Boston Harbor water quality, 1994 to 2014

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Boston Harbor Water Quality
1994-2014 
Massachusetts Water Resources Authority
Environmental Quality Department
Report 2015-05

Citation 
Taylor DI. 2015. Boston Harbor Water Quality 1994-2014 . Boston: Massachusetts Water
Resources Authority. Report 2015-05. 11 pp.

BOSTON HARBOR WATER QUALITY
(1994-2014) 
Prepared by 
David Taylor
Environmental Quality Water and Wastewater Dept
Massachusetts Water Resources Authority
100 First Avenue, Charlestown Navy Yard,
Boston MA 02129
June 2015 
Technical Report No. 2015-05 
Acknowledgements: Kelly Coughlin, Laura Ducott, Kristy McLean, Eric Sanderson,
Roxann Phelan and Chris Goodwin

TABLE OF CONTENTS
EXECUTIVE SUMMARY…………………………………………. 1
1.0 INTRODUCTION……………………………………………. 2
2.0 RESULTS
2.1 WATER QUALITY
2.1.1 Amounts and types of nutrients………….……. 3
2.1.2 Amounts of phytoplankton…………………….. 5
2.1.3 Suspended particulate material………….……. 6
2.1.4 Transparency……………………………..……. 7
2.1.5 Bottom-water DO………………………………. 7
2.1.6 Pathogen indicator counts……………….……. 7
2.2 PHYSICAL CONDITIONS
2.2.1 River inflows, salinity and water
temperatures…………………………….…….. 8
References……………………………………………………...……...11

1 
EXECUTIVE SUMMARY 
Water quality in Boston Harbor is affected by a large number of factors, among them infrastructure
projects that have been and continue to be implemented by the MWRA. In support of these projects,
MWRA monitors water quality in the harbor. This report documents 2014 water quality, and compares it
with water quality during the past 20 years. The report addresses issues associated with over-enrichment
(algae, concentrations of N and P, transparency and dissolved oxygen) and microbial contamination of the
harbor (pathogen indicator counts). It focuses on the main body of the harbor, the region that best
integrates the effects of all upstream infrastructure projects. Important findings from this report include: 
 Boston Harbor water quality has improved substantially during the past 20 years, and the
improvements were sustained during 2014. 2014 was a relatively dry year, with river inflows to
the harbor the second lowest since 1990. 
 2014 nitrogen (N) and phosphorus (P) concentrations were again much lower than during the
years the harbor received Deer Island and Nut Island plant discharges. N concentrations were the
fourth lowest since the discharges ended; P concentrations were the lowest since monitoring
began in 1995. N:P concentration ratios were higher than other years since the discharges were
discontinued. 
 Phytoplankton or microalgae biomass during this dry year was lower than during years the
treatment facilities discharged to the harbor, but the third highest since the discharges to the
harbor were discontinued. 
 Total suspended solids (TSS) concentrations were the highest, and transparency among the
poorest, since the discharges to the harbor were discontinued. Shoreline and salt marsh erosion
known to be a problem in the south harbor may have been responsible for the solids increase. 
 Bottom-water dissolved oxygen (DO) concentrations, which have also improved since 1994,
easily met the State Standard in 2014 (6 mg l -1 ). Bottom-water DO concentrations have been
consistently high since 2009. 
 2014 Enterococcus counts were among the lowest observed since 1996, and easily met the State
swimming standard. Enterococcus counts too have declined during the past 20 years. 
 Water quality in the main body of the harbor continues to be much improved.
.

2 
1.0 INTRODUCTION 
During the past 25 years the MWRA has
undertaken a series of engineering projects to
better collect, treat and dispose of the
wastewater discharged from the City of Boston
and surrounding communities to the harbor and
its tributary rivers. These projects have included
the Boston Harbor Project (Fig. 1, Taylor 2010),
the combined sewer overflow Control Plan
(MWRA 2014), the TRAC pretreatment
program, and programs to decrease infiltration
into the sewer system. 
Fig. 1. Deer Island wastewater treatment
facility with City of Boston in background. 
Over the same period, in support of the
engineering projects, MWRA has monitored
water quality in Boston Harbor. In this report
we document the harbor water quality during
2014. The report focuses on the main body of
the harbor, because water quality in this region
integrates the impacts of pollutant inputs from
all sources. Water quality data from the
tributary rivers are reported in MWRA (2014).
This report addresses three water quality issues:
the over-enrichment of the harbor (measured as
amounts of algae, nutrient concentrations and
bottom-water dissolved oxygen concentrations),
water transparency (measured as total suspended
solids concentrations and attenuation
coefficients) and pathogen indicator counts
(measured as Enterococcus ).
This report presents data collected by MWRA at
12 harbor locations (Fig. 2). The data were
collected as part of MWRA’s Boston Harbor
Water Quality Monitoring (BHWQM) project.
Most of the 12 locations have been sampled
weekly or every two weeks since 1994. The
sampling and analytical procedures used are
described in detail in Rex and Taylor (2000).
All water samples were collected from
MWRA’s sampling vessel, the Merganser (Fig.
3, 4). 
Fig. 2. Boston Harbor showing the 12
sampling locations, and the Inner (IH) and
Outer Harbor (OH) regions of the harbor. 
All data in the report are averaged for either the
harbor as a whole, or for particular regions of
the harbor. Stations 137, 138 and 24 were
located in the Inner Harbor (IH), and stations
106, 124, 139, 140, 141 and 142 in the Outer
Harbor (OH). The horizontal bar at the top of
each Figure shows the 14 years since the

3 
wastewater treatment facility discharges to the
harbor were discontinued in September 2000. 
Fig. 3. MWRA’s sampling vessel, the 
Merganser . 
Fig. 4. Water sample collection using a Niskin
bottle. 
2.0 RESULTS
2.1. WATER QUALITY
2.1.1. Amounts and types of nutrients 
The harbor’s total N (N) concentrations in 2014
(20.6 μmol l -1 ), were higher than certain years
since the Deer Island and Nut Island discharges
to the harbor were discontinued, but lower than
during the six final years the harbor received the
discharges (Fig. 5). This applied for all nine
locations shown in Figure 6. 2014 total P (TP)
concentrations (1.2 μmol l -1 ) were the lowest
since 1995. Total N: total P concentration
ratios, which measure the amount of N relative
P, and can determine whether algae build up in
coastal systems or not, were the highest since
2000, the year the discharges were diverted
offshore. 
Fig. 5. Annual average total N and total P
concentrations and total N:total P
concentration ratios, 1995-2014. 
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
10
20
30
40
50 Post-diversion
AVERAGE TN CONC.
(  MOL L -1 ) 
Total N
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.
(  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

4 
Fig. 6. Annual average total N concentrations partitioned into the ammonium (NH4) and non-
ammonium fractions at nine locations, 1995-2014. 
For all four fractions making up the total N,
2014 concentrations fell within the range seen
since 2000 (Fig. 7). Total N concentrations in
the OH were again lower than in the IH, and in
both regions were much lower than during years
the harbor received the discharges (Fig. 8). N:P
concentration ratios were the highest since 2000.
Total N refers to dissolved inorganic N (DIN)

5 
+ particulate nitrogen (PN) + dissolved organic
N (DON), and DIN refers to NH4 + NO3+2. 
Fig. 7. Annual average concentrations of the
four fractions making up total N (N), 1995-
2014.
Fig. 8. Annual average total N concentrations
in the Inner Harbor and Outer harbor, 1995-
2014.
2.1.2. Amounts of phytoplankton 
2014 summer phytoplankton biomass (measured
as chlorophyll a) at all locations combined
averaged 4.9 μg l -1 (Fig. 9). 2014 concentrations
were slightly lower than in 2013, but the third
highest since the discharges to the harbor were
discontinued. The slightly elevated chl-a
concentrations during 2014 were observed at all
locations, and especially at the locations in the
IH (Fig. 10). 
Fig. 9. Summer average phytoplankton
biomass measured as chl-a, 1995-2014.
Summer = Jun, Jul, Aug, Sept. 
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
2
4
6
8
10 Post-diversion
AVERAGE NH 4 CONC.
(  MOL L -1 ) 
AMMONIUM
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
2
4
6
8
10 Post-diversion
AVERAGE NO 3+2 CONC.
(  MOL L -1 ) 
NITRATE + NITRITE
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
2
4
6
8
10 Post-diversion
AVERAGE PART. N CONC.
(  MOL L -1 ) 
PARTICULATE N
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
5
10
15
20 Post-diversion
AVERAGE DON CONC.
(  MOL L -1 ) 
DISSOLVED ORGANIC N
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
10
20
30
40
50
OH 
AVERAGE TN CONC.
(  MOL L -1 ) 
IH
Total N 
Post-diversion
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
2
4
6
8
2013 
Post-diversion 
2011
2009
2007
2005
2003
2001
1999
1997
1995
Summer average chl-a conc.
(  g l -1 ) 
PHYTOPLANKTON BIOMASS
(summer)

6 
Fig. 10. Summer average chl-a, 1995-2014.
2.1.3. Suspended particulate material 
2014 TSS concentrations were by far the highest
observed since 1996 (Fig. 11). TSS increases in
the OH, and especially Stations 140, 139 and
124 were responsible for the increases (Fig. 12). 
Particulate organic C (PC), a measure of the
organic content of the TSS, was also elevated in
2014, but not to the same extent as TSS. 2014
PC concentrations were the highest since 2000,
but lower than during years the harbor received
wastewater discharges. PC expressed as percent
TSS was the lowest since 1996.

7 
TSS was the lowest since 1996 
Fig. 11. TSS, PC and PC as % TSS, 1996-
2014. 
2.1.4. Transparency 
Consistent with the harbor’s elevated TSS, water
transparency during 2014 was the poorest since
1996 (the first year for which harbor-wide
attenuation coefficient data were available (Fig.
13). Harbor attenuation coefficients in 2014
averaged 0.63 m -1 . Note, the attenuation
coefficients, as reported, are reciprocal values,
so the higher the value, the more rapid light
attenuation is, and the poorer the transparency. 
2.1.5. Bottom-water DO 
Minimum monthly average bottom-water DO
concentrations in 2014 (7.6 mg l -1 ) were among
the highest since 1994 (Fig. 14). Bottom-water
DO has increased since 1994, and the elevated
2014 concentrations were a continuation of this
trend. Both in the IH and the OH, the minimum
monthly DO concentrations easily met the State
Std of 6 mg l -1 (Fig. 15). DO was measured by
lowering YSI or Hydrolab sondes from the
sampling vessel into the water (Fig. 16). 
2.1.6. Pathogen indicator counts 
Recreational use of the harbor requires
monitoring for pathogen indicator bacteria. 
Enterococcus counts in 2014 were low and
averaged 3 colony forming units 100 ml -1 (Fig.
17). Counts in the IH were higher than in the
OH, as has been the case in all years since 1995.
Counts in both regions easily met State
Standards, and in the IH the 2014 counts were
the lowest since monitoring was started in 1995
(Fig. 18, 19). 
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
2
4
6
8
10 
ANNUAL AVERAGE TSS CONC.
( MG L -1 ) 
TSS 
Post-diversion 
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
10
20
30
40
50
60 
ANNUAL AVERAGE PC CONC.
(  MOL L -1 ) 
PC 
Post-diversion 
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
5
10
15
20
25
30 
ANNUAL PC as % TSS 
PC as % TSS 
Post-diversion

8 
Fig. 12. Annual average TSS concentrations, 1996-2014.
2.2. PHYSICAL CONDITIONS
2.2.1 River inflows, salinity and water
temperature 
2014 river flows averaged 1.34 x10 6 m 3 d -1 , the
second lowest since 1990 (Fig. 20).
Accordingly, salinity both in the IH and the OH 
were greater than in most years (Fig. 21). Water

9 
Fig. 13. Annual average attenuation
coefficients, 1997-2014
Fig. 14. Minimum monthly harbor-wide
average bottom-water DO concentrations
observed each year, 1994-2014
Fig. 15. Minimum monthly average bottom-
water DO concentrations in IH and OH. 
Fig. 16. Sampling equipment preparation
onboard the Merganser .
Fig. 17. Average Enterococcus counts by
year, 1994-2014.
Fig. 18. Average geometric mean 
Enterococcus counts in the IH and OH, 1994-
2014. 
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9 
ANNUAL AVERAGE K ( M -1 ) 
TRANSPARENCY 
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. 
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
3
4
5
6
7
8
9
OH 
Minimum monthly average bottom-water DO
( MG L -1 ) 
IH
BOTTOM-WATER DO 
Post - diversion
State
std 
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
2
4
6
8
10
12
14
16
18
20 Post-diversion
AVERAGE GEOMETRIC MEAN COUNTS
( CFU 100 ML -1 ) 
Enterococcus 
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
0
2
4
6
8
10
12 
Post-diversion 
OH 
AVERAGE GEOMETRIC MEAN COUNTS
( CFU 1OO ML -1 ) 
IH
ENTEROCOCCUS

10 
Fig. 19. Annual geomean Enterococcus counts, 1994-2014. 
temperatures during late winter/early spring
2014 were lower than average, but the opposite
applied during June and from August through
October (Fig. 22).

11 
Fig. 20. Annual average river inflows into
Boston Harbor. Data are sum of discharges
from Charles, Mystic, Neponset and
Weymouth- Weir rivers (data from USGS). 
Fig. 21. Comparison of annual average
salinity in the IH and OH, 1994-2014.
Fig. 22. Average water temperatures by
month. Blues lines show data for 2001-2013. 
References 
MWRA 2014. Combined Sewer Overflow
Control Plan: Annual Progress Report 2013.
Massachusetts Water Resources Authority,
Boston.
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. 
1990
1992
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
3.5
2013
2011
2009
2007
2005
2003
2001
1999
1997
1995
1993
ANNUAL AVERAGE RIVER FLOWS
(x10 6 M 3 D -1 )
1991 
RIVER DISCHARGE 
Post-diversion 
1994
1996
1998
2000
2002
2004
2006
2008
2010
2012
2014
24
26
28
30
32
34 Post-diversion 
OH 
AVERAGE SALINITY
( PSU ) 
IH
Salinity 
0 1 2 3 4 5 6 7 8 9 10 11 12 1 3
-4
0
4
8
12
16
20
24
2014
D S N F M O M A A J J
MONTHLY AVERAGE TEMP.
( o C )
J 
WATER TEMPERATURE