 1% of the total flow
but about 10% of the total nitrogen load.

9 
3. Water Column 
Water-column monitoring evaluates relevant physical oceanographic processes, water
quality, and phytoplankton and zooplankton communities at stations in Massachusetts
Bay, at the mouth of Boston Harbor, and in Cape Cod Bay (Figure 3-1). Ship-based
field surveys are augmented by measurements from instrumented buoys and satellite
imagery. 
Figure 3-1. Water-column monitoring stations and instrumented buoys in Massachusetts and
Cape Cod bays.

10
Nine regular surveys were conducted in February–October 2019. Five stations are in
the nearfield (the 10- by 12-kilometer area around the outfall where some effects of
the effluent were expected and have been observed) and nine are in the farfield,
including stations at the mouth of Boston Harbor, in Cape Cod Bay, and near the
Stellwagen Bank National Marine Sanctuary. Seven additional surveys were
conducted during May–July, triggered by elevated abundance of the toxic
dinoflagellate Alexandrium catenella . These Alexandrium Rapid-Response Study
surveys (Libby et al. 2013) provided in situ hydrographic data and water samples for
measuring dissolved oxygen, inorganic nutrients, and Alexandrium abundance from
up to 19 stations, including all MWRA water-column stations except Station N21.
Data from another set of ten stations in Boston Harbor, sampled as part of MWRA’s
harbor water-quality monitoring were included in analyses when sampling dates were
within a few days of the outfall-monitoring surveys.
The program continued to benefit from collaboration with the Center for Coastal
Studies at Provincetown, Massachusetts, which conducts an independent monitoring
program in Cape Cod Bay and, as part of the MWRA program, samples the water-
column stations in Cape Cod Bay and near the Stellwagen Bank National Marine
Sanctuary. Regulators have set a target that, whenever possible, sampling in Cape
Cod Bay should occur within 48 hours of the Massachusetts Bay sampling. All 2019
surveys were completed within that target.
As in past years, the field monitoring program was supplemented by measurements
on two instrumented buoys: the Northeastern Regional Association of Coastal and
Ocean Observing Systems (NERACOOS) Buoy A01 and the National Oceanic and
Atmospheric Administration’s National Data Buoy Center (NDBC) Buoy 44013.
The National Aeronautics and Space Administration provided Moderate Resolution
Imaging Spectroradiometer satellite imagery of chlorophyll and sea-surface
temperature. 
Physical Conditions 
Monitoring has shown that the water quality in the vicinity of the outfall and
throughout Massachusetts and Cape Cod bays is heavily influenced by weather, river
inflows, and other physical factors. Information about physical conditions has proven
key to interpreting the annual water-column monitoring data.
As in 2018, the Boston area experienced heavier than average rainfall in 2019 (see
Figure 2-1 in Section 2, Effluent), with higher than average flow from both the
Merrimack and Charles rivers during much of the year (Figure 3-2, Libby et al.
2020). The spring freshet, the high flow during snow melt, from the Merrimack
River was especially strong, cresting in April with flows greater than 1,000 cubic
meters per second. As a result, relatively low surface-water salinities were measured
in the nearfield throughout the spring and summer, one factor that can contribute to
lower bottom-water oxygen levels.

11 
Figure 3-2. Flows of the Merrimack (top) and Charles (bottom) rivers. Note differences in scales.
Dark red lines are 2019 data. Results from 1992–2018 are in light blue. The quarterly percentiles
represent the 2019 flows in comparison to the entire 28-year record.
Warm water temperatures can also contribute to lower dissolved oxygen levels.
Surface-water temperatures, important influences on water quality and measured
continuously at the NDBC Buoy, were average at the beginning of the year, but
especially warm during the summer, reaching a record 22˚ Celsius at the end of July
and remaining high through the end of the year (Figure 3-3). Since 1990, both air and
surface-water temperatures have increased at the NDBC Buoy, but water
temperatures have risen more quickly, suggesting the increases were caused by a
change in regional water circulation in the Gulf of Maine (Figure 3-4).
A May 15 storm with winds from the northeast created ideal conditions to transport
cells of the nuisance algal species Alexandrium catenella from the western Gulf of
Maine into Massachusetts Bay (see further discussion below). The autumn was also
stormy, with greater than six-meter waves during one storm in early December.

12 
Figure 3-3. Surface-water temperature at the NDBC Buoy in 2019 compared to prior years .
Vertical dashed lines denote timing of the MWRA surveys.
. 
Figure 3-4. Annual average mid-June through mid-August air and surface-water temperatures
at the NDBC Buoy, 1992–2019. Water temperatures in 1995 were omitted due to data gaps.

13
Spring and summer stratification of the Massachusetts Bay water column into distinct
shallow and deep layers was more intense than average (Figure 3-5). In spring 2019,
the high river flows and resulting low surface-water salinity promoted especially
strong early stratification. The record warm summer surface-water temperatures
contributed to a second peak, which persisted into September. Buoy data (not shown)
indicated that the water column did not become well mixed in deeper offshore waters
until mid-November. 
Figure 3-5. Stratification at selected stations 2019 compared to prior years. The black points and
lines are results from 2019; the blue lines and shading are results from 1992–2018: the line is the 50 th
percentile, dark shading spans the 25–75 th percentiles, and the light shading spans the range.

14 
Water Quality 
Water quality measurements for 2019 included quantification of nutrients,
phytoplankton biomass, and dissolved oxygen. Results continued to confirm
predictions of measurable outfall influence in some parameters, but only at stations
very near the outfall. There were no unexpected or environmentally adverse findings
(Libby et al. 2020). 
Nutrients 
Dissolved inorganic nutrient concentrations (nitrogen, phosphorus, and silica) in the
nearfield stayed mostly within the ranges measured in previous years. Nitrogen is the
most important nutrient affecting phytoplankton growth in Massachusetts Bay.
Ammonium is the largest fraction of the total nitrogen in wastewater (see Figure 2-6,
above), making it a good effluent tracer.
The 2019 outfall ammonium signature was typical of the years since the discharge
relocation (Figure 3-6). As in other years since the outfall began to discharge in
September 2000, episodic peaks in ammonium concentrations were detected at
Station N21, located just 60 meters from the outfall; at Station N18, 2.5 kilometers to
the south; and during some surveys, at Station F15, nine kilometers to the southeast.
Ammonium concentrations were consistently low at Station F23 at the mouth of
Boston Harbor, at other Massachusetts Bay stations, and in Cape Cod Bay.
Concentrations at Station F23 remained well below those measured when wastewater
was discharged into Boston Harbor.

15 
Figure 3-6. Station average ammonium concentrations at selected stations in 2019 compared to
prior years. Black points and lines are results from individual surveys in 2019. Red lines and shading
show data from Boston Harbor discharge years (1992–September 2000). Results from Massachusetts
Bay discharge years (September 2000–2018) are in blue. Line is the 50 th percentile, dark shading spans
the 25 th to 75 th percentile, and light shading spans the range.
.
As predicted by numeric model runs in the 1990s and observed each year of
monitoring, the effluent plume’s ammonium signature was evident in surface waters
during the winter and spring when the water column was relatively well-mixed
(Figure 3-7). The plume was confined beneath the pycnocline and below depths of
maximum phytoplankton growth during the summer, stratified season (Figure 3-8).
The distances where the ammonium signature could be detected during both stratified
and unstratified seasons remained consistent with predictions made during planning
for the outfall. (See Section 6, Special Studies, for additional analysis of nutrient
inputs and the detectable signatures during 2011–2019.)

16 
Figure 3-7. (Left) Surface- and bottom-water ammonium at selected stations on March 20, 2019,
during mixed 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 at selected stations on July 17, 2019,
during stratified conditions. (Right) Cross-sections of concentrations throughout the water
column along transects connecting selected stations.

17 
Phytoplankton Biomass 
Despite the ammonium concentration increases that have been observed since the
outfall began to discharge, no increases in phytoplankton biomass (measured as
chlorophyll and particulate organic carbon), have been detected, even at stations
closest to the outfall, and none were measured in 2019 (Figure 3-9). Regionally,
elevated chlorophyll levels occurred offshore and in Cape Cod Bay in February,
followed by an increase in Massachusetts Bay in April and May. As in previous
years, diatoms ( Guinardia delicatula and Thalassiosira spp. in 2019) were
responsible for the spring blooms. Chlorophyll concentrations were variable during
the summer and then increased at all stations in September, with a bloom of the
dinoflagellate Karenia mikimotoi . The September Karenia bloom was especially
prominent at Station F23 just offshore from Boston Harbor. (See further discussion
of the Karenia bloom below.) 
Figure 3-9. Station average areal chlorophyll concentrations at selected stations in 2019
compared to prior years. (For some stations, historic data extend later in the year than the current
survey schedule.) The black points and lines are results from 2019; the blue lines and shading are
results from 1992–2018: the line is the 50 th percentile, dark shading spans the 25–75 th percentiles, and
the light shading spans the range.

18 
Dissolved Oxygen 
Massachusetts Bay bottom-water dissolved oxygen concentrations began the year
close to the historic medians for February and March (Figure 3-10). Levels declined
and were lower than average in May and June, a result of the strong water-column
stratification. Mixing in July re-aerated bottom waters throughout the region, and
oxygen concentrations remained typical of the historic record throughout the late
summer and early fall. The usual fall overturn and return to oxygenated waters was
somewhat delayed in 2019, but measurements from the instrumented buoys indicated
that the minima were moderate, typical for the monitoring program. (Data from the
NERACOOS buoy are presented in Figure 3-18 on page 26.) 
Figure 3-10. Near-bottom water dissolved oxygen concentrations (milligrams per liter) in 2019
compared to prior years. (For some stations, historic data extend later in the year than the current
survey schedule.) The black points and lines are results from 2019; the blue lines and shading are
results from 1992–2018: the line is the 50 th percentile, dark shading spans the 25–75 th percentiles, and
the light shading spans the range.

19
Cape Cod Bay stations exhibited similar patterns in dissolved oxygen concentrations
during most of the year, with an early decline due to strong stratification and then a
recovery in July. However, levels fell steeply in late August and early September,
reaching 4–5 milligrams per liter at MWRA stations sampled by the Center for
Coastal Studies (Figure 3-11). Even lower concentrations were found by other
researchers in shallow, southern coastal waters, leading to lobster and crab deaths.
This hypoxia event in coastal Cape Cod Bay waters is further discussed in Section 6,
Special Studies. 
Figure 3-11. Near-bottom water dissolved oxygen concentrations (milligrams per liter) at Cape
Cod Bay stations in 2019 compared to prior years. The black points and lines are results from 2019;
the blue lines and shading are results from 1992–2018: the line is the 50 th percentile, dark shading
spans the 25–75 th percentiles, and the light shading spans the range. 
Phytoplankton Communities 
As in recent years, 2019 total phytoplankton abundances remained somewhat low
throughout Massachusetts Bay (Figure 3-12, Libby et al. 2020). In the nearfield,
overall abundance was 61% of the long-term mean, ranking 23 rd out of 28 years of
monitoring. The relatively low abundance can be partially explained by a lack of a
large winter-spring diatom bloom during the survey season and by the continued
absence of a bloom of the nuisance colonial flagellate Phaeocystis pouchetii in
Massachusetts Bay which has occurred in many years.

20 
Figure 3-12. Total phytoplankton abundance (million cells per liter) at selected stations in 2019
compared to prior years . (For some stations, historic data extend later in the year than the current
survey schedule.) The black points and lines are results from 2019; the blue lines and shading are
results from 1992–2018: the line is the 50 th percentile, dark shading spans the 25–75 th percentiles, and
the light shading spans the range. 
Diatom abundance was low, with centric diatom totals ranking 23 rd of 28 years.
Centric diatom abundance has been below the long-term mean since 2006.
Microflagellates continued to be the most abundant species group, comprising about
60% of the total phytoplankton counts, but were present at only 77% of their long-
term average, another factor in the low overall phytoplankton abundance.
Conversely, dinoflagellate abundance increased substantially in comparison to 2018,
and 2019 abundance ranked third out of the 28 years of monitoring (Figure 3-13) . 
The late summer and fall bloom of the dinoflagellate Karenia mikimotoi was largely
responsible for this overall increase. This species has been reported in New England
to the Gulf of Saint Lawrence region for many years (Blasco et al. 1996). It was not
observed in MWRA samples until 2017, when it had a maximum abundance of about
300,000 cells per liter, and it was present again in 2018, but in lower numbers. In
September 2019, Karenia mikimotoi abundance reached a maximum of 850,000 cells
per liter at Station F23 at the mouth of Boston Harbor and briefly discolored the water
within the harbor. Its presence in southern Cape Cod Bay may have contributed to
the hypoxia event further discussed in Section 6, Special Studies. Although its
toxicity is not well understood, anoxia and benthic mortalities have been associated
with this species in other locations.

21 
Figure 3-13. Total dinoflagellate abundance (100,000 cells per liter) at selected stations in 2019
compared to prior years . (For some stations, historic data extend later in the year than the current
survey schedule.) The black points and lines are results from 2019; the blue lines and shading are
results from 1992–2018: the line is the 50 th percentile, dark shading spans the 25–75 th percentiles, and
the light shading spans the range.
A large and prolonged bloom of the toxic dinoflagellate Alexandrium catenella 
prompted a series of seven rapid-response surveys over two months in 2019 (Figure
3-14). The 2019 bloom was comparable in magnitude and duration to blooms in
2005 and 2008. Large Alexandrium catenella blooms can cause paralytic shellfish
poisoning (PSP), a life-threatening condition for marine mammals and humans who
consume shellfish. Alexandrium blooms in Massachusetts Bay, when they have
occurred, have originated from cells from established cyst beds off the coast of
Maine. The cells typically enter Massachusetts Bay when winds from the northeast
push water masses from coastal Gulf of Maine waters into the bay, conditions that
occurred in the spring of 2019.

22 
Figure 3-14. Nearfield abundance of Alexandrium catenella , 1992–2019. Note log scale. 
The timing and north-to-south progression of the bloom was typical for
Massachusetts Bay (Figure 3-15). Very low abundances were detected during the
April MWRA survey, and in early May, there were indications that a bloom was
underway in the Gulf of Maine. During the May 16 survey, MWRA detected 
Alexandrium cells at all ten stations sampled, with a maximum level greater than 100
cells per liter at the northeast offshore Station F22, sufficient to trigger weekly rapid-
response surveys. From May 30 through July 17, high cell counts, greater than 5,000
and reaching a maximum of 24,000 cells per liter, were observed at the 19 stations
sampled. By July 31, counts had decreased to fewer than 100 cells per liter, and the
rapid-response surveys were curtailed.
Progression of PSP toxicity associated with the bloom was also typical, appearing
first in the north. On May 9, the New Hampshire Department of Environmental
Services detected a large increase in PSP toxicity in their state waters. PSP toxicity
remained undetected or low in Massachusetts Bay until June 18, when the
Massachusetts Department of Fisheries closed shellfishing from Boston to Plymouth.
When the peak cell count for the bloom occurred in a July 17 offshore sample, PSP
toxicity in the coastal areas had already declined, and the Massachusetts shellfishing
closure was lifted on July 19.
Modeling carried out by the federal National Centers for Coastal Ocean Science
suggests that the strong stratification in 2019, a result of spring freshwater inflow and
warm surface waters, and the region-wide availability of nutrients at the pycnocline
were key factors in determining the magnitude and duration of the bloom. In August,
the Woods Hole Oceanographic Institution detected Alexandrium cysts in
Massachusetts Bay, a potential concern for 2020. (A modest Alexandrium bloom did
occur in 2020 but did not result in shellfishing closures or a Contingency Plan
exceedance.)

23 
Figure 3-15. Alexandrium abundance in surface- and mid-depth samples during the 2019 bloom. 
The upper half of the symbols indicates abundance in surface waters; the lower half indicates
abundance at about 10 meters.
The potentially toxic genus of pennate diatoms, Pseudo-nitzschia , was also present in
somewhat elevated numbers in 2019, although higher abundances occurred in the
1990s. At particularly high abundance, domoic acid produced by some species of 
Pseudo-nitzschia can cause amnesic shellfish poisoning (ASP), a life-threatening
illness. Pseudo-nitzschia delicatissima , the species that dominated in 2019, does not
produce much toxin, and there were no closures due ASP toxicity.

24 
Zooplankton Communities 
Annual peak abundances of total zooplankton were higher than in many years of the
monitoring period and within in the 25–75 th percentile range at most stations during
most surveys (Figure 3-16, Libby et al. 2020). There were no extreme peaks
coinciding with survey dates, such as the bivalve veliger larvae that drove total
abundance peaks to record highs in July and August of 2015. In 2019, zooplankton
communities continued to be dominated by the typical mix of larval, young, and adult
copepods and by meroplankton, those animals that are planktonic for only a portion
of their lives. The small copepod Oithona similis continued to be the most abundant
species in most samples, with Acartia spp. dominating in Boston Harbor. 
Figure 3-16. Total zooplankton abundance (10,000 animals per square meter) at selected stations
in 2019 compared to prior years. (For some stations, historic data extend later in the year than the
current survey schedule.) The black points and lines are results from 2019; the blue lines and shading
are results from 1992–2018: the line is the 50 th percentile, dark shading spans the 25–75 th percentiles,
and the light shading spans the range.
Trend analysis has shown a sustained decrease in total zooplankton abundance during
2000–2006, followed by an increase in 2006–2017, and then a decrease in 2018 and
2019. The trend in phytoplankton abundance mirrors this pattern, suggesting that
zooplankton grazing is one factor determining abundances of both phytoplankton and
zooplankton populations (Figure 3-17).

25 
Figure 3-17. Trends in abundance of total phytoplankton (green triangles) and total zooplankton
(orange circles) in the nearfield. Lines are smoothed using a moving average of about four years. 
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 the Stellwagen
Bank National Marine Sanctuary. Water column Station F22 is in Stellwagen Basin,
just to the west of the sanctuary and is considered to be representative of northern,
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, for example, Figure 3-6, above). Levels have also remained low at
Station F06, located 29 kilometers offshore of the outfall and west of the sanctuary.
Sampling at Station F22, as well as data from the NERACOOS Buoy and satellite
imagery, detected no unusual chlorophyll levels in offshore regions in 2019. No
effects on chlorophyll levels in the offshore, including the sanctuary, were predicted
and none have been measured.
Deepwater dissolved oxygen concentrations at Station F22 in Stellwagen Basin were
healthy throughout 2019. Both survey observations and data from the NERACOOS
Buoy showed the typical decline during the stratified season (Figure 3-18). Data
from the buoy documented the rapid return to oxygenated conditions following fall
mixing events. 
20,000
40,000
60,000
80,000
100,000
400,000
800,000
1,200,000
1,600,000
2,000,000
1995 2000 2005 2010 2015 2020 
Total Zooplankton (animals m ‐ 3 )
Total Phytoplankton (cells L ‐ 1 ) 
Total Phytoplankton
Total Zooplankton

26 
Figure 3-18. Deepwater dissolved oxygen at the NERACOOS Buoy A01 and Station F22 in
Stellwagen Basin. 
Boston Harbor Water Quality 
Water quality in Boston Harbor has greatly improved during the past 20 years, and
those improvements were sustained in 2019. MWRA’s in-house Boston Harbor
monitoring program confirmed that harbor-wide concentrations of total nitrogen and
phosphorus remained low, as they have since effluent discharges to the harbor ended.
Perhaps the most dramatic improvement in Boston Harbor has been the decrease in
ammonium levels (see Figure 3-6, above). Ammonium concentrations 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, the result of over-stimulation of
phytoplankton growth in urban waters (Taylor 2020, and reviewed in the 2017 outfall
monitoring overview, Werme et al. 2018).

27 
Contingency Plan Thresholds 
There were no water-column threshold exceedances for dissolved oxygen or
chlorophyll parameters in 2019, but there was a caution level exceedance for presence
of the nuisance algal species Alexandrium catenella (Table 3-1). The Alexandrium 
bloom was region-wide, was first detected at northern stations, and exhibited higher
PSP toxicity in the north than at more southern stations. These results were
consistent with past blooms and not considered indicative of an outfall effect. 
Table 3-1. Contingency Plan threshold values and 2019 results for water-column monitoring. 
Parameter Baseline Caution Level Warning Level 2019 Results
Dissolved oxygen 
Nearfield
concentration 6.05 mg/L <6.5 mg/L <6.0 mg/L 7.18 mg/L
Nearfield percent
saturation 65.3% <80% <75% 81.2%
Stellwagen
concentration 6.23 mg/L <6.5 mg/L <6.0 mg/L 7.35 mg/L
Stellwagen percent
saturation 67.2% <80% <75% 79.0%
Nearfield depletion
rate 0.024 mg/L/d >0.037 mg/L/d >0.049 mg/L/d 0.011 mg/L/d 
Chlorophyll 
Annual 72 mg/m 2 >108 mg/m 2 >144 mg/m 2 92 mg/m 2
Winter/spring 50 mg/m 2 >199 mg/m 2 None 112 mg/m 2
Summer 51 mg/m 2 >89 mg/m 2 None 57 mg/m 2
Autumn 90 mg/m 2 >239 mg/m 2 None 132 mg/m 2 
Nuisance algae nearfield Pseudo-nitzschia 
Winter/spring 6,735 cells/L >17,900 cells/L None 18 cells/L
Summer 14,635 cells/L >43,100 cells/L None 598 cells/L
Autumn 10,050 cells/L >27,500 cells/L None 523 cells/L 
Nuisance algae nearfield Alexandrium catenella 
Any nearfield
sample
Baseline maximum
163 cells/L >100 cells/L None
24,342 cells/L
caution level
exceedance
PSP toxin extent NA New incidence None No new incidence 
Dissolved oxygen caution and warning levels represent numerical criteria, with the caveat “unless
background conditions are lower.” Results are therefore compared to the baseline rather than to the
caution and warning levels. Dissolved oxygen concentrations and percent saturation for the year are
the lowest survey means. 
Alexandrium catenella count is the highest sample abundance for all surveys.
PSP = paralytic shellfish poisoning
NA = not applicable

28 
4. Sea Floor 
Seafloor monitoring in 2019 included sampling and analysis of soft-bottom sediment
conditions, effluent tracers, and infauna at 14 stations and sediment-profile imaging at
23 stations (Figures 4-1 and 4-2). Anthropogenic contaminants analyses and video
assessment of 23 hard-bottom stations have occurred at three-year intervals, most
recently in 2017. 
Figure 4-1. Soft-bottom monitoring stations. Also shown are the instrumented buoys, the MWRA
outfall diffuser, and the Stellwagen Bank National Marine Sanctuary.

29 
Figure 4-2. Sediment-profile imaging stations. Also shown are NDBC Buoy 44013 and the MWRA
outfall diffuser. SPI = sediment-profile imaging

30
Soft-bottom sediment sampling was completed in August 2019, with samples
analyzed for grain-size distribution, the effluent tracer Clostridium perfringens 
spores, total organic carbon, and benthic infauna. The 14 stations included four
nearfield stations within two kilometers of the outfall (NF13, NF14, NF17, NF24);
six nearfield stations in western Massachusetts Bay but farther from the outfall
(NF04, NF10, NF12, NF20, NF21, NF22); one station in the “transition” area
between Boston Harbor and the nearfield stations (FF12); and three farfield reference
stations in Massachusetts Bay and Cape Cod Bay (FF01A, FF04, and FF09). For the
purposes of threshold testing, “nearfield” included the transition station, as well as
both nearfield groups, for a total of eleven stations.
Sediment-profile imaging was also completed in August 2019. Triplicate images
from 23 stations were used to measure the apparent reduction-oxidation (redox)
potential discontinuity (RPD) depth, an approximation of the depth that oxygen
penetrates the sediments as determined by color changes, and to assess the status of
the bottom community. 
Sediment Characteristics and Tracers 
As in past years, sediment grain-size distributions in 2019 varied broadly among
stations, ranging from silt and clay at some stations (particularly Station FF04 within
Stellwagen Basin) to almost entirely sand at others (Nestler et al. 2020). Sediment
grain-size distributions have remained generally consistent at individual stations over
the years of the monitoring program. When changes have occurred, they have been
mostly preceded by large storms with wave-driven currents sufficient to resuspend
bottom sediments.
As in other years since the offshore outfall began to discharge, it was possible to
detect elevated levels of the effluent tracer Clostridium perfringens spores at some
stations located closest to the outfall (Figures 4-3). Clostridium are anaerobic
bacteria that are found in mammalian (including human) digestive tracts and that
form persistent spores in oxygen-rich conditions. In 2019, the average Clostridium 
abundance at stations located within two kilometers of the outfall remained elevated,
but only at stations closest to the outfall. Clostridium abundance has declined over
time or remained similar to the baseline at stations further from the outfall.
Percent organic carbon content analyses were also consistent with past results, with
no increased organic carbon in any area, even the station group closest to the outfall
(Figure 4-5). 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 concentrations continue to show no
signs of organic enrichment from the outfall.

31 
Figure 4-3. Concentrations of Clostridium perfringens spores corrected for sediment grain size, in
2019. 
Figure 4-4. Total organic carbon at selected stations, 1992–2019. 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.

32 
Soft-bottom Communities 
The 14 soft-bottom samples collected and analyzed in 2019 yielded 26,614
organisms, classified into 185 species and 28 other discrete taxonomic groups
(Nestler et al. 2020). Total abundance of organisms was lower in 2019 than in 2018
across all regions except for the nearfield stations within two kilometers of the outfall,
where numbers were slightly higher, about the same as 2017 (Figure 4-5). The
numbers of species per sample and diversity measures were slightly higher than in
2018, but remained within the ranges measured throughout the monitoring program.
Polychaete worms continued to dominate at most stations, and the spionid polychaete 
Prionospio steenstrupi remained the numerically dominant species at several
nearfield stations; it has accounted for 25% of the total number of organisms sampled
over the course of the monitoring program. The tube-building amphipod 
Crassicorophium crassicorne , which prefers sandy sediments, was the most abundant
species at Station N17, very close to the outfall. 
Figure 4-5. Total abundance by region, 1992–2019 . 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. 
Community analyses continued to show no effects of the outfall on relative
abundance or community composition. A series of multivariate analyses assessed
spatial and temporal patterns in the soft-bottom benthic communities and found no
particular species or type of community specifically associated with the outfall.

33
A cluster analysis identified two main infauna assemblages and one outlier group:
Group I dominated by amphipods and polychaete worms, Group II dominated by
polychaetes, and the outlier Group III, representing the station located within
Stellwagen Basin, which has consistently supported a unique community. Ordination
analysis continued to show no indication of any relation of species composition to
proximity to the outfall, with stations closest to the outfall represented in the two
larger main assemblages (Figure 4-6). Analyses further continued to demonstrate that
variations in species distributions largely followed differences in sediment grain size
and depth (Figure 4-7). 
Figure 4-6. Ordination plot of 2019 Massachusetts Bay samples by location. Each point on the plot
represents one of the 14 stations; similarity of species composition is indicated by proximity of points
on the plot. Faunal assemblages (Groups I-III, and sub-groups) identified by cluster analysis are circled
on the plot. Locations 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. Stress is a measure of how well the ordination results represent the raw data; a stress of 0.05
indicates excellent representation.

34 
Figure 4-7. Percent fine sediments (top) and depth (bottom) superimposed on the ordination plot
of the 2019 infauna samples. Each point on the plot represents one of the 14 stations; similarity of
species composition is indicated by proximity of points on the plot. Faunal assemblages (Groups I-II,
and sub-groups) identified by cluster analysis are circled on the plot. Stress is a measure of how well
the ordination results represent the raw data; a stress of 0.05 indicates excellent representation.

35 
Sediment-profile Imaging 
Sediment-profile images continued to show no adverse effects of the outfall (Nestler
et al. 2020). Rough topography and physical processes in the nearfield remained the
more important factors in determining benthic habitat quality.
As in past years, the 2019 average RPD was deeper than the average measured during
the baseline period (Figure 4-8), with a mean depth of 4.8 cm for all stations where
RPDs could be measured. At eight of the 23 stations, the RPD was deeper than the
bottom of the images, either because of sandy sediments or sediment compaction.
The environmental concern before the outfall began to discharge was that the RPD
would become shallower, due to increases in organic matter causing stress on
sensitive sediment-dwelling organisms. The deep RPD in 2019 continued to indicate
there has been no adverse effect from the discharge. 
Figure 4-8. Annual apparent color RPD depth (± standard deviation) for nearfield stations. The
mean RPD has been deeper than in baseline years, a strong indication of no adverse effect from the
discharge.
Along with the deepening RPD, nearfield stations have shown an increase in the
organism sediment index (OSI; Figure 4-9), a measure that integrates RPD depth with
the successional stage of the infauna community. This general increase in OSI has
documented increasingly good habitat quality throughout the nearfield. Another
measure of biological activity, the number of biogenic structures, such as burrows and
voids, has decreased. This decline appears to be related to the number of winter
storms occurring within the year rather than to any outfall effect.

36 
Figure 4-9. Trend in the Massachusetts Bay organism sediment index over time. Points are
averages for all 23 nearfield stations. Green line is a two-year moving average. Blue line is a linear
regression line, R 2 = 0.60, p = <0.001. An OSI > 6 is considered to represent good benthic habitat.
In general, monitoring has shown that physical rather than biological processes, such
as storms and storm-induced sediment transport, can be primary stressors on the
Massachusetts Bay sea floor, lessening the chances of any effects of the
Massachusetts Bay outfall. At Station FF13 to the southwest of the outfall, for
example, biological processes were evident in 1997 and 1998, prior to outfall startup,
while physical processes have been particularly evident in recent, stormier years.
Section 6, Special Studies, presents further analysis of sediment habitat quality, and
Section 7, Monitoring Plan Revisions, provides rationale for ending sediment-profile
imaging studies, as well as sediment-contaminant analyses, in Massachusetts Bay. 
Stellwagen Bank National Marine Sanctuary 
The NPDES permit to discharge from Deer Island Treatment Plant into
Massachusetts Bay requires annual reports on results relevant to the 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 could be detected if they were to occur.
Station FF04 is typical of the deep waters offshore from the outfall, representative of
a number of stations monitored in earlier years of the program, and it continues to
support an infauna community typical of what had been found at the larger suite of
deep-water stations. The deep-water stations, including Station FF04, have always
shown distinct differences from those found at shallower stations, probably due to
their depth, their fine-grained sediments, and their distance from shore.
Superimposing percent grain size and depth on the ordination plot for 2019 infauna
samples continued to show these natural differences (see Figure 4-7, above).

37 
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 have greatly improved and
continue to improve in Boston Harbor, a result of the Boston Harbor Project, more
recent enhancements to treatment, and remediation of combined sewer overflows.
MWRA has conducted ongoing seafloor monitoring in Boston Harbor since 1991.
Annual sediment and infauna samples are taken from nine stations (Figure 4-10), and
sediment-profile imaging is conducted at 61 stations throughout the inner and outer
harbor. 
Figure 4-10. Soft-bottom sampling stations in Boston Harbor. Nine stations are sampled each year
for sediment characteristics and infauna analyses. Sediment-profile images are taken from 61 stations
throughout the harbor.

38
Concentrations of total organic carbon and Clostridium perfringens spores in harbor
sediments have declined over time, reflecting the improvements made throughout the
Boston Harbor Project. During the same time, number of species per sample (Figure
4-11, Rutecki et al. 2020) and infauna diversity measures (not shown) have increased,
a response to continued improvement in benthic habitat conditions. As in past years,
the samples showed differences between stations in the sandier stations of the outer
harbor, finer sediments of the inner harbor and Quincy Bay, and a persistently a
unique fauna at the most polluted location, Station T04, at the mouth of Savin Hill
Cove. 
Figure 4-11. Mean number of species per sample in Boston Harbor, 1991–2019. Eight stations,
T01–T08, were included in the analysis.

39
Sediment-profile imaging has also confirmed an inner- to outer-harbor gradient and
clearly documented improvements to habitat conditions throughout the Boston
Harbor Project. The harbor-wide OSI has improved since the early days of the
monitoring program, remaining higher than 6, considered indicative of good habitat
quality, for the past 17 years (Figure 4-12). 
Figure 4-12. Organism sediment index at 61 sediment-profile stations in Boston Harbor, 1992-2019 .
An OSI > 6 is considered to represent good benthic habitat. 
Sediment-profile imaging has also documented continued presence of eelgrass at
Deer Island Flats, another sign of recovery of the harbor following the outfall
diversion. An eelgrass bed was first detected in 2008 and persisted in the 2019
images.
The 2018 and 2019 images showed evidence of dredging, part of a channel-deepening
project by the U.S. Army Corps of Engineers. Dredging was underway at the time of
the 2018 survey, and because this disturbance completely removed parts of the
seafloor community, the OSI at Deer Island Flats, located within the dredged area,
was far lower than in 2017. Dredging continued in the area after the 2018 MWRA
survey concluded. Effects were still visible in 2019, although there were indications
of recolonization and recovery at some stations.

40 
Contingency Plan Thresholds 
There were no Contingency Plan threshold exceedances for seafloor parameters in
2019 (Table 4-1). The average RPD remained deeper than the thresholds and also
deeper than baseline values. Diversity and other benthic community parameters were
higher than Contingency Plan limits, and the percent opportunistic species remained
far below any level of concern, all signs of continued healthy seafloor habitat. 
Table 4-1. Contingency Plan threshold values and 2019 results for sea-floor monitoring. 
Parameter Baseline Caution Level Warning Level 2019 Results
Sediment parameters 
RPD depth NA <1.18 cm None 4.85 cm 
Benthic community parameters 
Species per
sample NA <42.99 None 64.1
Fisher’s log-series
alpha NA <9.42 None 12.9
Shannon diversity NA <3.37 None 3.88
Pielou’s evenness NA <0.57 None 0.65
% opportunists NA >10% >25% 0.28% 
HMW = high molecular weight; LMW = low molecular weight
NA = not applicable; RPD = redox potential discontinuity

41 
5. Fish and Shellfish 
MWRA monitors winter flounder health each year and conducts chemical
contaminant analyses of flounder and lobster meat tissues and cage-deployed blue
mussels every three years, most recently in 2018. Sampling and deployment sites
vary by species (Figure 5-1). Annual flounder monitoring, the only fish and shellfish
study conducted in 2019, focuses on external condition and the presence of liver
disease and tumors (neoplasia) in fish collected from near the former Boston Harbor
outfall at Deer Island Flats, off Nantasket Beach, the Massachusetts Bay outfall site,
and eastern Cape Cod Bay. 
Figure 5-1. Fish-and-shellfish monitoring stations. Only flounder were sampled in 2019. Also
shown are the two instrumented buoys, the MWRA outfall diffuser, and the boundaries of the
Stellwagen Bank National Marine Sanctuary.

42 
Flounder Health 
Annual flounder monitoring for external condition and the presence of liver disease
and tumors was hampered in April and May 2019 by a barge laying a new cable to
Deer Island, weed clogging, and abandoned lobster gear, which can require cutting
the flounder net (Figure 5-2). Only 40 fish were taken at Deer Island Flats and only
20 off Nantasket Beach, with the full complement, 50 fish, taken at the outfall site
and eastern Cape Cod Bay. 
Figure 5-2. Lobster gear in flounder net trawl. Photo credit Michael Moore, Woods Hole
Oceanographic Institution

43
Across the sites, mean age of fish ranged from 4.0 to 4.8 years, and standard length
ranged from 276 to 303 millimeters, within the ranges observed in recent years
(Moore et al. 2020). As in past years and as is common throughout northeast coastal
populations, the catches were dominated by females (reviewed in Moore et al. 2016).
Measures of external condition (such as occurrence and severity of fin erosion)
continued to suggest improved conditions since the 1980s and 1990s, and there
continued to be no evidence of neoplasia. Tumors have not been observed by the
monitoring program since 2004 and have never been found in fish taken from the
outfall site. Incidence of fin erosion, often an indicator of excess ammonium and
other pollutants, continued to be highest in fish from Deer Island Flats (32.5%) and
was lowest in fish from eastern Cape Cod Bay and off Nantasket Beach (10%).
Incidence of fin erosion has been highly variable at all sites, with no obvious long-
term trend and no correlation with liver conditions. Blind-side ulcers, a condition that
remains poorly understood, were present in small numbers of fish from Deer Island
Flats, off Nantasket Beach, and the outfall site.
The incidence of centrotubular hydropic vacuolation (CHV), a mild condition
associated with exposure to contaminants and a tumor precursor, remained lower than
the baseline observations at all sites (Figure 5-3). CHV incidence remained lower
than in any baseline year at the outfall site and somewhat elevated in comparison to
some recent years at Deer Island Flats, although also lower than levels found prior to
the Boston Harbor Project. Average severity of CHV also remained highest at Deer
Island Flats but at lower than levels seen in the early 1990s. Section 7, Monitoring
Plan Revisions, provides rationale for reducing future flounder-health monitoring. 
Figure 5-3. Annual prevalence of centrotubular hydropic vacuolation (CHV), 1991–2018. 
DIF = Deer Island Flats, ECCB = eastern Cape Cod Bay, NB = Nantasket Beach, OS = outfall site

44 
Contingency Plan Thresholds 
There was no Contingency Plan threshold exceedance for the only threshold
parameter measured in 2019 (Table 5-1). Incidence of CHV, the most common
indicator of liver disease in winter flounder of the region, was 6% in fish taken from
the vicinity of the outfall, much lower than the 44.9% caution threshold and the
24.4% baseline average. 
Table 5-1. Contingency Plan threshold values and 2019 result for fish-and-shellfish monitoring. 
Parameter Baseline Caution Level Warning Level 2019 Results
Flounder disease 
Liver disease
(CHV) 24.4% >44.9% None 6% 
CHV = centrotubular hydropic vacuolation

45 
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 long-term analyses of nutrient discharges into
Massachusetts Bay, sediment-habitat structure in Boston Harbor and Massachusetts
Bay, and the summer 2019 hypoxia event in southern Cape Cod Bay. 
Nutrient Discharges into Massachusetts Bay 
MWRA recently completed an updated assessment of nutrient inputs and nutrient and
phytoplankton biomass gradients in Massachusetts Bay (Libby et al. 2020). The
assessment focused on 2011–2019, years when water samples from each of eleven
stations were analyzed for full suite of parameters nine times per year. (Before 2011,
some stations included only a partial list of parameters, and some stations were
sampled just six times per year.) The study confirmed earlier studies that had first
predicted and then confirmed that the nutrient signature of the outfall would remain
localized and there would be no effect on phytoplankton biomass (for example, Libby
et al. 2009). Increased phytoplankton biomass in response to the discharge, were it to
occur, could contribute to eutrophication and result in low dissolved oxygen levels.
The new assessment found that total nitrogen, dissolved inorganic nitrogen
(ammonium, nitrate, and nitrite), and ammonium levels were each highest at Station
N21, located directly over the outfall (Figure 6-1). The proportions of total and
dissolved inorganic nitrogen made up of ammonium were also highest at Station N21,
as expected, because ammonium makes up the major part of the nitrogen discharge.
Concentrations of ammonium, as well as total and dissolved inorganic nitrogen, fell
precipitously with distance from the outfall, declining to background levels within 7.5
to 10 kilometers.
Concentrations of total and dissolved inorganic phosphorus (not shown) were
similarly highest at Station N21, declining even more quickly with distance from the
outfall. Dissolved inorganic silica (silicate) concentrations (also not shown) did not
vary with distance from the outfall. Phytoplankton biomass, measured as chlorophyll
(Figure 6-2) and particulate organic carbon, varied throughout the year and did not
vary with distance from the outfall.
It was not surprising that the study confirmed past predictions and analysis, showing
increased ammonium in the immediate vicinity of the outfall but not within greater
Massachusetts Bay or Cape Cod Bay and no detectable effect on phytoplankton
growth or biomass. While the MWRA effluent is considered nutrient-rich, exchange
with offshore waters provides about 15 times more total nitrogen to Massachusetts
Bay than the outfall discharge.

46 
Figure 6-1. Depth-averaged nitrogen concentrations (μM) and declines with distance from the
Massachusetts Bay outfall . Data are from 2011–2019. Station numbers are in black. TN = total
nitrogen DIN = dissolved inorganic nitrogen NH4 = ammonium. Error bars are 95% confidence limits. 
Figure 6-2. Depth-averaged chlorophyll concentrations (μM per liter as fluorescence) and
distance from the Massachusetts Bay outfall . Data are from 2011–2019. Station numbers are in
black. Error bars are 95% confidence limits.

47 
Sediment-Habitat Structures 
The almost 30 years of monitoring sediment-habitat structures in Boston Harbor and
Massachusetts Bay has documented improvements in the harbor but identified no
adverse effects from effluent discharge in the bay (see Section 4, Sea Floor, above).
This long monitoring period has further allowed for an analysis of long-term trends
not associated with the MWRA outfall. Weather and climate may prove to be the
most important forces driving future changes in both the harbor and the bay.
Prior to the Boston Harbor Project, organic and nutrient loads were major factors in
determining sediment quality in Boston Harbor, dominant enough to obscure analysis
of climate-driven stresses. The harbor’s complex geomorphology further made
interpreting effects of storms difficult, sometimes dampening and sometimes
amplifying the predicted effects.
Declines in organic-matter loading to the harbor began in 1991, with the ending of
biosolids discharges and facility upgrades, starting a shift from anaerobic to aerobic
conditions and resulting in continually improving habitat quality. The outfall
diversion from the harbor further reduced the organic-matter load, allowing
burrowing amphipods to flourish, which accelerated the transition to aerobic
conditions.
With recovery of the harbor, effects of weather and climate have become more
apparent (Figure 6-3). For example, an increase in spring salinity levels during 1991–
2019 was likely sufficient to favor a new dominant tube-building amphipod species.
Around 2014, Ampelisca vadorum , a more coastal species that builds shorter and
wider tubes, replaced the earlier dominant, Ampelisca abdita . During the same
general period, the extent of amphipod tube mats became more obviously associated
with occurrence or absence of winter storms. Eight of the windiest winter storms
occurred during 2006–2019, leading to fewer amphipod mats than had been present
during earlier recovery stages of the Boston Harbor Project.
In Massachusetts Bay, weather and climate appear to be the driving forces, not only
for seafloor communities, but probably also in the water column (Figure 6-4). Storms
and climate change are likely important factors in observed increases in water
temperature and salinity over time. Storms with forces great enough to resuspend and
transport sediments affect species composition and overall habitat quality. Intense
winter storms can decrease the total number of infaunal organisms in the following
year or change abundance patterns among the most frequently occurring species. The
increasing storminess that has been documented over the last years of the monitoring
program is likely related to both regional variability and to long-term trends.

48 
Figure 6-3. Reducing past sewage loadings, a result of the Boston Harbor Project, has led to
recovery of benthic habitat and communities in Boston Harbor.
Figure 6-4. Storms and other climate-related factors continue to have the greatest effects on the
habitats and communities in Massachusetts Bay.

49 
Hypoxia in Cape Cod Bay 
Typically, dissolved oxygen concentrations in coastal bottom waters are high in the
winter and early spring, fall steadily through the summer season when the water
column is stratified, and return to winter conditions during the fall. This general
pattern occurred throughout MWRA’s Massachusetts and Cape Cod bays stations in
2019 (see Figures 3-10 and 3-11, above), however the oxygen minima at the Cape
Cod Bay stations reached unusually low levels, four to five milligrams per liter.
Monitoring by the Massachusetts Division of Marine Fisheries, using sensors at
shallow locations south of the MWRA stations, showed hypoxic and anoxic
conditions in early October (Figure 6-5), which led to fish and lobster mortality in
traps set in the immediate vicinity of the sensors. The hypoxic event came to an end
on October 5, when strong winds from the north mixed and re-oxygenated the water
column to the bottom at the most southern sensor locations. 
Figure 6-5. The hypoxia and anoxia dissolved oxygen event in southern Cape Cod Bay, 2019. 
(Top left) Map showing MWRA stations in black and bottom dissolved oxygen concentrations at the
Department of Marine Fisheries hypoxic/anoxic site sensors on October 4; (Top right) Wind direction
and intensity at Provincetown, showing strong winds from the north on October 5; (Middle) Bottom
temperature at the site sensors; (Bottom) Bottom-water dissolved oxygen concentrations at the site
sensors. Color coding of the lines matches site locations on the station map. DO = dissolved oxygen

50
This unusual hypoxia event was driven by the large August and September
dinoflagellate bloom, likely Karenia mikimotoi (see discussion in Section 3, Water
Column, above) , coupled with strong and prolonged stratification in the shallow
waters. Decomposition of dying dinoflagellate cells rapidly depleted oxygen levels in
bottom waters. Karenia mikimotoi is a relative newcomer to the region, and has been
known to cause fish kills in other geographic areas.
Similar strong stratification, coupled with southward coastal flow and long water
resident times, have led to localized low-oxygen areas in Cape Cod Bay in the past
(Jiang et al. 2007). In the fall of 2013, strong and persistent stratification resulted in
relatively low dissolved oxygen levels at MWRA’s Cape Cod Bay stations, with
October levels declining to less than five milligrams per liter at Station F02, similar to
what occurred in 2019. Unlike 2019, the bottom waters at Station F01 during the
same 2013 survey had already recovered to winter oxygenated conditions.
The effects on the fish and lobster resource in 2019 were unprecedented, leaving
questions about whether changing oceanographic conditions could lead to recurring
hypoxia in future years. As shown above, the Massachusetts Bay discharge has no
detectable effect on nutrient levels or phytoplankton biomass at locations as far away
as the shallow fish and lobster grounds. However, MWRA will continue to support
its partner, the Center for Coastal Studies, as well as the Department of Marine
Fisheries and the local lobstermen working in Cape Cod Bay as this issue continues to
be studied.

51 
7. Monitoring Plan Revisions 
The MWRA permit to discharge into Massachusetts Bay includes a process for
modifying the monitoring plan in response to changing conditions and past
monitoring results. The monitoring plan was intended to be a “living document,”
incorporating new scientific information and improved understandings from data
analyses into the most appropriate continued measurements. Since the permit went
into effect in September 2000, two changes to the monitoring plan have been
approved, the first in 2004 and the second in 2010. Both revisions were developed in
coordination with EPA, MassDEP, and OMSAP.
Plans for a third set of revisions began in 2018, when OMSAP hosted a large group of
scientists, regulators, public interest groups, and interested citizens to review past
monitoring results and the ongoing monitoring program. This workshop, “2300 Days
at Sea: Monitoring the Impacts of the Outfall on Massachusetts Bay,” also began to
identify new issues of environmental and public concern, such as microplastic debris
and chemical contaminants of emerging concern.
Following the workshop, OMSAP and a series of subcommittees met throughout
2019 to develop a framework for revising the monitoring plan. With participation
from OMSAP members, regulators, and the public, this framework identified and
evaluated monitoring studies that could end or be reduced, based on strong evidence
that the original monitoring questions had been answered and that there were no
indications of environmental harm.
Following the OMSAP and subcommittee findings, MWRA proposed a series of
changes to the existing monitoring plan: (1) ending monitoring of the existing suite of
chemical contaminants in sediments; (2) ending monitoring of the sediment RPD, a
visual assessment of the depth of the sediment-oxygenated layer, and (3) eliminating
two sampling areas (off Nantasket Beach and eastern Cape Cod Bay) from
monitoring of contaminant-associated liver conditions in winter flounder. These
changes are expected to be approved and incorporated into a revised monitoring plan
in 2020. The changes in sediment monitoring were implemented in 2020, and the
changes to flounder monitoring will take place in 2021.
OMSAP is continuing to evaluate issues related to contaminants of emerging concern.
Recommendations for approaches to address these concerns are expected to be issued
in late 2020 or early 2021.

52 
Sediment Contaminants 
Sediment-contaminant monitoring was included in the original monitoring plan, and
since 2002, sediment contaminants have been measured every third year, in
conjunction with the annual benthic infauna sampling and analyses. Contaminants
measured have included toxic metals, PAHs, banned organochlorine pesticides, and
PCBs. These studies have detected no increases in sediment-contaminant
concentrations in response to the MWRA discharge. Instead, contaminant
concentrations have slowly decreased over time. For example, since 2005, PCB
concentrations in the nearfield have been consistently lower than in any earlier years
of monitoring (Figure 7-1). 
Figure 7-1. Average total PCB concentrations in nearfield sediments, 1992–2017 . Error bars are ±
one standard deviation. Dotted green line marks the outfall startup.
MWRA believes that the sediment-contaminant monitoring can end, and OMSAP has
concurred. Going forward, MWRA will continue to monitor the same suite of
contaminants in its effluent. These analyses use low detection limits, designed to be
protective of the marine environment, and the results of these analyses are reported in
the annual outfall monitoring overviews. A technical report further documenting
contaminant concentrations in effluent was recently completed (Charlestra et al.
2020).

53 
Sediment-profile Imaging 
Each August, MWRA has used a sharp-edged prism and camera at 23 stations in
Massachusetts Bay to provide a rapid assessment of RPD depth and other physical
and biological parameters. (See Section 4, Sea Floor, for 2019 results.) The concern
during outfall planning and siting was that inputs of organic matter could lead to
eutrophication and a shallower RPD.
In contrast to that concern, the nearfield RPD has become steadily deeper over the
course of the MWRA monitoring program, and bottom habitats have remained
healthy (Figure 7-2 and see Figure 4-8, above). The deeper RPD and good habitat
quality have been strong indications that there has been no adverse effect of the
discharge on the health of the bottom communities of Massachusetts Bay. 
Figure 7-2. Sediment-profile image from Station NF17, just south of the outfall, with healthy
amphipod tubes in 2019. Light-colored, oxygenated sediments extended deeper than the bottom of
this image. Tick marks are one centimeter.
MWRA believes that the sediment-profile imagery measurements in Massachusetts
Bay can end, and OMSAP has concurred. However, MWRA will continue to
qualitatively document sediment conditions in its infauna grab samples, as has been
routine but little reported. Going forward, relevant observations will be included in
annual technical reports and the outfall monitoring overview.

54 
Winter Flounder Health 
Each spring, MWRA has collected winter flounder, a popular sport fish, from Deer
Island Flats in Boston Harbor, off Nantasket Beach and at the outfall site in
Massachusetts Bay, and in eastern Cape Cod Bay and examined them for external
health and contaminant-related liver conditions, including tumor precursors and
tumors. (See Section 5, Fish and Shellfish, for 2019 results.) Prior to the 2004
monitoring plan revisions, fish were also taken from Broad Sound, just to the north of
Boston Harbor in western Massachusetts Bay.
During the 1970s and 1980s, precancerous conditions and tumors were so prevalent
in Boston Harbor winter flounder that flounder health became a driving impetus for
the Boston Harbor Project. (See the 2018 outfall monitoring overview, Werme et al.
2019, for a discussion of the improved health of Boston Harbor winter flounder, one
of the environmental success stories of the Boston Harbor Project.) The concern
during the outfall planning and siting was that liver conditions observed in Boston
Harbor would increase in Massachusetts Bay.
Liver tumors and tumor precursors have not increased in Massachusetts Bay. Tumors
have never been observed in fish taken from the outfall site, and the incidence of
CHV, the most common tumor precursor, has decreased in those fish, as well as in
fish taken from Deer Island Flats, near the former MWRA Boston Harbor outfall
(Figure 7-3). 
Figure 7-3. Centrotubular hydropic vacuolation (CHV) incidence at Deer Island Flats and the
Massachusetts Bay outfall over time . Incidence at the outfall has remained well below the
Contingency Plan caution-level threshold of 44.9%. 
0
10
20
30
40
50
60
70
80
90
1986 1988 1990 1992 1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 2018 2020
Centrotubular Hydropic Vacuolation (percent) Deer Island Flats Outfall
Threshold 44.9%,
(Outfall results only)

55
MWRA proposed ending all winter flounder health assessments, but OMSAP
members felt that, because moderate levels of liver impairment persist in Boston
Harbor, some continued study was warranted. They agreed instead to end monitoring
of fish from off Nantasket Beach, which is just outside and to the south of Boston
Harbor, and from eastern Cape Cod Bay. Incidence of CHV has slowly declined over
time in fish from Nantasket Beach and has remained low throughout the course of the
monitoring program in fish from eastern Cape Cod Bay (see Figure 5-3 in Section 5,
Fish and Shellfish).

56 
References 
Blasco, D, Berard-Therriault, L and Vrieling, EG. 1996. Temporal and spatial
distribution of the ichthyotoxic dinoflagellate G yrodinium aureolum Hulburt in the
St. Lawrence, Canada. Journal of Plankton Research . 18: 1917-1930.
Charlestra L, Keay KE, Lambert MT. 2020. Assessing contaminant concentrations
and trends in Deer Island Treatment Plant effluent using survival analysis techniques.
Boston: Massachusetts Water Resources Authority. Report 2020-06. 47 p.
Ellis-Hibbett D. 2020. Technical survey of nitrogen removal alternatives for the Deer
Island Treatment Plant. Boston: Massachusetts Water Resources Authority. Report
2020-02. 45 p.
EPA. 1988. Boston Harbor wastewater conveyance system. Final Supplemental
Environmental Impact Statement (SEIS). Boston, Massachusetts. United States
Environmental Protection Agency Region I.
Jiang MS, Wallace GT, Zhou M, Libby S, Hunt CD. 2007. Summer formation of a
high-nutrient low-oxygen pool in Cape Cod Bay, USA. Journal of Geophysical
Research 112:C05006. 22 p.
Libby PS, Rex AC, Keay KE, Mickelson MJ. 2013. Alexandrium rapid response
study survey plan. Revision 1. Boston: Massachusetts Water Resources Authority.
Report 2013-06. 13 p.
Libby PS, Borkman DG, Geyer WR, Keller AA, Turner JT, Mickelson MJ, Oviatt
CA. 2009. Water column monitoring in Massachusetts Bay 1992-2007: focus on 2007
results. Boston: Massachusetts Water Resources Authority. Report 2009-04. 162 p.
Libby PS, Borkman DG, Geyer WR, Turner JT, Costa AS, Taylor DI, Wang J,
Codiga D. 2020. 2019 water column monitoring results. Boston: Massachusetts Water
Resources Authority. Report 2020-08. 60 p.
MWRA. 2001. Massachusetts Water Resources Authority Contingency Plan,
Revision 1. Boston: Massachusetts Water Resources Authority. Report 2001-ms-071.
47 p.
MWRA. 2010. Ambient monitoring plan for the Massachusetts Water Resources
Authority effluent outfall, Revision 2, July 2010. Boston: Massachusetts Water
Resources Authority. Report 2010-04. 107 p.

57
Moore MJ, McElroy AE, Geoghegan P, Siskey MR, Pembroke A. 2016. Flounder
monitoring report: 2015 results. Boston: Massachusetts Water Resources Authority.
Report 2016-05. 40 p.
Moore MJ, Nestler E, Rutecki DA. 2019. Flounder monitoring report: 2019 results.
Boston: Massachusetts Water Resources Authority. Report 2019-10. 21 p.
Nestler EC, Diaz RJ, Madray ME. 2020. Outfall benthic monitoring report: 2018
results. Boston: Massachusetts Water Resources Authority. Report 2020-10. 66 p.
Rutecki DA. Nestler EC, Diaz RJ. 2019 Boston Harbor benthic monitoring report.
Boston: Massachusetts Water Resources Authority. Report 2020-12. 68 p.
Taylor DI, Oviatt CA, Giblin AE, Tucker J, Diaz RJ, Keay K. 2020. Wastewater
input reductions revers historic hypereutrophication of Boston Harbor, USA. Ambio 
49:187–196.
Werme C, Rex AC, Hunt, C. 2012. Outfall monitoring overview background: 2012
update. Boston: Massachusetts Water Resources Authority. Report 2012-02. 59 p.
Werme C, Keay KE, Libby PS, Codiga DL, Taylor DI, Charlestra L, Carroll SR.
2019. 2018 outfall monitoring overview. Boston: Massachusetts Water Resources
Authority Report 2017–07. 53 p.

58 
List of Acronyms 
ASP Amnesic shellfish poisoning
cBOD Carbonaceous biochemical oxygen demand
CHV Centrotubular hydropic vacuolation
DDT Dichlorodiphenyltrichloroethane
DIF Deer Island Flats
DIN Dissolved inorganic nitrogen
DO Dissolved oxygen
ECCB Eastern Cape Cod Bay
EPA U.S. Environmental Protection Agency
FF Farfield
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
NF Nearfield
NOEC No observed effects concentration
NPDES National Pollutant Discharge Elimination System
OMSAP Outfall Monitoring Science Advisory Panel
OS Outfall site
OSI Organism sediment index
PAH Polycyclic aromatic hydrocarbon
PCB Polychlorinated biphenyl
PIAC Public Interest Advisory Committee
PSP Paralytic shellfish poisoning
RPD Redox potential discontinuity
SEIS Supplemental environmental impact statement
SPI Sediment-profile imagery
TN Total nitrogen

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