Boston Harbor water quality, 1994 to 2015

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Boston Harbor Water Quality 
(1994-2015) 
Massachusetts Water Resources Authority 
Environmental Quality Department 
Report 2016-08

Citation: 
Taylor, DI. 2016. Boston Harbor Water Quality (1994-2015) . Boston: Massachusetts Water Resources
Authority. Report 2016-08. 14 p.

BOSTON HARBOR WATER QUALITY
(1994 - 2015) 
Prepared by 
David I. Taylor
Environmental Quality Water and Wastewater Dept.
Massachusetts Water Resources Authority
100 First Avenue, Charlestown Navy Yard,
Boston MA 02129
August 2016
Technical Report No. 2016-08 
Acknowledgements: Kelly Coughlin, Laura Ducott, Eric Sanderson, Chris Goodwin, Caitlyn Chafee,
Doug Hersh, Dillon Scott, Jianjung Wang

ii 
TABLE OF CONTENTS 
EXECUTIVE SUMMARY………………………………………………………… 1 
1. INTRODUCTION…………………………………………………………. 2 
2. NITROGEN AND PHOSPHORUS CONCENTRATIONS………………. 3 
3. PHYTOPLANKTON BIOMASS ………………………………………… 4 
4. SUSPENDED SOLIDS, PARTICULATE ORGANIC MATTER…………. 5 
5. TRANSPARENCY………………………………………………………….. 5 
6. BOTTOM-WATER DISSOLVED OXYGEN………………………………. 6 
7. PATHOGEN INDICATOR COUNTS……………………………………….. 7 
8. RIVER DISCHARGES, AND HARBOR PHYSICAL CONDITIONS …...... 7 
9. CONCLUSIONS……………………………………………………………… 8 
10. REFERENCES………………………………………………………………. 8 
APPENDIX ………………………………………………………………………….. 9

1 
EXECUTIVE SUMMARY 
The Massachusetts Water Resources Authority has monitored water quality in Boston Harbor since the
early to mid-1990’s in support of the Authority’s wastewater engineering projects, that have included
among others, the Boston Harbor Project, the CSO Control Plan, TRAC pretreatment program, and
programs to decrease infiltration into the sewer system. This report documents water quality in Boston
Harbor during 2015, and compares it with water quality during the preceding 20 years (1994-2014). The
aspects of water quality that were selected for examination are relevant to public use of the harbor
(microbial pathogen counts, water column transparency) and to the health of the harbor ecosystem
(nutrients concentrations, amounts of algae, particulate organic matter in the water, transparency
dissolved oxygen concentrations). In the late 1980’s, the harbor ecosystem was severely degraded, and in
many regions unsafe for human recreation use. 
Water quality in the harbor during the past 20 years has undergone significant changes (many of them
improvements), that have been the net result of the engineering projects plus background changes in
meteorology and river discharges to the harbor. Changes have included declines in water column nutrient
(nitrogen and phosphorus) concentrations, declines in pathogen indicator ( Enterococcus ) counts and the
amounts of microalgae in the water, and increases in bottom-water dissolved oxygen (DO)
concentrations. For certain aspects of water quality, specifically concentrations of nitrogen,
improvements coincided with the final Deer Island wastewater discharge diversion offshore, and values
since then have remained relatively constant. 
For other variables, including concentrations of phosphorus, bottom-water DO concentrations, and 
Enterococcus counts, conditions have progressively improved since the early 1990’s, with the
improvements continuing well after the Deer Island and Nut Island discharges to harbor were
discontinued. Annual average harbor salinity has shown a gradual increase, suggesting the marine
influence on the harbor has increased slightly during the past 20 years. This increased marine influence
may have contributed to the continued phosphorus, Enterococcus and DO improvements seen since the
discharges to the harbor were discontinued. 
Since 2011 the harbor has shown increases in phytoplankton biomass, total suspended solids and
particulate organic carbon concentrations, and s a light decrease in transparency. River discharges to the
harbor during three of the past four years during this period have been lower than average. The increased
hydraulic residence time caused by the lowered river inflows may have contributed to these recent natural
short-term changes.

2 
INTRODUCTION 
MWRA has monitored water quality in Boston
Harbor during the past 20 years in support of the
Authority’s wastewater engineering projects.
The projects have included, among others, the
Boston Harbor Project (BHP), the combined
sewer overflow (CSO) Control Plan (MWRA
2015), the TRAC pretreatment program, and
programs to decrease infiltration into the sewer
system. The BHP was implemented from 1991
through 2000, and the CSO Control Plan from
1996 to 2015. The Deer Island treatment
facility, the cornerstone of the BHP is shown in 
Figure 1. 
Fig. 1. Deer Island wastewater treatment
facility at the mouth of Boston Harbor 
In the late 1980’s Boston Harbor was viewed as
one of the most degraded coastal bays in the
USA. Figure 2 shows a conceptual model of
the changes that occur to coastal aquatic
ecosystems during degradation. Following the
large decreases in wastewater nutrient, organic
matter and microbial inputs brought about by the
BHP and CSO Control Plan, this historic
degradation of the harbor has been reversed. 
Nutrient (nitrogen and phosphorus)
concentrations and the amounts of algae (and
organic matter) in the water have decreased.
Bottom-water dissolved oxygen concentrations
have increased, and microbial pathogen
indicator counts have declined. The harbor’s
soft-sediments (and associated invertebrate
communities) have improved (Pembroke et al.
2015), and north harbor seagrass beds have
expanded (Costello and Kenworthy 2011). 
Fig. 2. Conceptual model of the changes that
occur to coastal aquatic ecosystems during
their degradation and specifically over-
enrichment. 
This report documents harbor water quality in
2015, and compares it with water quality trends
during prior years. It addresses three water
quality aspects pertinent to harbor ecosystem
health and to the health of the public using the
harbor, specifically: 
• system over-enrichment or
eutrophication (measured as amounts of
algae, nutrient concentrations and
bottom-water dissolved oxygen),

3 
• water transparency (measured as total
suspended solids and irradiance or light
attenuation coefficients), and 
• microbial pathogen indicator counts
(measured as counts of the enteric
bacterium, Enterococcus ). 
This report focuses on the main body of the
harbor, where the effects of the input changes
from multiple upstream sources are integrated.
Changes to specific locations along the
periphery of the harbor have been documented
elsewhere (MWRA 2015). 
The data we present here were collected at 9
locations as part of MWRA’s Boston Harbor
Water Quality Monitoring (BHWQM) project
( Fig. 3 ). Three locations were sampled in the
Inner Harbor (137, 138 and 24), the other six
locations were located in or at the mouth of the
Outer Harbor (106, 124, 139, 1409, 141 and
142). Station coordinates are shown in Table A-
1. 
Most locations were sampled weekly or every
two weeks. Sampling and analytical procedures
have been described in Rex and Taylor (2000).
All water samples collected from MWRA’s
sampling vessel, the Merganser ( Fig. 4 ). All
harbor-wide averages reported here are volume-
weighted by region, as described in Taylor et al.
(2011). Horizontal bars at the top of each graph
show the 15 years since the discharges to the
harbor were diverted offshore. 
2. NITROGEN (N) AND
PHOSPHORUS (P)
CONCENTRATIONS 
The BHP completed in 2001 caused harbor total
nitrogen (N) and total phosphorus (P)
concentrations to decrease ( Fig. 5 ). The bulk of
the N declines occurred between 1997/1998 and
2001, the three to four years that spanned the
two wastewater diversions, first to the harbor
mouth and then offshore. Nitrogen
concentrations since then have ranged between
18 and 22 μmol l -1 , about two thirds of what they
were during the discharges. Total nitrogen (N)
concentrations in 2015 averaged 20 μmol l -1 . 
Fig. 3. Boston Harbor showing the 9
sampling locations, and the Inner and Outer
Harbor regions of the harbor. 
Fig. 4. MWRA’s sampling vessel, the 
Merganser .

4 
Total phosphorus concentrations have shown a
progressive decline since 1995, continuing to
decline after the wastewater discharges to the
harbor were diverted offshore. Total P
concentrations in 2015 (1.2 μmol l -1 ) were the
third lowest since monitoring started. N:P 
Fig. 5. Annual average total N and total P
concentrations and total N:total P
concentration ratios, 1995-2015. 
concentration ratios declined when the
discharges were diverted offshore, but have
progressively increased since then. The 2015
N:P ratios averaged 16.5:1, similar to the
Redfield Ratio (16:1), and only slightly greater
than the average for the 15 post-diversion years. 
Approximately 90% of the total N concentration
decline brought about by the BHP was
contributed by an ammonium (NH4)
concentration decline. Ammonium was the N
fraction that made up most of the wastewater
total nitrogen discharged to the harbor pre-2001.
After the final wastewater diversion accounted
for 6% of the lowered total N. During the
discharges, ammonium contributed 21% of
water column total N. 
Declines in total N concentrations at all nine
locations in Figure A-1 (Appendix A) were
responsible for the overall harbor-wide average
N concentration decline. Ammonium
concentrations were also decreased at all nine
locations. At the three Inner Harbor locations
(137, 138 and 024), N concentrations have
continued to decline post-diversion; the lowered
concentrations at the Outer Harbor locations
during the same period have shown no trend. 
3. PHYTOPLANKTON BIOMASS 
Phytoplankton biomass in the harbor (measured
here as concentrations of chl-a) has decreased
during the past 20 years ( Fig. 6 ). Biomass
declined sharply when the wastewater
discharges were diverted offshore in 2000.
Biomass has shown a series of fluctuations since
then, when concentrations have exceeded or fell
within the biomass range during discharge years.
The first of the increases occurred two to three
years post-diversion, and the other, seven to
eight years later. The 2015 biomass values fell
on the ebb side of the latter increase. 
The N input declines brought about by the BHP
(Taylor 2010) were a major contributor to the
biomass declines that followed the discharge
diversion offshore. During neither of the post- 
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014 0
10
20
30
40
ANNUAL AVERAGE CONC.
( μ MOL L -1 ) 
Total N 
NON-NH 4
NH 4
Post-diversion 
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014 0.0
0.5
1.0
1.5
2.0
2.5
3.0 
Post-diversion
AVERAGE TP CONC.
( μ MOL L -1 ) 
Total P 
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014 0
5
10
15
20
25
30 Post-diversion
ANNUAL AVERAGE MOLAR
TN:TP RATIO 
N:P

5 
diversion increases were harbor nitrogen or
phosphorus concentrations greater than during
discharge years, suggesting processes other than
increased nutrient inputs were responsible for
the background biomass increases observed
post-diversion. 
Fig. 6. Annual (top) and summer (bottom)
average phytoplankton biomass measured as
chl-a, 1995-2015. Summer = J,J,A and S. 
The phytoplankton declines in the harbor were
evident at all except one of the nine sampling
locations ( Fig. A-2 ). Station 137 in the
uppermost Inner Harbor was the exception. The
2002-2003 phytoplankton increase was not
consistent among stations, but the biomass
increase later in the study was evident at all
locations, including 137, in fact, it was the
stations in the Inner Harbor (137, 138 and 24)
and western harbor (140) where the more recent
increases were observed. 
4. SUSPENDED SOLIDS,
PARTICULATE ORGANIC
MATTER 
Harbor total suspended solids (TSS)
concentrations increased during the period
spanned by this study ( Fig. 7 ). TSS
concentrations, which averaged 6.9 mg l -1 , were
the second highest since monitoring started. The
bulk of the increase started in 2007/2008,
reaching a maximum in 2014. All nine locations
showed the TSS concentration increases ( Fig. A-
3 ). Particulate organic C (POC) concentrations,
like the TSS concentrations, increased during the
second half of the study, but unlike for TSS,
POC concentrations at the end of the study were
lower than at the start. POC accounted for only a
small fraction of harbor TSS. The percent POC
content of TSS declined during the study,
indicating the bulk of the TSS increase was
caused by increased concentrations of suspended
inorganic rather than organic material. 
5. TRANSPARENCY 
Transparency, which in the harbor is high
compared to many other coastal systems, has
shown no trend during the past 20 years ( Fig. 8 ).
Transparency is reported here as attenuation
coefficients (k). These measure the rates at
which light attenuates as it passes through the
water column. The k values are presented as
reciprocal values, meaning the greater the value,
the greater the transparency. background
elevated TSS, POC and chl-a values observed
during these years (and shown earlier) may have
been contributing factors. 
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
2
4
6
8 
Post-diversion 
ANNUAL AVERAGE CHL-A
CONC. ( μ G L -1 ) 
PHYTOPLANKTON BIOMASS
(annual) 
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
2
4
6
8 
Post-diversion 
Summer average chl-a conc.
( μ g l -1 ) 
(summer)

6 
Fig. 7. POC, TSS and POC as % TSS (by
weight), 1996-2015. 
Transparency during the past three years (and
especially during 2013 and 2014) has been
slightly poorer than during many of the other
years since the discharges to the harbor were
discontinued. The 
Fig. 8. Vertical light attenuation coefficients,
a measure of transparency, 1996-2015. 
6. BOTTOM-WATER
DISSOLVED OXYGEN 
Summer bottom-water dissolved oxygen (DO)
concentrations in the harbor have increased
since the early 1990’s, and during 2015 the
minimum monthly-average concentrations (7.6
mg l -1 ) were the highest since monitoring started
( Fig. 9 ). During the final six years the harbor
received the discharges the minimum monthly
average DO concentrations fell below or
approached the State Standard of 6 mg l -1 . Since
then, the values averaged harbor-wide have
consistently met the standard. 
Fig. 9. Lowest monthly average bottom-
water DO concentrations observed each year,
1994-2015. 
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014 0
2
4
6
8
10
ANNUAL AVERAGE CONC.
( MG L -1 ) 
TSS 
NON-POC
POC
Post-diversion 
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
10
20
30
40
50
60 
ANNUAL POC CONC. ( μ MOL L -1 ) 
POC Post-diversion 
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
5
10
15
20
25
30 
ANNUAL POC as % TSS 
POC as % TSS 
Post-diversion 
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
-0.9
-0.8
-0.7
-0.6
-0.5
-0.4
-0.3 
ANNUAL AVERAGE PAR ATTENUATION
COEFFICIENTS ( M ) 
WATER CLARITY 
Post-diversion 
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
4
5
6
7
8
9
10 
Post-diversion
Minimum monthly bottom-water
DO conc. ( MG L -1 ) 
Bottom-water DO 
State
std.

7 
The DO increase during the period spanned by
the report was evident at all nine locations ( Fig.
A-4 ). The baseline concentrations from which
the increases occurred differed among locations.
At station 137, bottom-water DO concentrations
failed to meet the Standard during all of the final
six years the harbor received the discharges.
Since then, the standard has been met at this
location five of the 15 years. At four of the
locations, the standard was not met during only
one of the 15 years; at the remaining four
locations (three of them in the south harbor), the
standard was met during all fifteen post-
diversion years. 
7. PATHOGEN INDICATOR
COUNTS 
Harbor recreational use requires pathogen
indicator bacteria be monitored ( Fig. 10 ). 
Enterococcus counts in 2015 were the second
lowest since 1994, and averaged 3 colony
forming units 100 ml -1 . Counts <35 colony
forming units 100 ml -1 meet the State Standard
for recreational marine waters. 2015 counts at
all nine locations were well below levels seen
during the period the harbor received the
wastewater discharges ( Fig. A-5 ). 
Fig. 10. Annual average Enterococcus counts
by year, 1994-2015. 
8. RIVER DISCHARGES AND
HARBOR PHYSICAL
CONDITIONS 
Annual average river flows into the harbor
during 2015 (1.5 x10 6 m 3 d -1 ) were the third
lowest since 1990 ( Fig. 11 ). Flows during three
of the past four years (2015 included), have been
the lowest since 1990. Salinities during 2015
were the highest since 1990 ( Fig. 12 ). 
Fig. 11. Average river discharges, 1991-2015
(data from USGS). 
Fig. 12. Average harbor salinities, 1994-2015. 
From February through June water temperatures
during 2015 were 2 o C to 5 o C lower than during
the same months during all years since the
discharges were discontinued ( Fig. 13 ), though
October temperatures were the warmest ever
observed. 
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014 0
4
8
12
16
20 Post-diversion
GEOMETRIC MEAN COUNTS
( CFU 100 ML -1 ) 
Enterococcus 
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
2014
Long-term
average
including
2015
2012
2010
2008
2006
2004
2002
2000
1998
1996
ANNUAL AVERAGE RIVER FLOWS
(x10 6 M 3 D -1 )
1994 
RIVER DISCHARGE 
Post-diversion 
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
26
28
30
32
34
SALINITY (PPT) 
SALINITY 
Post-diversion

8 
Fig. 13. Average water temperatures by
month. Red line shows 2015 data; blue lines
shown 2001 to 2014. 
9. CONCLUSIONS 
Many of the harbor water quality improvements
observed during the implementation of the BHP
and the CSO Control Plan have been sustained
into 2015. The ending of the wastewater
discharges in 2000 caused harbor total nitrogen,
total phosphorus, and particulate organic C
concentrations, and phytoplankton biomass and 
Enterococcus counts to decline. 
During the 16 years since the discharges were
discontinued, total P concentrations and 
Enterococcus counts have continued to decline.
DO concentrations too have continued to
increase post-discharge. 2015 total P
concentrations and Enterococcus counts were
the lowest seen since 1994, and DO
concentrations the highest. 
Certain variables have shown fluctuations during
the years since the discharges were discontinued.
Phytoplankton biomass, POC and TSS
concentrations have all increase between about
1995/1996 (five to six years after the discharges
to the harbor were discontinued) to 2013 or
2014. 
Biomass, POC and TSS concentrations during
2015 were all higher than during most years
since the discharges to the harbor were
discontinued. 2015 TSS concentrations were the
second highest since monitoring started. 2015
chl-a and POC concentrations were elevated, but
lower than during most post-diversion years. 
10. REFERENCES 
Costello, CT, Kenworthy, WJ. 2011. Twelve-
year mapping and change analysis of eelgrass
( Zostera marina ) areal abundance in
Massachusetts Bay (USA) identifies statewide
declines. Estuaries and Coasts 34: 232-242. 
MWRA 2015. Combined Sewer Overflow
Control Plan: Annual Progress Report 2014.
Massachusetts Water Resources Authority,
Boston. 
Pembroke A, Diaz R, Nestler EC. 2015. Boston
Harbor benthic monitoring report: 2014 results.
Boston: Massachusetts Water Resources
Authority. Report 2015-10. 37 p. 
Rex A., Taylor D.I., 2000. Combined
Work/Quality Assurance Project Plan
(CW/QAPP) for Water Quality Monitoring and
Combined Sewer Overflow Receiving Water
Monitoring in Boston Harbor and Its Tributary
Rivers. Boston: Massachusetts Water Resources
Authority. Report 2000-ms-67. 48 p. 
Taylor D.I., 2010. The Boston Harbor Project
and large decreases in loadings of
eutrophication-related materials to Boston
Harbor. Marine Pollution Bulletin 60: 609-619. 
Taylor et al. 2011. Werme C, Keay KE, Libby
PS, Wu D, Taylor DI, Codiga DL, Coughlin K.
2015. 2014 Outfall monitoring overview.
Boston: Massachusetts Water Resources
Authority. Report 2015-11. 70p. 
0 1 2 3 4 5 6 7 8 9 10 11 12 13
-4
0
4
8
12
16
20
24
2015
D S N F M O M A A J J
MONTHLY AVERAGE TEMP.
( o C )
J 
WATER TEMPERATURE

9 
APPENDIX 
Table A-1. Boston Harbor sampling locations 
Station
Id 
Marine or
freshwater 3 Description Coordinates Monitoring
years 1 
024 Marine; Inner harbor mouth 42 20.66, 71 2.74 1993 – 2015+ 
106 Marine; Outer harbor, NE of Long Island 42 19.95, 70 57.54 1993 – 2015+ 
124 Marine; Hingham Bay, Crow Point flats 42 16.36, 70 53.86 1993 – 2015 3 
137 Marine; Mystic River mouth 42 23.21, 71 3.77 1993 – 2015+ 
138 Marine; 
l d b b 
Central inner harbor 42 21.56, 71 2.74 1993 – 2015+ 
139 Marine; Quincy Bay, SW of Hangman Island 42 17.20, 70 58.10 1993 – 2015+ 
140 2 Marine; 
l d b b 
Neponset River mouth/S. Dorchester Bay 42 18.35 71 2.43 1993 – 2015+ 
141 Marine; Outer harbor, NE of Peddocks Island 42 18.30, 70 55.85 1993 – 2015+ 
142 Marine; 
l d b b 
Outer harbor, President Roads, south
channel 
42 20.35, 70 55.89 1993 – 2015+

10 
Fig. A-1. Annual total N concentrations partitioned into the non-ammonium and ammonium
fractions at the nine sampling locations, 1995-2015.

11 
Fig. A-2. Summer average phytoplankton biomass (measured as chlorophyll-a) at nine harbor
sampling locations, 1995-2015, Summer = J, J, A and S.

12 
Fig. A-3. Annual total suspended solids (TSS) concentrations, 1995-2015.

MINIMUM BOTTOM-WATER DO *
(1994 - 2045)

Post-diversion

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14 
Fig. A-4. Lowest monthly average bottom-water DO concentrations, 1994-2015. Shaded areas
show years values failed to meet state Standard. 
Fig. A-5. Annual mean Enterococcus counts, 1994-2015.

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Boston, MA 02129
(617) 242-6000
www.mwra.com