The state of Boston Harbor: mapping the harbor's recovery, 2002

Massachusetts Water Resources Authority · from the MWRA · 45 pages · 8.4 MB
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BOARD OF DIRECTORS 
Robert A. Durand
John J. Carroll
Kevin L. Cotter
Joseph C. Foti
Lucile P. Hicks
Joseph A. MacRitchie
Vincent G. Mannering
Donald A. Mitchell
Andrew M. Pappastergion
Marie T.Turner
Special thanks to retiring member Robert D. Spinney 
EXECUTIVE DIRECTOR 
Frederick A. Laskey
THE STATE OF BOSTON HARBOR
MAPPING THE HARBOR’S RECOVERY 
PREPARED UNDER THE DIRECTION OF 
Michael J. Hornbrook, Chief Operating Officer 
PREPARED BY 
Andrea C. Rex
David Wu
Kelly Coughlin
Maurice Hall
Kenneth E. Keay
David I.Taylor 
EDITED BY 
Sally Rege Carroll 
DESIGN & GRAPHICS BY: 
Rita Berkeley 
GEOGRAPHIC INFORMATION SYSTEM ANALYSES & MAPPING BY 
Suh Yuen Liang 
ACKNOWLEDGEMENTS 
Keary Berger, James Blake, Michael Bothner, Jeanine Boyle,
Marilyn Buchholtz ten Brink, Michael Delaney, Robert Diaz,
Eugene Gallagher, Barbara Hecker, Douglas Hersh, Carlton Hunt,
Roy Kropp, Lisa Lefkovitz,Wendy Leo, Joseph Lobuglio, Nancy Maciolek,
Michael Mickelson, Nicole O'Neill, Richard Signell, Kelly Slater, and
Christopher W u. 
TECHNICAL REPORT NO. 2002-09
D E C E M B E R 2 0 0 2

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Enterococcus bacteria at Harbor Beaches, 1996-2001
Association between bacteria counts and rainfall at harbor beaches
Contaminants in flounder fillet, 1993-2001
Contaminants in mussel tissue, 1991-2001
Contaminants in lobster meat, 1992-2001
Bacteria counts at the bay outfall site 
F I G U R E S
TA B L E S
Introduction
Part I - The Boston Harbor Project 
Boston Harbor Project Timeline 
Part II - Mapping the Harbor’s Recovery 
Water Quality
The Floor of the Harbor
Fish and Shellfish 
Part III - Boston Harbor's Tributary Rivers 
River Bacteria
River Clarity
River Algae and Chlorophyll 
Part IV - After The Outfall: Changes in the Harbor
and Bay 
Changes in Boston Harbor
What is the Future of the Harbor?
Massachusetts Bay Monitoring 
References
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Table of Contents 
Map of Boston Harbor
The proportion of wastewater receiving secondary treatment, 1990-2000
Solids in MWRA discharges, 1988-2000
Metals in MWRA discharges, 1989-2000
Change in locations of harbor contamination sources
Model of tidal mixing in Boston Harbor
Modeled dilution patterns of treatment plant discharges into Boston Harbor
1939 Report on coliform bacteria 
Enterococcus bacteria in Boston Harbor
Annual pattern of high bacteria counts at Boston Harbor beaches, 1987-2001
Water clarity in Boston Harbor (contour maps), 1993-2000
Ammonium levels at the previous harbor outfall sites, 1997-2000
Summer chlorophyll in Boston Harbor (contour maps), 1995-2000
Dissolved oxygen in Boston Harbor
Daily cycle of dissolved oxygen
Boston Harbor sediment types (contour map)
U.S.G.S. metals sampling locations in Boston Harbor
Lead decreases over time in Boston Harbor sediments
Sediment oxygen demand in Boston Harbor, 1992-2000
Sediment profile imaging sites and sampling locations
Boston Harbor sediment profile images
Oxygen penetration into harbor sediments (contour maps), 1989-2000
Prevalence of Ampelisca in Boston Harbor, 1989-2001
Abundance and diversity of animals on the harbor floor, 1990-1999
Boston Harbor fish and shellfish monitoring locations
Liver disease in winter flounder, 1984-2001
PCBs in lobster hepatopancreas (tomalley), 1992-2000
Spatial pattern of river bacteria in 2000
Patterns of river bacteria compared to phases of CSO control
Comparison of water clarity in the rivers and the harbor
Spatial trend in Charles River water clarity
Comparison of chlorophyll in the rivers and the harbor
Locations of harbor contamination sources after September 2000
Trends in bacteria at the previous harbor outfall sites
Water clarity at the previous harbor outfall sites
Decreased ammonium levels after the bay outfall opened
Sampling sites throughout Massachusetts Bay
Model predictions of effluent dilution compared to monitoring results
Satellite images of chlorophyll in the southern Gulf of Maine
Seasonal chlorophyll levels near the bay outfall, 1992-2001
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Nut Island
Headworks
C. September 2000
Discharge sent to
Mass. Bay through
9.5 mile outfall
Deer Island
Treatment
Plant
discharge
Nut Island
Treatment
Plant
discharges
Nut Island
Headworks
A. Before July 1998 B. July 1998-September 2000
Deer Island
Treatment
Plant
discharge 
decade of environmental monitoring data is
displayed in maps that show both dramatic
and subtle changes in Boston Harbor's water,
sediment, and living natural communities since the
Massachusetts Water Resources Authority (MWRA)
first began the Boston Harbor Project in 1986.
From 1986 to 1995, there were marked improve-
ments in effluent discharges after MWRA upgraded
disinfection and primary treatment and then added
secondary treatment. MWRA also increased enforce-
ment of pretreatment of industrial wastewater, which
significantly reduced the amounts of metals and other
pollutants being sent to the treatment plants.
It is important to understand the effects that the
major components of the Boston Harbor Project had
on pollutant inputs to the harbor.The maps on this
page illustrate how, for three time periods, MWRA
minimized the impacts of sewage by improving treat-
ment and changing the location of effluent discharges.
A. Before July 1998: Poorly treated wastewater was
discharged from the Deer Island and Nut Island
Treatment Plants. Sewage solids (sludge) were dis-
charged into the northern harbor after digestion and
disinfection, a practice that ended in 1991.The first
battery of secondary treatment of sewage, which more
effectively removes solids and contaminants than pri-
mary treatment, was in place at Deer Island
Treatment Plant in 1997, and in 1998 up to 65% of
sewage was undergoing secondary treatment.
B. July 1998 to September 2000: With the comple-
tion of the inter-island tunnel from Nut Island to Deer
Island, South System sewage was sent to Deer Island
for secondary treatment, and the Nut Island Treatment
Plant was closed, ending direct discharges to the
southern harbor. Another battery of secondary treat-
ment was in place by September 2000, when 85% of
the sewage was receiving secondary treatment.
C. After September 2000: The third and final bat-
tery of secondary treatment is in place.The new outfall
transports cleaner effluent out of the harbor complete-
ly and into Massachusetts Bay for greater dilution.
Now, no treatment plants are discharging directly into
the harbor.
So far, data gathered on the quality of sediments,
water, and sea life in Boston Harbor and Mass-
achusetts Bay show that the new outfall has been func-
tioning as anticipated–providing rapid dilution to the
effluent–with no significant adverse impacts. Harbor
data show even further improvements as nutrients
decrease to levels more typical of a natural estuary.
Now that effluent discharges have moved from the
harbor to the bay, a significant fraction of remaining
pollution entering the harbor comes from its tributary
rivers. Although there have been some improvements
in river water quality, including lower bacteria levels in
the Charles River, other problems, like eutrophication
(high levels of nutrients), are more difficult to control.
Rivers, runoff, and other
“non-point” sources used to be
relatively minor contributors
of contamination to the har-
bor. In the absence of treat-
ment plant discharges, these
sources now constitute the
major inputs to the harbor,
and must in turn be addressed
to continue the “Boston
Harbor clean-up”. 
Go back to the Table of Contents OR Go to the next page 1 
A 
Introduction

his “State of Boston Harbor: Mapping the
Harbor’s Recovery” report arrives as MWRA
marks the completion of the Boston Harbor
Project. This report illustrates changes in the
waters, sediments, and living natural communi-
ties of this urban marine ecosystem, which is
recovering from centuries of receiving Greater
Boston’s sewage.
In 1985, a federal court order set an ambi-
tious schedule for the newly formed MWRA to
plan and construct new sewage treatment facili-
ties. These facilities would end the discharge of
untreated and partially treated sewage to
Boston Harbor. This undertaking, the “Boston
Harbor Project,” included four major construc-
tion projects: 
FACILITIES AT FORE RIVER SHIPYARD IN QUINCY 
to process sewage sludge into commercial
fertilizer pellets, ending the discharge of sludge
into the harbor. 
A NEW SECONDARY WASTEWATER
TREATMENT FACILITY, the new Deer Island
Treatment Plant (DITP), to replace the failing
and undersized primary treatment plants at
Deer Island and Nut Island (NITP). 
A TUNNEL FROM NUT ISLAND TO DITP to trans-
port South System sewage to DITP for sec-
ondary treatment, enabling flows from throughout
MWRA’s service area to receive secondary treat-
ment and greatly lessening pollution to the harbor. 
AN OUTFALL-DIFFUSER SYSTEM to discharge
treated effluent 9.5 miles offshore into
Massachusetts Bay, increasing dilution and mini-
mizing potential environmental impacts in the bay.
In addition to taking on these major construc-
tion projects, MWRA is addressing the problem
of combined sewer overflows (CSOs), which dis-
charge a mixture of stormwater runoff and
sewage directly into the harbor during heavy
rainstorms. In the 1980s, 88 CSOs in the harbor
and its tributary rivers discharged an estimated
3.3 billion gallons of partially treated or raw
combined sewage annually. By 2008, MWRA’s
CSO Plan proposes to close 36 CSOs, reduce
annual discharges to 0.4 billion gallons, and pro-
vide treatment to 95% of those discharges from
remaining CSOs that are necessary as safety
valves to prevent sewage flooding and backups
into streets and homes. 
1
2
3
4 Combined Sewer Overflows (CSOs)
Boston, Cambridge, Chelsea, and Somerville have
combined systems that carry sewage and
stormwater runoff in the same pipe. During heavy
rainstorms, the volume of flow is sometimes
more than the pipes can carry, causing mixed
stormwater and sewage discharges from outfall
pipes into Boston Harbor and its tributary rivers.
Sanitary Sewer Overflows
Sanitary (not combinrd) sewer systems are not
designed to carry stormwater runoff. Heavy rains
leaking into sewer pipes can cause these systems
to overflow into a stream or other body of water.
Stormwater
Drainage systems collect rainwater runoff from
streets and channel it to a nearby river or harbor.
Unfortunately, storm drainage is frequently
contaminated with sewage from leaking pipes or
illegal sewer connections from buildings. Animal
waste on the streets also contaminates stormwa-
ter, as does car exhaust, street dirt, and litter.
The Boston Harbor Project 
FROM 1986 TO 2000 THE BOSTON HARBOR PROJECT GRADUALLY
REDUCED TREATMENT PLANT DISCHARGES TO THE HARBOR 
T 
2 
PA RT O N E

Milton
Quincy
Hingham
Hull
Winthrop 
Dorchester Bay 
Moon Island 
Fort
Point
Channel
Massachusetts Bay
Northern Harbor
Deer Island Flats 
President Roads 
Long Island 
Mystic River
Charles River
Inner Harbor
Winthrop
Bay
Quincy Bay Hingham Bay 
Fore River
Hull Bay Southern Harbor r
Nantasket Roads 
River r 
Chelsea Revere
Everett 
Somerville 
NUT ISLAND HEADWORKS S S 
(FORMER SITE OF NUT ISLAND (F ( (F 
NT PLANT) 
INTER-ISLAND 
TUNNEL 
CLOSED NITP 
OUTFALLS 
CLOSED DITP 
OUTFALLS 
CLOSED NITP 
SLUDGE OUTFALL LL 
OUTFALL TUNNEL 
R ISLAND R 
ATMENT PLANT AT TREAT TREAT 
DIFFUSER 
9.5 MILES 
LOGAN 
AIRPORT 
SOMERVILL 
MARGINAL 
TREATMEN 
FACILITY 
PRISON S 
FOX 
CSO 
FACIL 
FIGURE I-1. MAP OF BOSTON HARBOR
showing major geographic features and
some MWRA facilities.

200
150
100
50
0
00 99 98 97 95 96 94 93 92 91 90 89 88
Sludge
Nut Island
Deer Island
SOLIDS DISCHARGES
Tons per day 
July 1985 Following the
passage of its enabling act
in 1984, MWRA assumed
responsibility for the
Metropolitan District
Commission’s water and
sewer systems. 
May 1986 Judge A.
David Mazzone ordered
a 13-year schedule to
the construct a new
Deer Island Treatment
Plant (DITP) and related
facilities. 
December 1988 Interim
repairs and upgrades to
the old DITP included
the provision of a more
reliable disinfection sys-
tem. Also, sewage scum
was landfilled instead of
being discharged into the
harbor. 
1989-1998 Pumping
capacity increased from
about 700 million gallons
per day (mgd) in 1989 to
900 mgd in 1998, sending
more wastewater for
treatment and reducing
CSO discharges. 
December 1991 Sludge
discharges into the
harbor from the old
Deer Island and Nut
Island treatment plants
ended. Sludge-to-fertilizer
pelletizing began at the
new Fore River plant. 
January 1995 First
components of
improved primary treat-
ment put into service at
the new DITP. 
1992 Solids discharged
to the harbor
decreased by 40 dry
tons per day.
Decrease in bio-
chemical oxygen
demand (BOD), nitro-
gen (N), phosphorous
(P), and bacteria in the
harbor. 
1995 Drop in total
solids discharged, as well
as further decreases in
bacteria, BOD, N, and P. 
1988 Scum
removal left less
oil, grease, and
floating matter in
effluent. Better
disinfection
resulted in fewer
bacteria. 
project milestones effects on discharges 
0
100
200
300
400
500
00 99 98 97 96 95 94 93 92 91 90
Secondary-treated Flows
Primary-treated Flows
Million gallons per day
PRIMARY AND SECONDARY TREATED FLOWS
FIGURE I-2.THE PROPOR-
TION OF WASTEWATER
RECEIVING SECONDARY
TREATMENT (1990-2000)
has climbed since the
phasing in of secondary
treatment started in 1997.
Secondary treatment
increases the removal of
solids and toxic
pollutants.
FIGURE I-3. SOLIDS IN
MWRA DISCHARGES
(1988-2000) have fallen
steadily since the beginning
of the Boston Harbor
Project. Sludge discharges to
the harbor ended in
December 1991, and sec-
ondary treatment at DITP
began in 1997, resulting in an
80% decrease in solids by
2000.
boston harbor project timeline 1985-2001 
4 
Bunker demolition
at Fort Dawes,
Deer Island
THE BOSTON HARBOR PROJECT

the 1995 State of Boston Harbor report
or visit our web site at
www.mwra.com/sewer/html/
sewditp.htm).
One of the earliest improvements at
the old Deer Island plant was the repair
of the disinfection system. Once repairs
were completed, the number of days per
year that the discharge had high bacteria
counts dropped from 130 days in 1988
to 4 days by 2000. By comparison, other
results due to better primary and second-
ary treatment have been relatively grad-
ual: Figure I-2 shows how the proportion
of sewage undergoing secondary treat-
ment, which removes at least 85% of
solids (primary treatment removes about
half), increased after 1997. Therefore,
significant drops in solids discharges
(Figure I-3) correspond to both the end
of sludge discharges to the harbor in
1991 and the beginning of secondary
treatment.
Effluent toxic metals decreased early
on in the Boston Harbor Project (Figure
I-4), largely because of MWRA’s
increased enforcement of industrial
requirements to pre-treat wastewater,
preventing metals and other toxic
pollutants from entering the
sewage system. Since metals
attach to solids, increased
solids removal further
decreased effluent metals.
ischarges of solids, toxic chemicals, and
bacteria decreased as MWRA improved
sewage treatment.
The major milestones of the Boston Harbor
Project and the resulting effects on wastewater
discharges are shown on the timeline
above. Increased pumping, the end
of scum and sludge discharges,
upgraded disinfection, and bet-
ter primary and secondary
treatment resulted in a
cleaner harbor by the year
2000. (For further expla-
nation of how the treat-
ment plant operates, see 
FIGURE I-4. METALS IN
MWRA DISCHARGES
(1989-2000) have dropped
dramatically, largely because
of effective industry source
reduction programs, an
outreach program aimed at
residential customers, and
the effects of secondary
treatment. Now, most
remaining metals are from
household sources. 
D 
August 1997 Startup of
Battery A, the first of
three batteries of
secondary treatment at
DITP. 
March 1998 Battery B
of secondary treatment
started up at DITP. 
July 1998 Inter-island
tunnel completed. South
System flows transferred
to DITP from the Nut
Island Treatment Plant
(NITP), allowing most
flow to receive second-
ary treatment. NITP was
later demolished, and
replaced by a headworks
facility and a park. 
September 2000 Start-
up of new ocean outfall
diffuser; effluent now
discharged through a
9.5-mile outfall into
Massachusetts Bay. 
1997 The beginning of sec-
ondary treatment marked a
dramatic decrease in BOD
and continuing declines of
bacteria, solids, N, and P . 
1998 End of effluent
discharges from NITP to
the southern harbor.
Continued declines in
TSS, BOD, N, P, and
bacteria. 
2000 End of effluent
discharges to Boston
Harbor; effluent receives
much better dilution in
Massachusetts Bay. 
March 2001 Last bat-
tery of secondary treat-
ment placed in operation
at DITP. 
0
200
400
600
800
1000
1200
00 99 98 97 96 95 94 93 92 91 90 89
Silver
Nickel
Chromium
Lead
Copper
Zinc
METALS DISCHARGES
Average pounds per day discharged 
5 
2001 Treatment
optimized at DITP.
Discharge consistently
meets effluent quality
standards. 
Multiple ports on diffuser heads
help dilute the effluent dis-
charged into Massachusetts Bay. 
Back to Table of Contents OR Go to Part Two-Mapping the Harbor's Recovery

Deer Island
Treatment
Plant
Nut Island
Treatment
Plant
A. Before July 1998
Deer Island
Treatment
Plant
Nut Island
Headworks
B. July 1998-September 2000 
6 MAPPING THE HARBOR’S RECOVERY 
I 
n this section, we report on the health of Boston
Harbor’s marine environment over the past decade as
the Boston Harbor Project progressed. Monitoring
data help answer the questions of greatest public con-
cern: Is it safe to swim and to eat shellfish? Is the
ecosystem healthy, and are aesthetics protected?
Changes in bacteria, water clarity, nutrients, dissolved
oxygen, toxic contaminants, and other indicators
provide a picture of how the harbor is recovering.
To compare “before” and “after” conditions, we
chose July 1998 as a turning point, the date the Nut
Island Treatment Plant (NITP) was decommissioned
and its flow re-routed to the Deer Island Treatment
Plant (DITP) for secondary treatment. After July
1998, most of the wastewater discharged to the har-
bor received secondary treatment, except during the
highest flow periods caused by rainstorms.This point
also marks when MWRA discharges to the southern
harbor ended (Figure II-1).
By September 2000, virtually all the major mile-
stones of the Boston Harbor Project were complete,
except for the new Massachusetts Bay outfall and
one remaining battery of secondary treatment. For
many data analyses in this section,“before” is the
period up to July 1998, and “after” is the period July
1998-September 2000, representing the near-comple-
tion of the Boston Harbor Project.
Part II is organized into three sections, focusing on
the harbor’s water, sediments, and fish and shellfish.
The health of each of these ecosystem “compart-
ments” is closely intertwined with the others through
the physical movement of water and sediments, and
biological interactions. 
FIGURE II-1. CHANGE IN LOCATIONS OF HARBOR CONTAMINATION SOURCES. A: BEFORE JULY 1998. The
major wastewater sources in Boston Harbor were the Deer and Nut Island Treatment Plants (big arrows). Rivers,
CSOs, and runoff (indicated by small arrows) contributed significant but smaller amounts of contaminants.
B: JULY 1998-SEPTEMBER 2000. NITP closed in July 1998 and all flows were transferred to the new DITP, which
became the harbor’s main point source of treated wastewater.Average discharges from Deer Island increased from
250 to 350 million gallons per day. Rivers, CSOs, and runoff remained.
Mapping the Harbor’s Recovery 
Inside the inter-island
tunnel that carries
wastewater from Nut
Island to Deer Island
PA RT T W O
THE STATE OF BOSTON HARBOR BEFORE THE BAY OUTFALL STARTED UP IN SEPTEMBER 2000

FIGURE II-2. MODEL OF
TIDAL MIXING IN
BOSTON HARBOR.
R. Signell of the U.S.
Geological
Survey used a
computer model
to investigate
tidal flushing of
Boston Harbor.
A: SHOWS THE
HARBOR AT
MODEL START
TIME. Boston
Harbor water is indicated
in red, Massachusetts Bay
water in blue.
B:THE EFFECT OF TIDAL FLUSHING AFTER 3.6 DAYS, OR 7 TIDAL CYCLES.
Most of the water in the harbor has mixed with bay water. However, the inner harbor and the shoreline remain
relatively unmixed.The shoreline takes longer to flush than the deep channels at the harbor’s mouth. For a movie
of this mixing process, go to the web at http://woodshole.er.usgs.gov/operations/modeling/movies/fli/boston.html. 
he harbor’s patterns of pollution depend on
the movement of water within the harbor–its
physical oceanography. The harbor is relative-
ly shallow with an average depth of about 15 feet,
and is well flushed by strong tides. The average resi-
dence time of water in Boston Harbor is short;
Massachusetts Bay and river waters replace all the
harbor water in five to seven days. When MWRA
effluent was discharged into the harbor, traces were
detected six miles out in the bay.
Computer modeling by the United States
Geological Survey (USGS) shows that the deep
channels at the mouth of the harbor are most rapid-
ly flushed, while the Inner Harbor and shoreline
areas are flushed more slowly (Figure II-2). As solids
and attached pollutants can accumulate in calmer
areas, Boston Harbor shoreline embayments and the
Inner Harbor tend to be most affected by pollution.
Early on, engineers did well to site the old DITP
and NITP outfalls near deep shipping channels at
the mouth of the harbor where strong tidal currents
would dilute and flush waste out to the bay, lessen-
ing the impact. Figure II-3 shows what happened to
wastewater discharged from DITP and NITP
through the former harbor outfalls. DITP dis-
charges were flushed offshore and diluted relatively
rapidly, but a significant portion of the discharge
flowed toward the Inner Harbor on the incoming
tide. NITP discharges were rapidly carried out
Nantasket Roads, but a portion of the discharge,
more poorly diluted, entered Hingham Bay. 
7 MAPPING THE HARBOR’S RECOVERY:WATER QUALITY
water quality
FIGURE II-3. MODELED DILUTION PATTERNS OF
TREATMENT PLANT DISCHARGES INTO
BOSTON HARBOR. In this computer model, yellow
and red areas represent less dilution, green and blue
are more diluted. Wastewater from DITP was swept
northeast, with some of the discharge returning on
the incoming tide. In the southern harbor, waste-
water from NITP was not as well diluted as from
DITP (Signell, 1992 USGS).
PHYSICAL OCEANOGRAPHY OF THE HARBOR TIDAL CURRENTS CAN MOVE POLLUTION FAR FROM ITS SOURCES 
T 
A. Model
Start Time=0
B. Model
Time=3.6 Days 
President Roads
Nantasket Roads
Inner
Harbor
Quincy
Bay Hingham
Bay 
DITP
discharge
site
NITP
discharge
site
1992

ntreated or poorly treated sewage can carry
disease-causing microorganisms (pathogens):
bacteria, viruses, and parasites. These
pathogens can threaten public health if sewage con-
taminates swimming areas or shellfish. Indicator
bacteria like
Enterococcus and fecal coliform are
found in sewage. If high numbers of these indicator
bacteria are present in the water, there is a risk of
disease. Historically, poorly treated wastewater and
discharges of sewage solids, or sludge, were signifi-
cant sources of bacteria to the harbor, documented
as far back as the 1930s (Figure II-4).
Figure II-5 compares the patterns of
Enterococcus
in the harbor, averaged over time.
Enterococcus is
the measure of recreational marine water quality
recommended by the U.S. Environmental Protection
Agency (EPA). From 1987 to 1998, bacteria counts
were high around Deer Island, Nut Island, and the
sludge outfalls; they were also high in the Inner
Harbor, along the shoreline, and in the rivers.
From July 1998 to August 2000, (when all
wastewater was receiving secondary treatment
and updated disinfection at Deer Island and
being discharged to the harbor), bacterial
water quality improved so much that most of
the harbor met EPA’s most stringent swim-
ming criteria.
Sources of bacterial pollution to the harbor
are now local: stormwater, CSOs, boats, ani-
mals, and birds all potentially contribute to
the problem. These local sources of pollution primari-
ly affect the harbor’s shoreline and beaches, the least
well-flushed areas of the harbor.“Hot spots” of bacte-
ria persist at the mouth of the Neponset River and
southern Dorchester Bay; in the Inner Harbor, espe-
cially Fort Point Channel; the mouth of the Mystic
River, and along Wollaston Beach. Beach water quali-
ty is discussed in more detail on pages 10 and 11. 
BACTERIAL POLLUTION IN THE HARBOR 
U 
INDICATOR BACTERIA SHOW DECREASE IN PUBLIC HEALTH RISK
FIGURE II-4. A 1939 REPORT ON COLIFORM
BACTERIA shows levels in excess of 1,000 colonies
per 100 ml over large portions of the harbor. Areas
over 3,000 colonies per 100 ml were recorded around
Deer Island, Moon Island, and parts of Quincy Bay,
caused by the discharges of untreated sewage in these
areas (Commonwealth of Massachusetts, 1939). 
8 
C O P Y R I G H T D E N N I S K U N K E L M I C R O S C O P Y , I N C . 
Enterococcus faecium magnified 2, 345 times
MAPPING THE HARBOR’S RECOVERY:WATER QUALITY

DITP outfalls Fort
Point
Channel
Mystic River 
A. 1987-1998 
Inner Harbor 
Inner Harbor 
Neponset River 
NITP outfalls 
Enterococcus 
Colonies/100ml
0-5
5-35
35-104
104-158
158-275
275-500
>500
no data
outfall
closed outfall
DITP outfalls
Closed
NITP outfalls
B. 1998-2000 
Fort
Point
Channel
Neponset River 
FIGURE II-5. ENTEROCOCCUS BACTERIA IN BOSTON HARBOR. Enterococcus is the indicator recommended by EPA for monitoring
the quality of marine recreational waters.The maps show contours generated from average Enterococcus counts collected during
MWRA’s harbor surveys (since 1989) and from MDC’s beach monitoring (since 1987).The contours are drawn at the detection limit (5
colonies/100 ml), and at the EPA guidelines for a designated bathing beach (35 colonies/100 ml), moderate use (158 colonies/100 ml),
light use (276 colonies per 100 ml) and infrequent recreational use (500 colonies/100ml).
A: 1987-1998. Data averaged from 1987-1998 show that Boston Harbor as a whole was generally within swimming standards.The con-
tour plots show a pattern of elevated bacteria levels around the treatment plant outfalls. Most of these high counts were in the early
part of this period. Bacteria were elevated at the shoreline, in embayments, and the Inner Harbor.The highest bacteria levels were in the
rivers and in Fort Point Channel.
B: 1998-2000. Data averaged from July1998-August 2000 show the cumulative impact of the Boston Harbor Project and early CSO con-
trol projects, even before the new ocean outfall came on-line in 2000.The addition of south system flows to DITP discharges was
accomplished without increasing bacterial contamination around DITP outfalls. Now, almost all the outer harbor is at or below the
detection limit or within the swimming standard. However, problems still remain along the shoreline, especially in the rivers. 
9 MAPPING THE HARBOR’S RECOVERY:WATER QUALITY

eaches in Boston Harbor are generally swimma-
ble.Table II-1 shows that bacteria counts typical-
ly are well within standards. However, swimming
advisories are still posted at harbor beaches each sum-
mer, with some beaches posted more frequently than
others.There are two parts of the swimming standard:
the water should have an average (geometric mean) Enterococcus count of less than 35 colonies/100 ml,
and there should be no more than 104
Enterococcus
colonies/100ml in a single sample.
High bacteria counts, when they do occur, may
result from a variety of different sources, which can
include CSO discharges, storm drain and street runoff,
illegal boat discharges, and even bird waste.
The causes of variations in water quality are not
obvious. For example, Carson Beach in
South Boston is the second cleanest beach in
the harbor, but has seven CSO outfalls and
storm drains. On the other hand,Wollaston
Beach in Quincy—one of the most contami-
nated beaches in the harbor—has no CSO or
other sewage discharges but has eight storm
drains which discharge along its shoreline.
At beaches affected by CSO discharges and
storm drains, rainfall has a major impact on beach
water quality. Heavy rains are often followed by high
bacteria counts. However, high counts during dry
weather also occur at all beaches. In fact, most elevat-
ed bacteria counts occur in dry weather or light rain,
as is shown in Table II-2 (facing page).The proportion
of high counts to low counts in dry weather, though,
remains low overall.The sources of dry weather con-
tamination are not completely understood, but likely
include animal waste and cross-connections of sewer
pipes into storm drains.
Figure II-6 shows the percent of bacterial samples
failing to meet the swimming standard for
Enterococcus for each swimming season since 1987.
Water quality is generally good, but there is no clear
trend, with year to year variations at each beach.The
effect of rainfall is complicated.Tenean Beach, for
example, shows an increased frequency of high
counts during rainy summers, but Wollaston
does not.
While posting frequencies remain variable,
efforts by MWRA and communities have sig-
nificantly reduced the volume of untreated
CSO discharges to the harbor since the late
1980s. Implementation of MWRA’s CSO
Control Plan closed its CSO treatment facility near
Constitution Beach, eliminated CSO discharges to the
Neponset River, and will eliminate the remaining CSOs
in South Dorchester Bay (near Tenean and Malibu
Beach).With community input, MWRA is developing
the CSO plan for North Dorchester Bay (Carson
Beach) to determine how best to control CSOs and
protect beaches there.
Treatment plant discharges and much of the com-
bined sewage in the harbor have been eliminated,
revealing the importance of other sources of coastline
contamination. Identifying and eliminating cross-con-
nections, controlling CSO, and maintaining local storm
and sewer systems will be essential to realizing the full
benefits of the Boston Harbor project. 
BEACHES 
B 
HARBOR BEACHES ARE SWIMMABLE MOST OF THE TIME. WATER QUALITY VARIATIONS REFLECT A COMPLEX URBAN COASTLINE. 
10 MAPPING THE HARBOR’S RECOVERY:WATER QUALITY 
The L-Street
Brownies
swim in the
harbor even
in winter 
Pleasure Bay
Carson
Constitution
Short
Winthrop
Tenean
Malibu
Wollaston
4
5
6
9
9
11
12
13
95%
94%
92%
92%
96%
86%
96%
87% 
TABLE II-1. ENTEROCOCCUS BACTERIA AT
HARBOR BEACHES, 1996-2001.

WINTHROP W 
SHORT S 
CONSTITUTION CONSTITUTI 
PLEASURE 
BAY 
CARSON 
MALIBU 
NEAN TEN 
WOLLASTON WO 
30 
20 
10 
0 
89 91 99 0 01 
Malibu lib 
30 
20 
10 
0 
87 89 91 9 99 01 
Pleasure Bay 
30 
20 
10 
0 
Wollaston 
87 89 91 93 95 97 97 99 99 01 
30 
20 
10 
87 89 91 93 95 97 99 01 01 
Carso Carson 
30 
20 
10 
0 
Ten 
87 89 91 93 95 97 99 01 
12 
8 
4 4 
0 nches in 
87 89 91 93 95 97 99 01 
Summer Rainfall Summer Rai 
87 87 91 93 95 97 99 01 
Short 
50 
0 
0 
20 
10 
0 
percent of samples failing ercent of s percent of samples failing percent of samples failing percent of samples failing percent of samples failing 
30 
20 
10 
Winthrop 
01 
FIGURE II-6. ANNUAL PATTERN OF HIGH BACTERIA 
COUNTS AT BOSTON HARBOR BEACHES, 1987-2001. The 
percent of samples failing to meet the Enterococcus limit of 104 
past 13 years there has been no clear trend over time, even as 
the Boston Harbor Project remediated high bacteria counts near 
sewage and sludge outfalls. Shoreline sources are the dominant 
cause of contamination at beaches. 
# of samples 
meeting i 
standards 
g
d d 
# of samples 
failing f ili 
standards 
g
d 
Total 
% failing 
1,829 
99 
1,928 
5% 
1,616 
161 
1,777 
9% 
386 
191 
577 
33% 
3,821 
451 
4,282 
11% 
TABLE II-2. ASSOCIATION BETWEEN BACTERIA COUNTS AND 
RAINFALL AT HARBOR BEACHES. Enterococcus samples were collected 
daily monitoring between 1996 and 2000. “ 
above the single sample limit of 104 colonies/100 ml. CSOs generally do 
percent of samples failing percent of samples failing 
30 30 
20 
10 
0 
97 99 01 
Constitution 
11

ater clarity is one of the factors that determine whether people swim in a body of water like Boston
Harbor. It also determines how much light reaches the plants in the water. These plants, which
include algae and seagrasses, are important to the ecology of the harbor.
Measurements of clarity in the harbor (and anecdotal observations by the public) indicate
that water clarity has improved since 1993. One of the measurements that has shown this
improvement is Secchi depth. This is the depth at which a white disk, a Secchi disk, lowered
into the water is no longer visible.
Water clarity shows a west-to-east increasing gradient across the harbor. This can be seen
in Figure II-7. Water is more turbid toward the rivers and shallow margins of the harbor, and
clearer (deeper Secchi depths) toward the mouth of the harbor and bay. Water in Dorchester
Bay is naturally turbid, because it is a shallow depositional area for sediments carried down
by the Neponset River. Figure II-7 compares water clarity across the harbor during the peri-
ods 1993-1998 and 1998-2000. Water clarity improved off NITP and in Nantasket Roads after 1998. 
DITP outfalls
A. 1993-1998 
Neponset
River
Dorchester
Bay 
NITP
outfalls Nantasket Roads
Hull Bay 
Secchi Depth (meters)
0-2
2-3
>3
no data
outfall
closed outfall 
Inner Harbor 
FIGURE II-7.WATER CLARITY IN
BOSTON HARBOR. Water clarity
showed noticeable improvements after
South System flows were transferred
to DITP for secondary treatment in
July 1998.
A: BEFORE. Up to July 1998, Secchi
depths were generally >2 meters (6.6
feet) over most of the harbor, but were
noticeably shallower around the Nut
Island outfalls and in Dorchester Bay.
B:AFTER the closing of NITP in July
1998, Secchi depths increased by more
than a meter near the old NITP out-
falls. In other parts of the South
Harbor, the increase in clarity was
smaller, ranging from 0.2 to 0.6 meters
(8 inches-2 feet).Water clarity off DITP
showed no decrease, despite the added
flows from the South System; second-
ary treatment increased solids removal,
compensating for the increased flows.
WATER CLARITY 
W 
WATER CLARITY INCREASED IN SOME PARTS OF THE HARBOR 
A Secchi disk is used to measure
water clarity in Boston Harbor. 
N A D I N E S M O S K E 
12 MAPPING THE HARBOR’S RECOVERY:WATER QUALITY 
Neponset
River 
DITP outfalls 
Nantasket Roads 
Closed
NITP
outfalls 
Hull Bay
Inner Harbor
Dorchester
Bay 
B. 1998-2000

utrients such as nitrogen and phosphorus are
familiar as the
active ingredi-
ents in lawn and
agricultural fertil-
izers. In marine
environments
such as Boston
Harbor, excessive
amounts of nutri-
ents—especially
nitrogen—can stimulate
the overgrowth of phytoplankton and seaweed.
Ammonium is the form of nitrogen that most stimu-
lates this overgrowth.
Figure II-8 shows the changes in ammonium con-
centrations at the former Deer Island and Nut Island
outfalls. Note the very large decrease in ammonium
at the NITP outfall site after discharges from NITP
ended (II-8B). Now, ammonium at this site shows a
typical, low seasonal cycle seen in healthy estuaries.
Ammonium increased at the DITP outfalls after
the south system flows were added to the discharge;
this was expected. The increase was not as great as
the decrease at Nut Island because of the greater
dilution of wastewater near Deer Island. After the
Massachusetts Bay outfall went on-line in September
2000, ammonium in both the north-
ern and the southern harbor
dropped to a more pristine level. 
N 
FIGURE II-8. AMMONIUM LEVELS AT THE PREVIOUS HARBOR OUTFALL SITES, 1997-2000.
A: DEER ISLAND OUTFALL SITE. Before July 1998, measurements around the two outfalls sometimes reached
very high levels, up to 100 micromoles per liter. Healthy ammonium values in estuaries are typically less than 5
micromoles per liter. After July 1998, ammonium levels around Deer Island increased.
B: NUT ISLAND OUTFALL SITE. Ammonium levels around Nut Island dropped to nearly zero after MWRA divert-
ed flows to DITP.Ammonium levels also decreased elsewhere in the southern harbor.There was a dramatic drop at
the DITP outfalls in late 2000 after the new outfall came into use (discussed further in part IV of this report). Excess nutrients can cause the overgrowth
of algae like this microscopic diatom. 
13 MAPPING THE HARBOR’S RECOVERY:WATER QUALITY 
NUTRIENTS
NUTRIENT CONCENTRATIONS HAVE
DECREASED 
Deer Island
Treatment
Plant
Nut Island
Headworks
since 1998 
80
100
120
140 
M B. AMM M 
liter

14 MAPPING THE HARBOR’S RECOVERY:WATER QUALITY 
s expected, one of the changes we found was
a decrease in the amount of microscopic algae
(phytoplankton) in the water. Figure II-9 com-
pares concentrations of chlorophyll across the harbor
before and after NITP flows were transfered to DITP
for secondary treatment. Chlorophyll, a photosynthet-
ic pigment in algae cells, is used to measure quanti-
ties of algae. The amounts of chlorophyll in the water
decrease away from the shoreline toward the bay.
After harbor discharges from NITP ended, chloro-
phyll in the South Harbor decreased to
more natural levels.
The North Harbor showed only a
small increase in chlorophyll con-
fined to the region near Deer
Island. Overgrowth of algae was
offset by the greater dilution of
effluent at this site. The outer North
Harbor is the region where we expect to see the
largest decreases in algae in the years to come. 
Seagrasses: Can the nurseries
of the harbor recover?
Dense meadows of seagrass are characteristic of
pristine, shallow depositional environments in
New England. A century ago, seagrass meadows
covered hundreds of acres of subtidal flats of
Boston Harbor. Important nursery areas for
young fish and shellfish, these meadows had all but
vanished by the late 1980s, victims of turbid water,
viral diseases, and excessive nutrients which pro-
mote the growth of algae on seagrass leaves.
Boston Harbor now supports only small areas of
seagrasses in Hingham Bay and in the North
Harbor near Logan Airport. Until recently, nutri-
ent concentrations in the harbor have been very
high, and the water in most areas has not been
clear enough for seagrasses.With the reduction in
nutrients in the water and the increase in clarity,
especially in the South Harbor, we might expect to
see recolonization of the harbor floor by these
important habitats in the years to come.
CHLOROPHYLL & ALGAE ALGAE HAVE DECREASED TO MORE NATURAL LEVELS 
A 
N A D I N E S M O S K E
R O B E R T M I C H E L S O N 
A close-up of tiny
animals on blades
of seagrass.
Dave Kaplan from MWRA's Deer Island
laboratory samples water in the harbor. 
T R A C Y V I L L A R E A L

Quincy Bay
Hingham Bay
Inner
Harbor 
DITP outfalls
Chlorophyll (ug/L)
<6
6-7
7-9
>9
no data
outfall
closed outfall
NITP outfalls 
Neponset
River 
A. 1995-1998
DITP outfalls 
Neponset
River
Quincy Bay
Hingham Bay
Inner
Harbor 
Closed NITP outfalls
B. 1998-2000
DITP outfalls
FIGURE II-9: SUMMER CHLOROPHYLL IN BOSTON
HARBOR. Changes in the amounts of algae in the harbor
have been seen since 1995.
A: AUGUST 1995-JULY 8,1998. While both DITP and
NITP were discharging, chlorophyll had a west-to-east
decreasing gradient, with the highest levels in Quincy Bay
and at the mouth of the Neponset River.
B: JULY 9, 1998-AUGUST 2000. With the transfer of South
System flows to DITP, the shape of chlorophyll contours
shifted subtly, with lower chlorophyll levels in the southern
harbor and a small, localized increase in chlorophyll at the
outer North Harbor. 
15 
J O S E P H I N G O L D S B Y 
MAPPING THE HARBOR’S RECOVERY:WATER QUALITY 
Mouth of the Neponset River

ne of the early perceptions about the effects of
pollution in Boston Harbor was that dis-
solved oxygen (DO) in the water was too low.
We now know that, except for a few isolated locations,
DO levels in the harbor were high enough to support
healthy marine life even before the Boston Harbor
Project began.This change in perspective is not only
based on more monitoring data, but also on new stud-
ies by the EPA showing that DO requirements for
marine life are actually lower than previously thought.
DO levels in Boston Harbor have benefited from
the harbor being so well-mixed and well-flushed.
MWRA’s monitoring has revealed little change in DO
concentrations in the harbor’s waters over the past
10 years. Figure II-10 illustrates Boston Harbor’s
summer pattern of dissolved oxygen, which is high
even at the end of the summer, when DO is typically
at its lowest. DO concentrations increase with dis-
tance from the shoreline. The lowest levels are in the
Inner Harbor and the mouths of rivers. Figure II-11
shows data from a moored instrument in the Inner
Harbor, illustrating the daily pattern of DO. 
DISSOLVED OXYGEN
DISSOLVED OXYGEN IN THE HARBOR REMAINS AT HEALTHY LEVELS 
O 
M a s s a c h u s e t t s w a t e r quality stan-
dards for dissolved oxygen in marine waters are 5 mil-
ligrams per liter (mg/l) for class SB, and 6 mg/l for class
SA, the same as for fresh water. EPA’s new recommend-
ed marine dissolved oxygen standard (at present appli-
cable only from Cape Cod south to Cape Hatteras) is
an average of 4.8 milligrams per liter, with a minimum of
2.3 milligrams per liter.
Most of Boston Harbor is Class SB; parts of
Dorchester and Quincy bays are SA.
Under water quality standards, marine class SA is des-
ignated an excellent habitat for fish and other aquatic
life, and class SB is good. 
MWRA uses this
water quality
meter to measure
dissolved oxygen,
salinity, pH, depth,
temperature, and
turbidity.
Smelt schooling in the
harbor’s Fore River.These
fish require high oxygen
levels in spawning areas. 
N A D I N E S M O S K E
R O B E R T M I C H E L S O N 
16 MAPPING THE HARBOR’S RECOVERY

FIGURE II-10: DISSOLVED OXYGEN IN BOSTON HARBOR. This map shows the average pattern of DO in the bottom waters of
the harbor during the summer. DO is typically lowest in the summer, and in the bottom water. DO levels in the harbor are healthy,
ranging from 4.9 milligrams per liter in the Mystic River/Inner Harbor, to 8.1 mg/l in the South Harbor. DO is lower in the river basins
and the Inner Harbor. Note, DO shows a decreasing east-west pattern, reflecting effects of different levels of tidal flushing. 
17 MAPPING THE HARBOR’S RECOVERY 
6.0
5.8
6.7 6.0
6.0
6.7
7.0
6.8 7.3
6.1
6.3 6.7 7.1
7.3
7.7
7.7
7.4 6.3
7.2
7.2
6.1
8.5
7.9 7.9
7.5
7.4 7.2
7.3
7.5
7.9 8.0
7.8
8.1 8.1
7.6
7.6
7.8 7.8
8.1
7.9
7.6
7.6
7.9 7.4
Bottom Dissolved
Oxygen (mg/l)
5-6
6-7
>7
no data
sampling location
moored DO meter 
South Harbor
Inner Harbor
Mystic
River
New
England
Aquarium 
7.2
7
6.8
6.6
6.4
midnight 4 am 8 am noon 4 pm 8 pm midnight
DO (millligrams per liter) 
Aurelia , a common
jellyfish in Boston
Harbor.
FIGURE II-11. DAILY CYCLE OF DISSOLVED OXYGEN IN THE
BOTTOM WATERS OF THE INNER HARBOR in September
2000.A moored instrument near the New England Aquarium
shows DO in the water decreases at night, and increases through
the day. Note that even in the early morning when DO is lowest,
concentrations are greater than EPA’s new recommended standard
for marine waters (an average of 4.8 mg/l).

18 MAPPING THE HARBOR’S RECOVERY 
ince the Boston Harbor Project began,
some of the most surprising stories have
been about the rapidity of change in the
sediments at the bottom of the harbor. For
example, U.S. Geological Survey studies
found that levels of lead and other heavy metals in
the harbor’s sediments are about half of what they
were 20 years ago. There is less organic matter set-
tling on the harbor floor, and the sediments are more
oxygenated, both of which are good for the bottom-
dwelling community, or benthos. The benthos is not
only increasingly abundant, it is more diverse. These
are truly signs of a recovering Boston Harbor. 
Tiny worms are
important parts of
a healthy seafloor
community. 
n depositional areas, weak tidal currents or
depressions in the seafloor allow solids
to settle and become soft sediments.
These areas are most affected by pollu-
tion because toxic materials and oxygen-
consuming organic matter tend to adhere
to solid particles and settle with them.
Such contaminants are often swept away
from erosional areas, which have strong
tides and lots of water movement. Intermediate areas
are sometimes depositional and sometimes erosional,
depending on changing currents and waves. Figure II-
12 shows where different sediment types are in
Boston Harbor.
The locations of the Deer Island and Nut Island
outfalls in erosional areas minimized the local impacts
of those discharges on the sediments, because the
solids were carried to depositional areas elsewhere in
the harbor or further offshore. Depositional sediments
in the harbor can collect contaminants from quite dis-
tant sources. A University of Massachusetts study con-
ducted in the late 1980s illustrates this phenome-
non.The study found that contaminants in a
muddy area of Dorchester Bay did not come
from a nearby CSO as expected, but from
sewage sludge discharged from the Nut Island
Treatment Plant—more than 4 miles away.
Sediment type determines where different ben-
thic animals and plants live, and their exposure to
contamination. The benthos is particularly vulnerable
to contaminants in the sediments because most benth-
ic organisms are immobile or move very little—they
cannot escape if environmental conditions deteriorate.
In contrast, fish and other mobile animals will actively
try to move to a higher quality habitat when condi-
tions get worse—for example, if dissolved oxygen
drops to stressful levels.
Soft-bottom benthic communities that live in
potentially more contaminated, depositional areas
include worms, crustaceans, clams, and other animals,
mostly living below the surface of the sediments.
Because these communities have the potential for
more exposure to pollution, MWRA’s benthic moni-
toring in the harbor focuses on soft sediment habitats
and investigates:
1. sediment contamination,
2. sediment metabolism, and
3. the benthic community. 
SEDIMENT TYPES IN BOSTON HARBOR 
I S of the floor the harbor 
Tiny worms are
important parts of
a healthy seafloor
community. 
D R . J A M E S B L A K E

19 MAPPING THE HARBOR’S RECOVERY
FIGURE II-12. BOSTON HARBOR SEDIMENT TYPES. The types of sediment in Boston Harbor determine the
biology of the seafloor ecosystem and also correlate with pollutant impacts.This map categorizes harbor sedi-
ments into three types: erosional, depositional, and intermediate. Land contours, currents, and waves create these
different sedimentary environments. Erosional areas include much of the harbor’s shoreline as well as the Outer
Harbor islands. In Boston Harbor, these are typically rocky and support seaweeds and animals like snails, blue
mussels, barnacles, and sea urchins. Large areas of the central, southern, and north-
western harbor are depositional.These muddy bottoms are home to animals
like worms, clams, and crustaceans. Intermediate environments have some
characteristics of erosional and depositional areas, depending on weather.
MWRA’s monitoring focuses on depositional environments, which can
accumulate contaminants attached to particles that settle to the bottom.
Note: shoreline sediment types are estimated based on very limited data.
(Map after Knebel et al 1991.) 
Sediment Type
depositional
intermediate
erosional
no data
outfall
NITP sludge outfall
Sewage sludge discharges
ended in 1991.
Before 1991, the solids and scum removed during
sewage treatment were treated in a very different
manner from the way they are today.As part of pri-
mary treatment, wastewater is channeled into set-
tling tanks, where heavy particles (sludge) sink to the
bottom of the tank.Anything that floats, such as plas-
tics,fats,cooking oils,and sticks,is called scum.Before
the Boston Harbor Project, the sewage solids and
floating material was digested–broken down by bac-
teria–to reduce its volume and oxygen-demanding
organic matter. Then, the digested sludge and scum
were simply re-combined with chlorinated effluent
and discharged into the harbor on the outgoing tide.
The sludge-scum mixture from NITP was digested
and then pumped to an outfall about 5 miles away off
Long Island (see Figure I-1, page 3).This black, smelly
substance, adorned with pieces of trash, represented
the worst results of the old treatment plants, and the
most memorable ones for boaters. Today, scum is
landfilled.Sludge is processed into fertilizer pellets for
gardening and landscaping. The days of scum and
sludge in the harbor are, fortunately, long-gone. 
Sludge from the Deer
Island Treatment
Plant is now made
into fertilizer pellets.

acteria and other organisms metabolize organic
matter, depleting oxygen. If the sediments use
up oxygen too quickly, it can mean that they are
polluted by excess organic matter. In the early 1990s,
Boston Harbor sediments showed some of the highest
rates of oxygen use ever measured in any sediments!
In the decade since MWRA stopped discharging
sludge, rates of metabolism in the harbor’s sediments
have dropped to levels that
are more typical of a
healthy ecosystem
(Figure II-15). 
300
250
200
150
100
50
0
92 93
Millimoles of oxygen per square meter per day
94 95 96 97 98 99 00
former NITP
sludge site
sampling
station 
he United States Geological Survey has been monitoring trends in metals concentrations at four locations
in Boston Harbor (Figure II-13). This study showed that, over the last two decades, lead has decreased
approximately 50% in harbor sediments (Figure II-14), as have most other heavy metals at the four sites
sampled. This is related to a decrease in metals inputs from many sources, including sewage discharges. 
FIGURE II-14. LEAD DECREASES OVER TIME IN
BOSTON HARBOR SEDIMENTS. From data col-
lected at four stations throughout Boston Harbor,
USGS scientists have shown a distinct downward
trend in lead concentrations in surface sediments
since the late 1970s. (Bothner et al . 1998) 
3
4
10
8
HEAVY METALS ARE LOWER IN RECENT YEARS SEDIMENT CONTAMINATION 
T 
FIGURE II-13. USGS METALS SAMPLING LOCATIONS
IN BOSTON HARBOR.
SEDIMENT METABOLISM
FIGURE II-15. SEDIMENT OXYGEN DEMAND IN
BOSTON HARBOR, 1992-2000.The rate at which
sediments use up oxygen indicates if they are
degraded by too much organic matter.This graph
shows the change in sediment oxygen demand from
1992-2000 near the former NITP sewage sludge
discharge site near Long Island. Extremely high rates
were recorded in 1993, and even higher rates in
1995, as burrowing and feeding activities by benthic
animals ventilated the sediments, making more oxy-
gen available to bacteria. Metabolism rates have
declined in recent years to normal levels—indicat-
ing that the sediments have been “mined out” of
organic matter. (Tucker et al . 2001) 
B 
1.2
Relative concentration (background corrected)
1.0
0.8
0.6
0.4
0.2
0.0 0 2 4 6 8 10 12 14 16
Years since first sample (1977 or 1978)
Station 3
Station 4
Station 8
Station10 
SEDIMENT METABOLISM MEASURES THE EFFECT OF ORGANIC MATTER ON THE HARBOR FLOOR 
20 
USGS sediment
core sampler
MAPPING THE HARBOR’S RECOVERY

ome of MWRA’s most exciting findings in
Boston Harbor have come from two studies of
the soft-bottom benthic community—sediment
profile imaging (SPI) and benthic sampling—that
examine benthic species diversity and abundance.
The biggest changes became evident a few years after
the end of sludge discharges to the harbor in
December 1991.
Once each summer, large amounts of data on sedi-
ment quality are quickly gathered at more than 50 sta-
tions (Figure II-16) in Boston Harbor by photograph-
ing a cross-section of the top several inches of the sedi-
ment. Sediment profile imaging can measure oxygen
penetration, an important measure of benthic health,
as “redox potential discontinuity” (RPD) depth. Figure
II-17A shows that, at a heavily polluted site, little or no
oxygen penetrates into the sediments and few benthic
animals survive. At a recovering site (Figure II-17B),
there is a thick surface layer of light-colored oxygenat-
ed sediment and abundant evidence of animal activity.
Figure II-18 shows average RPD depths in the har-
bor. In 1989 and 1990 (Figure II-18A), sediment
imaging showed minimal oxygen penetration at the
sludge discharge sites and other heavily polluted loca-
tions.There was little evidence of benthic animal
activity at such stations. By 2000, conditions had
improved, with deeper oxygen penetration and greater 
THE BENTHIC COMMUNITY 
S 
AFTER DECADES OF POLLUTION, THE BENTHIC COMMUNITY IS RECOVERING
Sampling station
SPI only
SPI and detailed
studies
FIGURE II-16. SEDIMENT PROFILE IMAGING SITES
AND SAMPLING LOCATIONS for detailed studies of
bottom-dwelling animals.
FIGURE II-17. BOSTON HARBOR SEDIMENT PROFILE IMAGES. The depth of
oxygen penetration (RPD) is indicated by the thickness of light-colored, oxygenated
sediments on top of black, sulfide-rich anoxic sediments. A: UNHEALTHY SEDI-
MENTS This photograph shows mostly dark sediments—these are oxygen-deprived.
The RPD is shallow, and there is no visible life on the surface. In this extreme case,
hydrogen sulfide produced by anaerobic bacteria feeds mats of sulfur bacteria that
build up on the sediment surface. Underneath is black, anoxic mud. B: RECOVERING
SEDIMENTS This photograph shows a recovering site that has developed a deep
RPD. Individual Ampelisca tubes protrude from the surface. Ampelisca pump water
into their tubes, thereby aerating the sediments below. 
B. 1998
water 
Ampelisca tubes surface 
water
A. 1990
surface 
R O B E R T D I A Z 
21 
Sediment
Profile Imaging
camera
MAPPING THE HARBOR’S RECOVERY

B. 1992-2000
AFTER SLUDGE DISCHARGES
ENDED
DITP outfalls
NITP sludge outfall (closed 1991)
NITP outfalls (closed 1998) 
Oxygen penetration (RPD)
(depth in cm)
0-1
1-2.7
2.7-4.5
4.5-7.4
no data
outfall
NITP sludge outfall
closed outfall
A. 1989-1990
DURING SLUDGE DISCHARGES
INTO THE HARBOR
DITP outfalls
NITP sludge outfall
NITP outfalls 
RPD (Figure II-18B). Scientists attribute some of this improvement to a tiny,
shrimp-like crustacean called
Ampelisca.
Ampelisca is a sensitive indicator of sediment conditions.While this animal can
tolerate moderate levels of organic matter and oxygen loss, it is vulnerable to con-
tamination from toxic metals and pesticides.Thus, its increase in the harbor after
many years may signal less contaminated sediments. In 1989-90,
Ampelisca tube-
mats were found at only 24% of the harbor sampling stations (Figure II-19). In sum-
mer 1991, harbor sediment samples indicated an environment under stress–diversity
was low, with an average of just 18 species per
sample.The total number of animals captured
was also quite low. By the mid-1990s, as the
Ampelisca communities spread and their
tubemats provided shelter to other organisms, the abun-
dance of benthic animals increased dramatically (Figure II-20). By 1996, sci-
entists found
Ampelisca at over 80% of stations in Boston Harbor,
and diversity more than doubled through the 1990s (Figures II-19 and II-20B). 
22 
Ampelisca 
MAPPING THE HARBOR’S RECOVERY
FIGURE II-18. OXYGEN PENETRATION INTO HARBOR SEDIMENTS, 1989-2000. These contour maps were created by averaging annual RPD data collected from 1989-1900
and 1992-2000, as measured by sediment profile imaging. A: 1989-1990. Early in the Boston Harbor Project the northern harbor and the southern harbor around the NITP out-
falls had very shallow RPDs. Nearly half of all stations had RPD depths of less than one centimeter. B: 1992 to 2000. Later data show better sediment oxygenation, especially in
the northern harbor, which had been more impacted by sludge discharges. One apparent factor in this improvement is the presence of Ampelisca tubemats.These mats, which pro-
mote the oxygenation of the sediments, correlate well with RPD depths of 2.7 centimeters or greater in the northern harbor, Nantasket Roads, and parts of Hingham Bay.

Ampelisca can also benefit the sediments.They
build tubes that can grow in thick mats on the
seafloor, and these mats often host other animal
species.
Ampelisca irrigate the sediments with oxy-
genated water, increasing the depth of oxygen penetra-
tion.The average August RPD depth contours from
1992 through 2000 (Figure II-18 B) closely track the
presence of the
Ampelisca-dominated communities—
stations with greater oxygen penetration consistently
supported these communities throughout the 1990s.
However,
Ampelisca tubemat communities have
been declining since 1996. Biodiversity in harbor
samples remained high, even as
Ampelisca started to
decline. It is likely that, as pollution inputs were
cleaned up, even more pollutant-sensitive species
were able to move in. Future sampling will show if
Ampelisca is in turn being replaced by a more
diverse community that is more typical of unimpact-
ed New England estuaries. 
90
80
70
60
50
40
30
20
10
0 90 91 92 93 92 94 95 96 97 98 99 00 01
Percent of harbor sampling stations
MAY
AUGUST
FIGURE II-19. PREVALENCE OF AMPELISCA IN
BOSTON HARBOR, 1989-2001. This graph shows
the percent of benthic monitoring stations with 
Ampelisca tubemats. Except for 1992, when results
are shown for May and August, all bars show results
from August. Ampelisca was found at increasing
numbers of stations through the early to mid-90s,
indicating that Boston Harbor sediments were
steadily recovering. In 1989-1990, Ampelisca tube-
mats were found at only 24% of the harbor sampling
stations. In May 1992, the tubemats were found at
fewer than 10% of the stations, with many stations
showing signs of disturbance from a major storm in
October 1991 (the “Halloween Nor’easter” or “The
Perfect Storm”).This storm caused the highest
storm surge in Boston Harbor in two decades, and
scoured soft sediments from the seafloor in many
parts of the harbor.This sediment transport and
mixing, together with a reduction in pollution inputs,
may have promoted the establishment of more vig-
orous benthic communities and set the stage for the
increases in abundance and diversity observed after-
ward. By August 1992 more than 50% of the harbor
stations contained Ampelisca tubemats, and this pro-
portion increased throughout the mid-1990s, peak-
ing at over 80% of stations in 1996.The recent
decline in Ampelisca abundance seems to be a result
of succession from Ampelisca to a more diversified
and healthy benthic community.
FIGURE II-20.ABUNDANCE AND DIVERSITY OF ANIMALS ON THE HARBOR FLOOR 1990-1999. Each
summer since 1991 MWRA has collected sediment samples at eight stations in Boston Harbor. At each station,
three sediment grab samples are collected, and the animals in these samples are preserved, identified, and count-
ed in the laboratory. These graphs are from averages of all eight stations. A: ABUNDANCE. The number of
animals brought up per sample has increased dramatically since 1991. In 1991, a single grab sample brought up
approximately 1,000 individual animals. By 1998, there were about 6,000 animals per sample. Increases were
most noticeable in the early 1990s, as communities quickly recovered after sludge discharges stopped in
December 1991. B: DIVERSITY. Measured by the number of different species found in a grab sample, diversity
has also climbed since 1991. In 1991, a grab sampler would bring aboard about 18 different species
per sample. By 1999, an average of 33 species per sample was collected.Thus, in less than a
decade, the biodiversity of the harbor almost doubled.Although the increases are not at all sta-
tions or in all years, a statistical analysis of the data confirmed that the overall increase is signif-
icant. As with many other benthic measurements, biodiversity
increased sharply in the 1990s after sludge
discharges to the harbor ended. 
9000
8000
7000
6000
5000
4000
3000
2000
1000
0 91 92 93 94 95 96 97 98 99
Individuals per sample
A. ABUNDANCE OF HARBOR
BENTHIC ANIMALS
91 92 93 94 95 96 97 98 99 
0
10
20
30
40
Spring
Summer
Average species per sample
B. DIVERSITY OF HARBOR
BENTHIC ANIMALS 
23 MAPPING THE HARBOR’S RECOVERY

WRA studies fish and shellfish from two aspects: the condition of the
animals themselves, and whether their contaminant levels pose a
health threat to consumers. Since 1992, MWRA has monitored win-
ter flounder, lobster, and blue mussels. Flounder and lobster are
important biomonitoring tools because locally, these two species are
commercially important for food, and they live in close contact with potentially
contaminated bottom sediments. Mussels are used because they feed by filtering
particles out of the water, and can concentrate (bioaccumulate) toxic materials
from the water in their tissues.
Flounder and lobster for testing are collected near Deer Island. Mussels are col-
lected from relatively pristine sites and then transferred to cages which are placed
near Deer Island and in the Inner Harbor for up to 60 days, to permit bioaccumu-
lation of contaminants. (Monitoring locations are shown in Figure II-21.)
Flounder caught near Deer Island have a much lower prevalence of liver dis-
ease than those in the 1980s, and liver tumors are now rare. Levels of mercury,
PCBs, and pesticides in flounder fillet are well within U.S. Food and Drug
Administration (FDA) guidelines. Lobster also are healthy, and have low levels of
contaminants in the meat. However, PCBs in lobster hepatopancreas (tomalley)
are above FDA guidelines, consistent with existing advisories against consuming
tomalley. Mussels have lower levels of PAHs than in the early 1990s. PCBs and
pesticides in mussels remained relatively stable throughout the decade at levels
well within FDA guidelines. Overall, the contaminant data show that fish and
shellfish in the harbor are healthy and meet FDA guidelines. (For definitions of
PCBs and PAHs, see page 26.) 
er Harbor 
DEER
ISLAND
FLATS
Flounder/Lobster
Station
Mussel Station M 
fish shellfish & 
FIGURE II-21. BOSTON HARBOR FISH & SHELLFISH MONITORING LOCATIONS. 
24 
R O B E R T M I C H E L S O N 
MAPPING THE HARBOR’S RECOVERY

PCB
DDT
Mercury
24.9 - 72.9
3.1 - 7.2
40 - 90
Actual range of
annual averages
Parts per billion, wet weight
2,000
5,000
1,000
FDA limit 
lounder live on the bottom, eating worms and
other tiny animals that live in the sediments, and
thus can be exposed to sediment contaminants
directly through the skin and from feeding. In the
mid-1980s, a scientific paper identified Boston Harbor
flounder as having among the highest incidence of
liver tumors in the northeastern United States.
Since 1992, the flounder caught near Deer Island
have not exhibited gross abnormalities, such as fin
erosion, that had been observed during the mid-
1980s; the fish generally appear healthier. Of the
liver lesions, a type called “centrotubular hydropic
vacuolation” (CHV) has been the most common.
Figure II-22A shows that, on average, the rate of
CHV is about two-thirds of the levels found in the
1980s, although this may be partially explained by
the age of the fish: the tested fish from Boston
Harbor have been younger, and younger fish tend to
have lower CHV levels. Liver tumors, which indicate
more serious health effects, have not been observed
since 1996 (Figure II-22B).
The flounder livers are tested for levels of lead,
mercury, cadmium, copper, nickel, silver, zinc,
chromium, PAHs, PCBs, DDT, and ten other pesti-
cides. In order to test for potential human health
effects, mercury, PCBs, DDT, and seven other pesti-
cides are measured in the edible flounder fillets. For
many fish species, consumption advisories because of
mercury are a concern. However, mercury levels in
winter flounder have been stable at about 50-100
parts per billion, well below the FDA limit of 1,000
parts per billion. Levels of PCBs and DDT are also
well below FDA limits (Table II-3). 
FIGURE II-22. LIVER DISEASE IN WINTER FLOUNDER, 1984-2001.
Liver disease is a sensitive indicator of pollution effects on Boston Harbor flounder because the liver can be dam-
aged as contaminants are metabolized. A: EARLY LIVER DISEASE. On average, the rate of early liver disease (meas-
ured as centrotubular hydropic vacuolation or CHV) is about two-thirds the levels found in the 1980s, when nearly
70% of fish were affected. B: LIVER TUMORS. This more serious abnormality, once found at an unusually high inci-
dence, has not been seen since 1996 (when one tumor was found out of 16 fish collected). Other forms of liver
disease (not shown) also have dropped substantially since the late 1980s but seem to have leveled off over the last
decade.Although encouraging, these observations should be interpreted with caution, because the fish caught in
Boston Harbor recently have been younger, and younger fish tend to have a lower prevalence of liver disease.
TABLE II-3. CONTAMINANTS IN FLOUNDER
FILLET, 1993-2001. PCBs, DDT, and mercury in fillet
of flounder caught in the harbor have fluctuated
between years
with no clear
pattern.
However, all
these chemicals have
measured well below the U. S. Food and Drug
Administration (FDA) action limits. 
90
80
70
60
50
40
30
20
10
0 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01
Percent of flounders with disease (CHV) 
14
12
10
8
6
4
2
0 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 00 01
Percent of flounders with tumors 
WINTER FLOUNDER 
F 
BOSTON HARBOR FLOUNDER ARE IN GOOD HEALTH AND MEET FDA STANDARDS 
R O B E R T M I C H E L S O N 
A. FLOUNDER EARLY LIVER DISEASE B. FLOUNDER TUMORS 
25 
Flounder live in
contact with the
ocean floor.
MAPPING THE HARBOR’S RECOVERY 
R O B E R T M I C H E L S O N

WRA studies blue mussels to assess how
water quality may affect levels of toxic con-
taminants in marine animals. Mussels feed
by filtering large volumes of water, and can accumu-
late dissolved toxic metals and organic compounds
in their tissues. For this study, hundreds of mussels
from relatively clean areas in Gloucester and
Sandwich are put in cages and placed on moorings
for one to two months at two locations: the Inner
Harbor near the New England Aquarium, and Deer
Island Flats (Figure II-20). Upon retrieval, the mus-
sels are analyzed for lead, mercury, PCBs, PAHs,
DDT, and ten other pesticides. There has been little
change in PCBs and DDT over time, but PAHs in
mussels are lower than in the early 1990s. 
BLUE MUSSELS
PAH LEVELS IN MUSSELS HAVE
DECREASED BY MORE THAN 50% IN
THE LAST DECADE. 
M 
TABLE II-4: CONTAMINANTS IN MUSSEL TISSUE,
1991-2001. Blue mussels collected near Deer Island
have levels of PCBs, DDT, and PAHs that are below
FDA limits. Levels of other pesticides (data not
shown) are equal to, or lower than, DDT levels.
Recent PAH levels are less than half of amounts seen
in the early 1990s. 
PCBs
DDT
14.9 - 36.6
2.2 - 8.3
38 - 528
2,000
5,000
None PAH-low molecular
weight (ng/g dry)
Actual range of
annual averages
Parts per billion, wet weight
FDA limit 
PCBs: Polychlorinated biphenyls 
A group of banned toxic chemicals, formerly used in
a variety of commercial applications, including elec-
trical transformers and condensers, batteries, and
lubricants. PCBs are known to cause skin diseases
and suspected of causing birth defects and cancer. 
PAHs: Polycyclic aromatic hydrocarbons 
Complex organic chemicals found in petroleum and in
products of fossil fuel combustion. Many PAHs are
known carcinogens. 
R O B E R T M I C H E L S O N 
26 
Typical blue mussel bed
MAPPING THE HARBOR’S RECOVERY
Mussel cages
being deployed

ach year, MWRA tests 15 lobsters caught near
Deer Island. The lobsters are examined for exter-
nal signs of disease, such as black gill disease,
shell erosion, parasites, and tumors. The tail and claw
meat is tested for mercury, PCBs, DDT, and ten other
pesticides. The tomalley is tested for the same con-
taminants plus lead, cadmium, copper, nickel, silver,
zinc, chromium, and PAHs. Table II-5 shows the
average results of this testing for mercury, PCBs, and
pesticides in lobster meat. The levels of contaminants
in lobster meat are well below the FDA limit for
human consumption.
An unanticipated finding in the lobster study has
been a trend of increasing concentration of PCBs in
lobster hepatopancreas since 1993 (Figure II-23).
Industrial PCBs are potential carcinogens and were
phased out of production beginning in 1971.
Although PCB levels are extremely low in MWRA
discharges, PCBs break down very slowly and are
therefore very persistent in the environment; histori-
cal inputs of PCBs from a variety of sources have
accumulated in marine sediments.
MWRA examined whether the apparent increase
in lobster tomalley PCBs could be explained by the
better laboratory testing methods that have been
used recently, but the trend was found no matter
which method was used. One explanation for the
trend is that, due to the lower amount of sewage
solids in the harbor, lobster could be foraging less in
the Outer Harbor and more in the Inner Harbor and
Dorchester Bay, where there are more pollutants.
Another possible factor is that, in recent years, sam-
pling for lobster has been later in the year. This may
mean that the length of time the lobsters that were
sampled were exposed to PCBs in the harbor has
increased. No matter what the cause, the levels of
PCBs in lobster tomalley now are at, or slightly over,
the FDA limit. This finding confirms existing con-
sumer advisories against eating lobster tomalley. 
PCBs
DDT
Mercury
10.8 - 39.8
0.7 - 6.0
70 - 260
2,000
5,000
1,000
Actual range of
annual averages
Parts per billion, wet weight
FDA limit
TABLE II-5: CONTAMINANTS IN LOBSTER MEAT,
1992-2001. MWRA tests the tail and claw meat of
lobsters near Deer Island for PCBs (polychlorinated
biphenyls), DDT, and mercury.The levels of contami-
nants vary from year to year, yet are always well
under FDA limits. 
E 
FIGURE II-23: PCBs IN LOBSTER HEPATOPAN-
CREAS (TOMALLEY), 1992-2000. From 1993-1999
there was an upward trend in PCB levels in lobster
caught in the harbor. Scientists have been unable to
definitively explain this trend—there are several
plausible hypotheses (see text). Longstanding
consumer advisories against eating lobster tomalley
are supported by these MWRA data. 
4000
3500
3000
2500
2000
1500
1000
500
0 93 94 95 96 97 98 99 00 92 
LOBSTER
LOBSTER MEAT SHOWS LITTLE
CONTAMINATION, BUT THE TOMALLEY
EXCEEDS LIMITS FOR PCBs 
27 Back to Table of Contents OR Go to Part Three-Boston Harbor's Tributary Rivers 
R O B E R T M I C H E L S O N

oston Harbor is an estuary—a marine
ecosystem where freshwater enters the
ocean. The largest rivers draining into
Boston Harbor are the Charles, the
Neponset, and the Mystic. Since 1989,
MWRA has regularly monitored water
quality in these rivers, primarily to assess impacts of
combined sewer overflows (CSOs).The monitoring also
measures the effect of the rivers on harbor water quali-
ty. Measured water quality indicators include bacteria,
water clarity, chlorophyll, and dissolved oxygen. 
HE CHARLES RIVER meanders nearly 80
miles from its headwaters at Echo Lake in
Hopkinton before emptying into Boston Harbor.
Pollution sources to the lower Charles include
upstream community wastewater treatment plants,
contaminated stormwater runoff, and leaking septic
systems.Thirteen CSOs discharge to the lower Charles,
including MWRA’s Cottage Farm CSO treatment facil-
ity, which screens and disinfects wet-weather combined
sewage discharges. Historically, the Charles was heavi-
ly used for industrial waste disposal, and hotspots of
toxic contaminants remain in its sediments.
The river mouth, originally a tidal estuarine salt-
marsh, has been dammed since the early 1900s and a
new dam and locks system was built in 1978. This
dam controls river flow and flooding, and fills the
Charles River Basin, a popular urban recreational
area. However, the dam has some adverse impacts on
the river’s ecosystem. It prevents tidal flushing, trap-
ping pollutants in the basin. Seawater leaks upstream
into the river through the dam—in the summer the
heavy saltwater slides up the river bottom, forming a
cold saltwater “wedge” with freshwater above it. These
layers prevent vertical mixing, inhibiting replenish-
ment of oxygen from the air to the bottom waters.
Large amounts of decaying organic material in the
bottom sediments use oxygen, so that sometimes the
river bottom water has almost no oxygen at all. The
decay process also produces toxic sulfides, which pre-
vent a normal benthic community from developing
on the bottom. 
Boston Harbor’s Tributary Rivers 
INTRODUCTION TO BOSTON HARBOR’S THREE MAJOR RIVERS 
B 
Trees along the Charles River 
E R I C E N D L I C H 
An aerial view of the Neponset Estuary 
J O S E P H I N G O L D S B Y 
PA RT T H R E E 
T 
26 BOSTON HARBOR’S TRIBUTARY RIVERS

HE NEPONSET RIVER is 28 miles long, flowing from its headwaters in
Foxboro to the river mouth in central Boston Harbor. Unlike the Charles
and Mystic Rivers, the Neponset River mouth is not dammed, so an estuar-
ine habitat, the Neponset estuary, remains as Boston Harbor’s largest saltmarsh.
The marsh is important wildlife habitat and is also a natural filter of pollutants.
Just upstream of the saltmarsh is the harbor's largest smelt spawning area. In the
Neponset watershed are three Areas of Critical Environmental Concern (ACECs):
the Neponset Estuary, Fowl Meadow, and Ponkapoag Bog. ACECs are recognized
as especially sensitive and important regions for wildlife habitat, flood control, or
recreational and historical resources.
Water quality problems in the Neponset watershed include bacterial contami-
nation, eutrophication, and toxic chemicals in sediments. In recent years, CSOs in
the river have been eliminated, but the lower Neponset still receives contaminants
from leaking septic systems further upstream and from stormwater runoff. During
rainstorms, MWRA’s Commercial Point CSO Treatment Facility discharges
screened and disinfected combined sewage to southern Dorchester Bay at the
mouth of the river. 
HE MYSTIC RIVER 
flows from the Mystic
Lakes in Winchester and
Arlington, east through Medford,
Somerville, and Chelsea to
Boston Harbor.
Only five miles long, much of
the river flows through dense res-
idential and industrial areas, and
is impacted by pollution from
surrounding development. Like the Charles, the Mystic River is dammed at its
mouth where it enters Boston Harbor, but it does not suffer from the same saltwater
wedge and low dissolved oxygen that affect the Charles.
Water quality problems in the Mystic Basin include toxic pollutants in industri-
alized areas, eutrophication, and bacterial contamination from sanitary sewer over-
flows, stormwater, and eight CSOs.
Alewife Brook, a tributary to the Mystic in Cambridge and Arlington, is also
heavily affected by stormwater and combined sewage, and the brook is an addition-
al source of pollution to the Mystic. At the river mouth, MWRA’s Somerville
Marginal CSO Treatment Facility discharges screened, chlorinated combined sewage
during heavy rains. 
T 
T 
Bridge over the Mystic River 
E R I C E N D L I C H 
The Neponset Marsh 
J O S E P H I N G O L D S B Y 
Storm drain 
E R I C E N D L I C H 
29 BOSTON HARBOR’S TRIBUTARY RIVERS

n general, the harbor’s tributary rivers have poor-
er bacterial water quality than the harbor, reflect-
ing the impacts of CSOs and urban storm runoff
on relatively small water bodies. In contrast with
most of Boston Harbor, the rivers frequently do not
meet the Massachusetts state water quality standard
of average fecal coliform counts of less than 200
colonies per 100 ml. Figure III-1 shows the spatial
variation of bacteria counts along the Charles,
Mystic, and Neponset Rivers in the year 2000, aver-
aged for all weather conditions.
Figure III-2 shows changes in river bacteria over
three time periods corresponding to phases of
implementation of MWRA’s plan to control CSOs.
In the Charles, improvement in water quality over
the past ten years has been dramatic; fecal coliform
counts (geometric mean) fell by over five-fold.
Although the Mystic River shows slight improve-
ment over this period, the Mystic and Alewife Brook
are still plagued with contaminated stormwater and
CSOs. Implementation of MWRA’s CSO Plan will
control CSOs, but stormwater is a major source of
bacteria. Although closing CSOs and better CSO
treatment at MWRA facilities has reduced inputs of
bacteria to the Neponset, stormwater sources are so
much larger than were CSOs that water quality in
the lower Neponset has remained about the same
since monitoring began. 
RIVER BACTERIA
trends in river water quality 
I 
J O S E P H I N G O L D S B Y
E R I C E N D L I C H 
Neponset Marsh Homes along the Mystic River
Head of the Charles race 
E R I C E N D L I C H 
30 BOSTON HARBOR’S TRIBUTARY RIVERS

C
h
a
r
l
e
s
R
i
v
e
r
C
h
a
r
l
e
s
R i
v
e
r
B
a
s
i
n
Inner Harbor 
S O M E R V I L L E 
Cottage
Farm
CSO
(treated)
Watertown
Dam Laundry
Brook
Arsenal
Mall
B.U.
Bridge
Charles
River
Dam
Stony
Brook
CSO 
C A M B R I D G E
B O S TO N 
a
b c
d
e
f
g h i j k l
m n o
C H A R L E S 
A R L I N G TO N
M E D F O R D
S O M E R V I L L E
E V E R E T T 
Mystic Lakes
Malden River 
a b
c
d
e f
g
h
i
j
k
l
m 
Tobin
Bridge
Amelia Earhart
Dam (locks) Somerville
Marginal
CSO
(treated) 
A
l
e
w
i
f
e
B
r
o
o
k
Mystic
R
i
v
e
r 
M Y S T I C 
sampling location 
Fox Point
CSO
(treated)
Commercial Point
CSO (treated) 
N e p o
n
s
e
t
R i v
e r
Dorchester Bay
Quincy
Bay 
Q U I N C Y
B O S TO N 
N E P O N S E T
a
b
c
d
e f
g 
A. CHARLES: Most fecal coliform readings
hovered around or below the state standard
of 200 colonies per 100 milliliters. The area
between the Watertown dam and the Arsenal
Mall (upstream of any CSO discharges) was
the most consistently contaminated section
surveyed; and the Charles River Basin, the
important recreational area between
Cambridge and Boston, had the best bacterial
water quality.
B. MYSTIC: Bacterial counts in the Mystic
River vary greatly depending on location.A
tributary,Alewife Brook, is one of the most
contaminated water bodies in the Boston
area, mostly due to stormwater and CSOs.
Here, fecal coliform counts routinely fail to
meet the state standard. However, down-
stream, in the Mystic River proper, bacterial
water quality is fairly good, except for a
noticeable increase near Medford Square (h).
Counts decrease near the river’s mouth.
C. NEPONSET: Except near its mouth, the
Neponset River consistently fails to meet
state bacterial water quality standards.The
Baker Dam in Milton is affected by leaking
septic systems upstream and contaminated
stormwater. At the river mouth, where river
water mixes with the cleaner harbor water,
fecal coliform counts meet the standard.
Unfortunately, water quality does not consis-
tently meet standards near Tenean Beach or
the Commercial Point CSO Treatment Facility
outfall.Although the effluent from the facility
is effectively disinfected, these sites are
impacted by contaminated stormwater. 
2000
1500
1000
500
0 
Charles River 
Colonies/100 mL
Upstream
(Watertown) (North Station) 
State 
Standard 
a 
b 
c 
d e h j 
1500
1000
500
0
Colonies/100 mL
Upstream
(Arlington) Downstream
(Charlestown) 
Mystic River 
State 
Standard 
b 
a c 
d 
e f f 
g h 
i j k l 
m 
750
500
250
0 
Colonies/100 mL
Baker
Dam Granite
Ave. Neponset
Circle Tenean
Beach Com.
Point CSO Victory
Road River
mouth
Upstream
(Milton) Downstream
(Dorchester) 
Neponset River 
State 
Standard 
a 
b 
c 
d 
e 
f g 
31 BOSTON HARBOR’S TRIBUTARY RIVERS
FIGURE III-1. SPATIAL PATTERN OF RIVER BACTERIA IN 2000*
* Samples collected during all weather conditions.

0
0.5
1
1.5
2
2.5 
Mystic
River
Secchi Depth (meters)
Charles
River Neponset
River
Boston
Harbor 
FIGURE III-3. COMPARISON OF WATER CLARITY
IN THE RIVERS AND THE HARBOR. Average Secchi
depths in the rivers are roughly comparable, at about
one meter. However, clarity in the harbor is more than
double that of the clearest tributary, the Neponset.
RIVER CLARITY 
WRA tests for water clarity by measuring
Secchi depth in the rivers. Generally, the trib-
utary rivers are not as clear as the harbor M 
32 BOSTON HARBOR’S TRIBUTARY RIVERS 
PHASE I:
1989-1991
Early improvements
at DITP and
headworks increase
flow to DITP. CSO
decreases from 3.3
to 1.5 billion gallons
annually.
PHASE I1I: 1998-2008
Completion of 25 long-term CSO projects
decreases annual modeled CSO flow to 0.4 billion
gallons, with 95% of remaining flow treated.
PHASE I1: 1992-1997
CSO upgrades, full pumping
capacity at DITP further
decrease discharges to one
billion gallons annually.
4
3
2
1
0
87 88 89 90 91 92 93 94 95 96 97 98 99 00 01 02 03 04 05 06 07 08
Annual overflow volume (billion gallons)
A. Modeled Decrease in Annual CSO Overflow Volume: 1987-2008
B. Fecal Coliform Counts 
800
700
600
500
400
300
200
100
0
800
700
600
500
400
300
200
100
0
800
700
600
500
400
300
200
100
0
1989-1991 1992-1997 1998-2001
1989-1991 1992-1997 1998-2001
1989-1991 1992-1997 1998-2001 
Charles River 
Mystic River 
Neponset River
Geometric mean fecal coliform (colonies per 100 mL) 
FIGURE III-2. PATTERNS OF RIVER BACTERIA COMPARED TO
PHASES OF CSO CONTROL. Bacterial counts for the three rivers
are grouped in time by the three phases of the MWRA’s CSO Plan.
A: Model predictions for CSO discharges, CSO Control Plan.
B: Average bacteria levels in the Charles have decreased 80%, while
the Mystic and Neponset Rivers have shown little or no improve-
ment.The Mystic and Neponset are more affected by stormwater
than by CSO. Improved pumping and hydraulic capacity at DITP great-
ly decreased discharges from Charles River CSOs. Also, communities
along the Charles have been working to clean up stormwater dis-
charges. Although there have been local improvements at the mouth
of the Mystic River near MWRA’s Somerville Marginal CSO
Treatment Facility, the overall average water quality in the Mystic has
changed very little.
While CSOs have been eliminated in the Neponset, stormwater still
contaminates that river. (Lines above bars indicate margin of error.)

0
1
Upstream Downstream
(Boston)
Secchi depth (meters)
0.5 
hlorophyll concentrations are typically higher in the rivers than in the harbor, because nutrient levels are
higher in rivers. Also, the residence time of water is greater in the dammed portions of the rivers than in
the harbor. Both these factors allow more algae to build up. Algae levels are at their highest in the rivers
and the harbor in the summertime (Figure III-5). The Mystic and Charles Rivers have the highest amounts of
algae; the Neponset River the least. Since river chlorophyll monitoring began in 1992, there have been no signifi-
cant trends in algal blooms over time. 
RIVER ALGAE & CHLOROPHYLL
J F M A M J J A S O N D
70
60
50
40
30
20
10
0 
Charles River
Mystic River
Neponset River
Boston Harbor
Chlorophyll (ug/L)
Month 
C 
FIGURE III-5. COMPARISON OF CHLOROPHYLL IN
THE RIVERS AND THE HARBOR. Rivers have higher
chlorophyll levels than the harbor, but both ecosystems
are subject to dramatic seasonal fluctuations.
Chlorophyll levels are high in the summer when the
light is intense, and low in the dimmer winter months.
River chlorophyll is measured downstream near the
river mouth but before mixing with saltwater. Both the
Mystic and Charles are very eutrophied, with high aver-
age chlorophyll due to poor flushing and high nutrient
inputs.The Neponset has the lowest chlorophyll of all
the rivers, probably due to a relatively natural river flow
and lower nutrient inputs.
FIGURE III-4. SPATIAL TREND IN CHARLES RIVER
WATER CLARITY. Secchi depths along the Charles
River from Newton to downtown Boston show a
trend of increasing clarity in the downstream
stretches near Boston. As the river slows and
widens through Cambridge and Boston, the rate of
flow decreases, allowing solids to settle out. As a
result, Secchi depths increase downstream. 
because they have higher concentrations of particu-
lates and algae (Figure III-3). The water clarity in the
rivers has not changed significantly since monitoring
began in 1992. The Charles River has an interesting
pattern of water clarity: the water is more clear in the
urbanized basin than it is upstream (Figure III-4). 
Boating in the Mystic River is an
important recreational resource
for Greater Boston. 
E R I C E N D L I C H 
33 Back to Table of Contents OR Go to Part Four-After the Outfall

Deer Island
Treatment
Plant
Nut Island
Headworks 
OUTFALL TUNNEL
9.5 miles to
Massachusetts Bay 
R O B E R T M I C H E L S O N 
34 AF T ER THE OUTFALL 
he opening of the new 9.5-mile ocean outfall on September 6, 2000 relocated effluent away from
Boston Harbor to Massachusetts Bay. MWRA scientists have already noted a number of changes in
harbor water quality that appear to be related to the relocation. The most dramatic changes have
occurred near the former harbor outfalls, especially changes in bacteria, ammonium concentrations,
and water clarity. This section describes observations during the first four months after the DITP discharges to
the harbor ended. Now, the major sources of contaminants—especially nutrients—are from the rivers and
stormwater runoff, shown schematically in Figure IV-1. 
After the Outfall:
T
FIGURE IV-1. LOCATIONS OF HARBOR
CONTAMINATION SOURCES AFTER SEPTEMBER
2000. After the opening of the Massachusetts Bay
outfall in 2000, wastewater inputs to the harbor dra-
matically changed.Where large amounts of treated
wastewater had been discharged at the mouth of the
harbor, now only smaller sources still remain.
Typical habitat near MWRA’s
outfall in Massachusetts Bay is
rocky, supporting a variety of
sea life.
A tiny ocean pout rests on
pink corraline algae in
Massachusetts Bay.
PA RT F O U R
MONITORING RESULTS SINCE SEPTEMBER 2000 
B A R B A R A H E C K E R 
& Changes in the Harbor Bay

DITP outfalls
NITP
outfalls
Boston
Hull
Hingham
Chelsea
Everett Revere
Winthrop 
Hingham Bay
Inner Harbor 
B. BACTERIA AT DEER ISLAND OUTFALL SITE 
OUTFALL SITE
28
250
200
50
0
0 ml Water Quality Q y 
Standard 
Transfer
of flows
to DITP 
2,830 >2,000 250 
200 
150 
100 
50 
0 
colonies/100 ml 
1999 2001 
Water Quality 
Standard 
Start of 
Mass. Bay 
outfall 
ince DITP discharges to the harbor ended in
September 2000, bacteria counts at the former
harbor outfalls have been consistently low
(Figure IV-2). Counts decreased first at the NITP out-
falls in 1998, and then at the DITP outfalls in
September 2000. 
S 
BACTERIA
LOW FECAL COLIFORM COUNTS AT
THE FORMER HARBOR OUTFALLS 
During the first weeks after the bay outfall started up
and all harbor discharges ended, water quality
improved greatly near the former harbor outfalls.
During subsequent months, improvements were seen
harbor-wide. 
FIGURE IV-2.TRENDS IN BACTERIA AT THE PREVIOUS HARBOR OUTFALL SITES (shown as orange circles).
A: Fecal coliform levels at the old NITP outfalls dropped after 1998. B: Fecal coliform decreased at the DITP out-
falls after 2000. Since the closing of the NITP and DITP outfalls in July 1998 and September 2000 respectively, fecal
coliform counts have been consistently far below the state standard of 200 colonies per100 milliliters. 
35 AFTER THE OUTFALL 
K A R E N - J A Y N E D O D G E 
Digesters at the Deer
Island Treatment Plant
Changes in
Boston Harbor

20
15
10
5
0
J F M A M J J A S O N D
2000 
Range 
1993-1999
tfall Bay outfall
ened opened
Monthly mean ammonium conc. (umol/L)
FIGURE IV-3. WATER CLARITY AT THE FORMER
HARBOR OUTFALL SITES. A. NEAR DEER ISLAND,
clarity doubled in 2000, a direct result of the opening of
the bay outfall. B. SECCHI DEPTHS also increased at the
Nut Island outfall site first after the opening of the inter-
island tunnel in July 1998, and then after the opening of
the bay outfall.
1997 1998 1999 2000 2001
J F M A M J J A S O N D J F M A M J J A S O N D J F M A M J J A S O N D J F M A M J J A S O N D J F
1997 1998 1999 2000 2001
J F M A M J J A S O N D J F M A M J J A S O N D J F M A M J J A S O N D J F M A M J J A S O N D J F
Secchi depth (meters)
0
1
2
3
4
5
6
7
Secchi depth (meters)
0
1
2
3
4
5
6
7
NITP closed
A. DEER ISLAND OUTFALL
B. NUT ISLAND OUTFALL
DITP outfalls
closed and
Bay outfall
opened
DITP outfalls
closed and
Bay outfall
opened
NITP closed 
36 AFTER THE OUTFALL 
igure IV-4 compares average concentrations of ammonium by month,
1993-1999, with levels measured in 2000. The rapid, harborwide
decrease in ammonium after discharges ended was especially notable
in the winter months, the period when ammonium had formerly increased. 
AMMONIUM
80% LESS AMMONIUM AROUND THE FORMER OUTFALLS 
F 
FIGURE IV-4. DECREASED AMMONIUM LEVELS AFTER THE BAY
OUTFALL OPENED. Range of average ammonium levels harbor-wide
between 1993-1999 (shaded area) compared to 2000 (green line), the
year the bay outfall opened. The 2000 line after September decreases to
below the range of concentrations seen during harbor discharges.This
rapid and large decrease in ammonium may prove to be one of the
largest improvements in Boston Harbor. 
N A D I N E S M O S K E 
WATER CLARITY
WATER CLARITY HAS INCREASED AT THE FORMER OUTFALLS

WRA's discharge permit for the bay out-
fall has strict monitoring require-
ments designed to identify
unexpected impacts from
operation of the outfall.
There is little doubt that the Boston
Harbor Project benefits the marine envi-
ronment and the people of the region, but
moving the effluent outfall from the harbor to
9.5 miles out into Massachusetts Bay caused some
concern. To address these concerns, MWRA imple-
mented an extensive monitoring program to measure
the health of the bay (Figure IV-5). The monitoring is
managed by MWRA scientists and carried out by
teams from consulting firms, universities, research
institutions, and government agencies. These scien-
tists conduct oceanographic studies of the bay's
water, plankton, sediment, and fish and shellfish to
understand how the ecosystem functions, and to
measure environmental effects of MWRA pollution
abatement projects.
MWRA's goals for Boston Harbor and
Massachusetts Bay are based on concerns
expressed by the public during the planning
of the Boston Harbor Project. These goals
include beaches safe for swimming, healthy
marine resources, seafood safe for eating,
and protection of harbor and bay aesthetics.
The remainder of this report describes some
early observations of the environment of
Massachusetts Bay since the outfall began operating
in September 2000.
n the next decade, we expect that Boston Harbor
will continue to improve. Sewage effluent, which
formerly constituted 40% of the freshwater flow
into the harbor, is gone. Because the harbor is no
longer the receptacle for sewage effluent and sludge,
water quality will get better, the bottom sediments
will continue to cleanse themselves, and sea life will
grow healthier.
However, as the large and obvious problems in
the harbor are being resolved, other challenges have
become more apparent. Now, the Mystic, Charles,
and Neponset rivers are the major freshwater
sources to the Boston Harbor estuary—and the
rivers carry pollutants to the harbor from upstream
watersheds. Furthermore, Boston Harbor still expe-
riences pollution problems typical of any water body
near a major city. Contaminants from the air, storm
runoff, and combined sewer overflows have measura-
ble impacts, affecting people and wildlife.
These watershed protection and pollution preven-
tion problems are difficult to assess and require new
approaches that cross many traditional jurisdic-
tions—in a sense, they are even more challenging
than MWRA’s construction of modern wastewater
treatment facilities. The Boston Harbor Project has
helped to transform what was once called the “dirti-
est harbor in America” to the centerpiece of metro-
politan Boston. Realizing the full benefit of this
investment will require better technical understand-
ing of the remaining pollution sources and their
impacts, as well as coordinated efforts by local, state,
and federal agencies, businesses, and residents. 
I
What is the future 
of the harbor?
Massachusetts Bay monitoring 
M Alexandrium ,
also called red
tide
Outfall Monitoring Science
Advisor y Panel
An independent panel of scientists, the Outfall
Monitoring Science Advisory Panel (OMSAP), reviews
monitoring data and provides advice on key scientific
issues related to the discharge permit. OMSAP also
provides advice concerning any proposed modifications
to the monitoring or contingency plans. (Visit OMSAP’s
web page at: www.epa.gov/region01/omsap/).
Humpback whale in Massachusetts
Bay. Certified marine mammal
observers are on all MWRA surveys. 
R O B E R T M I C H E L S O N 
37 AFTER THE OUTFALL

ne of MWRA’s tasks was to determine if the
new outfall was working as expected–was the
effluent going where it should?
In July 2001, a major dye study of the effluent suc-
cessfully tracked the location and dilution of the
DITP effluent discharge in Massachusetts Bay.
The study measured the actual dilution fac-
tor at the outfall to confirm whether the
outfall is working as expected.The moni-
toring team added an environmentally
friendly, rose-colored dye (rhodamine) in a
measured amount at the DITP . The dilu-
tion of the dye at the outfall was followed by
tracking it and sampling with shipboard instru-
ments as the dye emerged from the outfall diffuser
and mixed with the surrounding water. Results from
the field data showed effluent initial dilution of about
100 to 1, at a minimum, within 50 meters of the dis-
charge.This was within the expected range. 
O 
Water quality
monitoring, nearfield
q y
Water quality
monitoring, farfield
q y
Flounder, lobster, or
mussel sampling
Soft sediment
bottom surveys
USGS mooring
Outfall diffuser
EFFLUENT PLUME STUDIES
A DYE STUDY SHOWED THAT THE
OUTFALL IS WORKING AS DESIGNED 
arly sampling studies also measured ammonium,
which is a useful tracer of the effluent plume.The
transfer of effluent discharge from the harbor to
the bay clearly affected concentrations close to the new
outfall. Prior to outfall start-up, ammonium was rela-
tively low throughout the nearfield. By late September,
concentrations were higher, indicating the presence of
effluent.The ammonium monitoring data showed a
pattern that was similar to the computer model’s pre-
diction of outfall dilution (Figure IV-6). 
WATER COLUMN STUDIES
MONITORING DATA MATCHED OUTFALL
PREDICTIONS FOR BEFORE AND AFTER
THE DISCHARGE BEGAN 
E 
38 AFTER THE OUTFALL
FIGURE IV-5. SAMPLING SITES THROUGHOUT MASSACHUSETTS BAY. As part of the permit that allows the
MWRA to operate its new Massachusetts Bay outfall, MWRA scientists and consultants have set up “nearfield” and
“farfield” stations.The nearfield stations are within about 3 miles of the outfall diffuser, to monitor any changes
occurring in the immediate vicinity of the discharge.The farfield stations are in Boston Harbor, Massachusetts Bay,
Cape Cod Bay, and the Stellwagen Bank National Marine Sanctuary to assess any changes that may be occurring
distant from the discharge.A cooperative USGS-MWRA project maintains a moored array of water and current
meters, and suspended sediment samplers near the outfall site. 
The “Tow-yo”
was used to make
water quality
measurements during
the dye-dilution test.

DILUTION AREA
(Square miles)
< 200
200 - 400
400 - 600
600 - 800
800 - 1000
>1000
3
30
151
48
54
A2. MODEL PREDICTION OF EFFLUENT DILUTION-
BAY OUTFALL LOCATION
DILUTION AREA
(Square miles)
< 200
200 - 400
400 - 600
600 - 800
800 - 1000
>1000
>16
12-16
8-12
4-8
background (less than 4)
no data
>16
12-16
8-12
4-8
background (less than 4)
no data
77
56
59
77
116
A1. MODEL PREDICTION OF EFFLUENT DILUTION-
HARBOR OUTFALL LOCATIONS
B1. ACTUAL MEASUREMENT OF AMMONIUM-
HARBOR OUTFALL LOCATION, OCTOBER 1999
B2. ACTUAL MEASUREMENT OF AMMONIUM-
BAY OUTFALL LOCATION, OCTOBER 2000
CONCENTRATION (micromoles per liter) CONCENTRATION (micromoles per liter)
FIGURE IV-6: MODEL
PREDICTIONS OF
EFFLUENT DILUTION
COMPARED TO MONI-
TORING RESULTS.
A:Averaged computer
model predictions of efflu-
ent dilution.These maps,
generated by USGS before
the outfall was built, show
dilution contours from the
harbor and bay outfall
locations.The harbor
model shows a large area
of highly concentrated
effluent centered in the
harbor but spreading east
and south, into
Massachusetts Bay and
south of Boston. In com-
parison, the bay outfall has
a small patch of effluent
centered around the dif-
fuser, with dilution rapidly
increasing away from the
outfall.
B:Ammonium concentra-
tions, a good tracer of
effluent, were measured
while the outfall was at
Deer Island, and after the
bay outfall went on-line.
The pattern of ammonium
concentration agrees well
with the model, giving sci-
entists and engineers con-
fidence that we under-
stand how the outfall is
functioning. A lesser area
is affected, and ammonium
levels in the harbor have
decreased dramatically. 
39 AFTER THE OUTFALL

here was an unusually large bloom of chloro-
phyll at the time the outfall began operating.
The detection of the event, and subsequent
use of data from many sources to understand it,
shows how MWRA’s monitoring was able to detect
an unusual environmental occurrence and discern if
it was outfall-related.
When the outfall began operation, chlorophyll
levels were already unusually elevated, and contin-
ued to increase during the fall of 2000.
Scientists compared chlorophyll levels near the
outfall to those elsewhere and found that chloro-
phyll was high throughout the region. Satellite
imagery confirmed that there was a region-wide
algal bloom that ranged from New Jersey to the
Bay of Fundy (Figure IV-7, last panel). Boston
Harbor, Cape Cod Bay, the coastal stations, and the
offshore stations had annual mean chlorophyll lev-
els that were higher in 2000 than had been
observed since 1992.
The monitoring team closely followed the
progress of this bloom throughout the fall, winter,
and following spring. Throughout this period, there
were no unusual elevations of nuisance algal
species, and dissolved oxygen in the water column
was somewhat higher than usual.
Factors causing this unusual fall bloom apparent-
ly did not last until spring. By the winter/spring of
2001, chlorophyll levels had declined to levels lower
than in 1998 and 1999 (Figure IV-8). All the evi-
dence suggested that this unusual bloom was inde-
pendent of the MWRA outfall and that there were
no adverse effects. 
250
200
150
100
50
0 92 93 94 95 96 97 98 99 00
Outfall
Start-up
Fall Mean
Fall Caution Level Threshold
A. FALL CHLOROPHYLL 1992-2000
Milligrams per square meter
CHLOROPHYLL A LARGE FALL BLOOM IN 2000
FIGURE IV-8. SEASONAL CHLOROPHYLL
LEVELS NEAR THE BAY OUTFALL, 1992-2001.
These are average nearfield chlorophyll levels for
each year by season.
A: FALL: In 2000, chlorophyll was very high, just as
the outfall started-up
B: WINTER/SPRING: Although the winter/spring of
1999 and 2000 had relatively high chlorophyll, the
winter of 2001 following the large fall bloom in 2000
had only average chlorophyll levels.
For both graphs, MWRA’s contingency plan thresh-
olds are indicated.When the threshold is exceeded,
this indicates an unusual occurrence that may war-
rant further study or other action. 
FIGURE IV-7. SATELLITE IMAGES OF CHLOROPHYLL IN THE SOUTHERN GULF OF MAINE show a region-
wide increasing trend in chlorophyll levels throughout the Gulf of Maine since 1997.This regional information is an
important aid to MWRA’s monitoring team in interpreting sampling data like the elevated chlorophyll measurements
in fall 2000. It is clear from the satellite image that the high chlorophyll was widespread, and not just near MWRA’s
outfall. Scientists are unsure what caused this pattern of increases, but suspect that an ocean-wide fluctuation in
nutrient levels may have been a factor. In 2001, chlorophyll levels declined (not shown). 
40 AFTER THE OUTFALL 
T 
250
200
150
100
50
0 92 93 94 95 96 97 98 99 00 01
Winter/Spring Mean
Winter/Spring Caution Level Threshold
B. WINTER/SPRING CHLOROPHYLL 1992-2001
Milligrams per square meter
Outfall
Start-up

sediment contaminant survey was conduct-
ed in the fall of 2000 after the outfall came
on line. Concentrations of organic and inor-
ganic contaminants were similar to those measured
prior to the outfall coming on line. In July 2001,
the monitoring team carried out the annual video
and photographic survey of the plant and animal
communities that live on rocks near the outfall.
Using a remotely operated vehicle, or “ROV,” scien-
tists were able to document abundant life on and
near active diffuser heads, including densely grow-
ing sea anemones, sea squirts, starfish, flounder,
cod, sponges and other animals, shown below. Data
gathered so far show that the outfall is functioning
as anticipated—providing rapid dilution to the
effluent—and no significant adverse impacts have
been observed. 
Before outfall
start-up 2.0
Fecal coliform
1.0 
Enterococcus 
After outfall
start-up
2.2 1.1
Geometric mean bacteria counts
(colonies/100 ml) at new outfall site 
WRA monitors bacterial water quality in the
bay to assure that the operation of the out-
fall does not adversely affect shellfish-grow-
ing waters. Every month, MWRA collects water
samples at twelve locations in the bay. The samples
are analyzed for the sewage indicator bacteria fecal
coliform and
Enterococcus. Fecal coliform and
Enterococcus counts in Massachusetts Bay have
remained low following the opening of the new out-
fall (Table IV-1). The study was able to detect a
slight increase at stations directly over the outfall
diffuser; no changes were found further away. 
41 
B A R B A R A H E C K E R 
Go back to the Table of Contents 
M 
TABLE IV-1: BACTERIA COUNTS AT THE BAY
OUTFALL SITE. The FDA shellfishing standard is less
than 14 fecal coliform colonies per 100 ml. 
A 
Chris Wu of MWRA’s
Department of
Laboratory Services
tests water samples
for bacteria. 
C L A U D I A O G I L V I E 
t is rewarding to witness the recovery of a
significant resource like Boston Harbor, but
this report makes clear that although the
“Boston Harbor Project” is finished, the
“Harbor Clean-up” is not.The removal of
treatment plant effluent from the harbor
exposed shoreline contamination.The har-
bor’s tributary rivers suffer from urban runoff
and low river flow. MWRA’s CSO Plan,
scheduled for completion in 2008, will reduce
wet-weather pollution at the shoreline and in
the rivers. But there are many causes of the
remaining pollution problems, some as simple
as a sewer pipe incorrectly connected to a
storm drain, and others as complex as
eutrophication in rivers caused by watershed-
wide patterns of water use and land develop-
ment. MWRA’s investment in environmental
quality continues beyond the Boston Harbor
Project, exemplified by extensive monitoring
in Massachusetts Bay for outfall effects, imple-
mentation of the CSO Plan, control of infiltra-
tion and inflow, and construction and mainte-
nance of the sewer system. MWRA’s work
must be complemented by continued efforts
by municipalities, advocacy groups, and regula-
tory agencies to understand and address
water quality problems, and to ensure the
continued recovery of the harbor and its
watershed. 
I 
Conclusion 
Anemones and other
animals growing on an
active outfall diffuser.
BACTERIA IN THE BAY
COUNTS REMAIN LOW
EARLY OBSERVATIONS ON
THE SEAFLOOR
ABUNDANT SEA LIFE AT THE OUTFALL

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