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24 months after offshore transfer, 2003

Massachusetts Water Resources Authority · from the MWRA · 95 pages · 2.5 MB
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24 months after ‘offshore transfer’:
an update of water quality
improvements in Boston Harbor
Massachusetts Water Resources Authority
Environmental Quality Department
Report ENQUAD 2003-04

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24 months after ‘offshore transfer’: an update of water
quality improvements in Boston Harbor 
prepared by 
David I. Taylor
MASSACHUSETTS WATER RESOURCES AUTHORITY
Environmental Quality Department
100 First Avenue
Charlestown Navy Yard
Boston, MA 02129
(617) 242-6000
July 2003
Report No: 2003-04

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Citation
Taylor D. I. 2003. 24 months after ‘offshore transfer’: an update of water quality improvements in
Boston Harbor. Boston: Massachusetts Water Resources Authority. Report ENQUAD 2003-04. 94 p

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TABLE OF CONTENTS 
Page
Executive Summary ……………………………………………… 5
Introduction ……………………………………………………… 8
Approach of the report……………………………… .…. 9
Methods
Field sampling and laboratory analytical procedures…… 12
Data and statistical analysis………………………………. 14
Results
Nitrogen concentrations...………………………………… 17
Concentrations of phosphorus ………………………….. 26
Molar ratios of N:P……………………………………….. 33
Phytoplankton biomass (chlorophyll-a)……………..…… 38
Suspended particulate material…………………………… 44
Water clarity.……………………………….……………. 50
Bottom-water dissolved oxygen (DO)……………………. 54
Sewerage-indicator bacteria……………………………… 57
Salinity and water temperature…………………………… 62
Discussion
Overview of changes during the 24-months versus
first 12-months……………………………………….. 68
Observed versus predicted changes.. ……………………. 76
Acknowledgements………………………………………………. 79
Literature cited …………………………………………………… 80
Appendix A ………………………………………………………. 84

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EXECUTIVE SUMMARY 
In September 2000, the wastewater discharges from the Deer Island treatment facility
(WWTF) to Boston Harbor were transferred 16 km offshore for diffusion into the bottom
waters of Massachusetts Bay. This transfer, here termed ‘offshore transfer’, ended over a
century of wastewater discharges from the City of Boston and surrounding communities
to Boston Harbor.
In 2002, we reported some of the improvements in water quality of the Harbor during the
first 12-months after offshore transfer. In this report, we update our previous report, and
document the changes in Harbor water quality for the first full 24-months after transfer.
Others will report on changes to components of the Harbor other than the water column,
and also to Massachusetts Bay.
In this report we compare water quality during the first 24 months after offshore transfer
(from September 7 2000 through August 31 2002), with water quality during a 3- to 7-
year ‘baseline’ period before transfer. This comparison means that the report only
identifies the relatively large changes that fell outside of the range seen in the Harbor
during baseline.
One of the improvements we observed in the Harbor water column was a reduction in
concentrations of N and P, the 2 nutrients most responsible for eutrophication (or over-
enrichment’ of aquatic systems. For both N and P, the decreases were highly significant
(p = or < 0.01), and observed over most of the area of the Harbor. They were also seen
during both 12-months making up the 24-months.
For both N and P, the dissolved inorganic fractions contributed most of the decreases;
these being the fractions that, in turn, contributed most of the N and P in the wastewater
discharged to the Harbor before transfer. Ammonium, the fraction that contributed most
of the dissolved inorganic nitrogen (DIN) in the wastewater, was, in turn, most
responsible for the decrease in DIN in the Harbor.

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The Harbor also showed a significant decrease in Harbor-wide average concentrations of
chlorophyll-a (chl-a) – a measure of phytoplankton biomass (p = or < 0.05, but > 0.011).
Based on the relationships demonstrated between chl-a and N loadings by others, the
decrease in chl-a was likely the result of the decrease in N loadings to the Harbor that
followed transfer. The decrease for chl-a was smaller and more localized than for most
nutrients.
We were also able to detect an improvement in water clarity in the Harbor over the 24-
months. We monitored two measures of clarity - vertical attenuation coefficient (k) and
secchi depth. For both we could not detect an improvement for the data averaged
Harbor-wide for the full 24-months, but we were able to detect improvements at
individual stations.
Bottom-water dissolved oxygen (DO) was also improved during the 24-months. For both
DO variables we monitored (DO concentrations and DO % saturation), the improvements
were focused in mid-summer, when DO in the Harbor tended to be lowest. As for most
nutrients and for chl-a, we were able to detect improvements for both variables for the
data averaged Harbor-wide. As for chl-a, but unlike for nutrients, the improvements were
focused in specific areas of the Harbor.
We were also able to detect decreases in counts of both types of sewerage-indicator
bacteria that we monitored – Enterococcus and fecal coliform. For Enterococcus, for
which we had a full 24-months of data after transfer, we observed highly significant
decreases for Harbor-wide average counts. As for chl-a and DO, the increases were
focused in specific areas of the Harbor – in this case, the outer, Outer Harbor.
For many of the variables that we monitored, the improvements we observed for the 24-
months (and have reported here) were as we saw for the first 12-months after transfer.
For many variables, including the total and dissolved inorganic forms of N and P, and the
molar ratios of N:P, the Harbor showed decreases over most of its area during the first
12-months, and we saw this again for the 24-months.

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For other variables, including especially the particulate variables (particulate N,
particulate P, chl-a and PC), and variables related to the particulates (e.g. water clarity),
the improvements were smaller and more localized for the 24-months than for the first
12-months. For these variables, the improvements seen during the first 12-months were
apparently ‘dampened’ during the second twelve
For other variables, including total P, nitrate + nitrite, mid-summer bottom-water DO and
counts of Enterococcus, the improvements for the 24-months were larger and more
extensive than during the first 12-months. For these, the changes over the first 12-months
were ‘accentuated’ during the second 12-months.
This report confirms the conclusion of our earlier report that water quality in Boston
Harbor has improved significantly since wastewater discharges to the Harbor ended. For
many variables, the improvements for the 24-months as a whole were very similar to the
improvements predicted by others using complex numerical models. They were also
similar to the decreases we observed during the first 12-months.
The differences in patterns of responses we observed between the first 12-months and 24-
months for certain variables, probably reflects interactions of the effects of offshore
transfer with the effects of natural, inter-annual changes in water quality. The
improvements in water quality that followed transfer were apparently modified, in certain
cases ‘dampened’, and in others, ‘enhanced’, during the drier second of the two 12-
months.

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INTRODUCTION 
September 2000 saw completion of one of the final and most conspicuous milestones of
the Boston Harbor Project (BHP), the transfer 16-km offshore of the wastewater formerly
discharged from the Deer Island wastewater treatment facility to Boston Harbor. This
transfer, here referred to as ‘offshore transfer’, ended over a century of direct discharges
of wastewater from the City of Boston and surrounding communities to the Harbor.
Numerical modeling studies conducted before the transfer by HydroQual 1995) and
others had predicted the offshore transfer would lead to improvements in the water
quality of Boston Harbor, with only minimal impacts on Massachusetts Bay.
Some of the improvements in the Harbor during the first 12-months after offshore
transfer were reported by Taylor (2002).
The improvements that we observed in the Harbor during the first 12-months included
Harbor-wide reductions in concentrations of N and P, and of chlorophyll-a (chl-a), a
measure of phytoplankton biomass. Also observed were localized increases in water
clarity and of bottom-water dissolved-oxygen (DO), and a Harbor-wide decrease in
water-column counts of sewerage-indicator bacteria. Libby et al. (2002), Werme and
Hunt (2002) and others have reported the changes in the Bay.
An additional 12-months have passed since wastewater discharges to the Harbor were
ended, and the purpose of this report was to update our earlier report, and document the
changes in the Harbor water-column for the first full 24-months after transfer. We also
compared the changes during the two 12-months making up the 24-months, to determine
any ‘inter-annual’ variability in the responses of the Harbor.
This report (like our previous report) focuses on the water column alone; others will
address changes to other components of the Harbor, including the sediments, and fish and
shellfish. The report addresses three aspects of the Harbor water column - indices of

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eutrophication (or over-enrichment) of the water column, water clarity (or transparency),
and counts of sewerage indicator bacteria in the water column.
These three aspects were addressed because of their relevance to the health of the public
using the Harbor, and to the ‘health’ of the Harbor ecosystem. Others will report changes
to other components of the water column, including the primary productivity and the
structure of the phytoplankton and zooplankton communities of the Harbor. 
Approach of the report 
The basic approach of the report was to compare Harbor water quality during the first 24-
months after ‘offshore transfer’, with water quality during a 3- to 7-year ‘baseline period’
before transfer. The ‘baseline period’ extended from August 1993 (or August 1997)
through 6 September 2000. The ‘post-transfer’ period extended from 7 September 2000,
the day after offshore transfer, through 31 August 2002.
The reductions in wastewater flows and loadings that followed ‘offshore transfer’ are
summarized in Table 1. Figure 1 provides a schematic of the effects of offshore transfer
on the sizes and locations of N loadings to the Harbor. In this report, we compare water
quality during the ‘post-transfer period’, represented by the bottom panel, with water
quality during the ‘baseline period’, represented by the top two panels.
As is evident in Figure 1, the baseline period encompassed periods before and after an
earlier transfer of wastewater flows, called ‘inter-island transfer’. Inter-island transfer
occurred in mid-1998. Unlike for ‘offshore transfer’, which ended wastewater flows to
the Harbor, inter-island transfer involved a transfer of wastewater flows within the
Harbor. Taylor (2001 b) reported the changes in Harbor water quality that followed
‘inter-island’ transfer.

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Table 1. Wastewater flows and loadings from the two treatment facilities to the Harbor
before and after offshore transfer. Values are monthly average + 1 x SD daily flows and
loadings. Estimates before transfer are for Sept 1 1995 through Aug 30 2000. Flows
and loadings from the two facilities to the Harbor after transfer, have been assumed to be
zero.
Variable Baseline Post-transfer
Flows (x 10 6 m 3 d -1 ), Flows (MGD),
nutrient loads (kmol d -1 ), nutrient loads
TSS and BOD (tons d -1 ) (kg d -1 )
Flow 1.42 + 0.3 375.2 + 79.3 0
TN 2314 + 305 32.4 + 4.3 0
DIN 1649 + 194 23.1 + 2.7 0
NH 4 1557 + 195 21.8 + 2.7 0
TP 133 + 21 4.1 + 0.2 0
DIP 76 + 13 2.4 + 0.2 0
DIN as %TN 72 + 9 as for molar loads 0
DIP as %TP 58 + 12 as for molar loads 0
Molar TN:TP 17.5 + 1.9 not applicable 0
Molar DIN:DIP 22.3 + 4.5 not applicable 0
TSS 59.6 + 31.7 not applicable 0
BOD 89.3 + 67 not applicable 0

<JULY 1998

DEER IS.
WWIF

BASELINE PERIOD
(< Sept. 2000)

24-MONTHS POST-
OFFSHORE TRANSFER
(Sept. 2000 through
Aug. 2002)

Figure 1. Changes in locations of discharges from the two WWTFs during the baseline
period, and between the baseline period and the first 24-months after offshore
transfer. Arrows indicate flows from the WWTFs, rivers and shoreline
non-point sources. Sizes of arrows are roughly in proportion to nitrogen (N)
loadings, N being one of the nutrients reponsible for historic eutrophication
of Boston Harbor (N-loading estimates from Alber and Chan 1994)

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In this report, we address the changes in water quality after offshore transfer, at two
levels. First, we examine the changes for the Harbor as a whole, and we do this by
comparing volume-weighted, Harbor-wide averages for the periods before and after
transfer. Second, we examine changes at each of the 10 stations we sampled in the
Harbor, and we did this to detect any spatial patterns to the changes. 
METHODS
Field sampling and laboratory analytical procedures 
To track the changes in the Harbor, we monitored water quality at 10 stations. The 10
stations were located in each of the four major regions of the Harbor (Fig. 2): 3 in the
Inner Harbor, 3 in the North West Harbor, 3 in the Central Harbor and 1 in the South East
Harbor. (Note: when the term ‘North Harbor’ has been used in the report, it refers to the
Inner Harbor + North West Harbor; ‘South Harbor’, to Central Harbor + South West
Harbor; and ‘Outer Harbor’, to the North West Harbor + Central Harbor + South East
Harbor).
Table 2 lists the names and coordinates of the 10 sampling stations. Each station was
sampled between August 1993 (or 1997 depending on variable and station), through
August 31, 2002 (24 months after offshore transfer). Each year, each station was
sampled weekly from May through October, and every two weeks from November
through April.
For most variables, measurements at each station were conducted at two depths; one
‘near-surface’ (at ca. 0.3 m below the water surface), and one ‘near-bottom’ (or ca. 0.5 m
above the sediment surface). For these variables, the data are reported in this report as
averages of the two depths. For total dissolved and particulate fractions of N and P,
samples were (for reasons of logistics) collected at ‘near surface’ depths alone.

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For dissolved oxygen (DO), only near-bottom data have been reported in this report.
Secchi depths obviously represent integrated measures through some portion of the
surface waters of the water column. Vertical attenuation coefficients (k) were computed
from measurements of photosynthetically-active radiation (PAR) measured at 1.0-m
intervals through the water column.
Table 3 summarizes the field procedures and analytical techniques employed in this
study. Further details of these are provided in Rex and Taylor (2000). The standard

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Table 2. Locations of the stations monitored to track the changes in Harbor water quality
that followed offshore transfer.
Station Station ID Latitude (N) Longitude (W) 
NORTH HARBOR 
Inner Harbor 
Mouth Mystic River 137 42 o 23.20 71 o 03.80
New England Aquarium 138 42 o 21.59 71 o 02.82
Mouth Inner Harbor 024 42 o 20.59 71 o 00.48 
North West Harbor 
Long Island 106 42 o 20.00 70 o 57.60
Calf Island 142 42 o 20.35 70 o 55.89
Neponset River/ 140 42 o 18.35 71 o 02.43
Dorchester Bay 
SOUTH HARBOR 
Central Harbor 
Inner Quincy Bay 077 42 o 16.51 70 o 59.31
Hangman Island 139 42 o 17.20 70 o 58.10
Nantasket Roads 141 42 o 18.30 70 o 55.85 
South East Harbor 
Hingham Bay 124 42 o 16.36 70 o 53.86

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Table 3. Summary of field and analytical methods.
VARIABLE METHOD
TDN a and TDP a
PN a
PP a
Ammonium b
Nitrate + nitrite b
Phosphate b
Chlorophyll a b ,
phaeophytin b
Secchi depth d
k d
TSS b
Dissolved oxygen c
Enterococcus b
Salinity b and water
temperature b
Solarzano and Sharp (1980b), Whatman G/F filters
Perkin Elmer CHN analyzer, Whatman GF/F
Solarzano and Sharp (1980a), Whatman GF/F
Fiore and O'Brien (1962), modified as in Clesceri et al.
(1998; Method 4500-NH3 H), Skalar SAN plus autoanalyzer,
Whatman GF/F filters
Bendschneider and Robinson (1952), modified as
in Clesceri et al. (1998; Method 4500-NO3 F),
Skalar SAN plus autoanalyzer, Whatman GF/F
filters
Murphy and Riley (1962), modified as in Clesceri et al.
(1998; Method 4500-P F), Skalar SAN plus autoanalyzer,
Whatman GF/F filters
After Holm Hansen (1965) as described in
EPA (1992). Sequioa Turner Model 450
fluorometer, Whatman GF/F filters
20 cm standard (all-white) secchi disc
Li Cor PAR sensor Model LI-193 SB
Clesceri et al. (1998, Method 2540D), using
nucleopore filters
YSI 3800 through July 1997, Hydrolab
Datasonde 4 thereafter
Clesceri et al. (1998, Method 9230C)
YSI 3800 through July 1997, Hydrolab
Datasonde 4 thereafter
a = surface samples only, b = samples/measurements taken surface plus bottom, c = measurement
taken at bottom only, d = profile through water column.

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operating procedures for all analytical techniques are archived at the MWRA Central
Laboratory, Deer Island, Winthrop, MA 02152. The data presented in this report are
stored in the EM & MS Oracle database, MWRA Environmental Quality Department,
Charlestown Navy Yard, Boston MA 02129. 
Data and statistical analysis 
We used the non-parametric Mann-Whitney U test to test for differences in water quality
between the periods before and after transfer (SPSS 8.0, SPSS 1995). We selected the
Mann-Whitney U test in preference to conventional Analysis of Variance (ANOVA),
because it was more conservative than ANOVA. It was also less sensitive to the non-
homogeneity of variance shown by certain data at certain stations.
The Mann-Whitney U test was applied to two sets of data; data averaged for the Harbor
as a whole, and data for each of the 10 stations. The Harbor-wide averages were
computed as volume-weighted averages; ‘volume-weighting’ was required to correct for
the different numbers of stations sampled per region. Volume-weighted, Harbor-wide
averages were computed as follows (after Sung 1991): 
Volume-weighted average = (a*0.119) + (b*0.418) + (c*0.342) + (d*0.12) 
where, a = average concentration for all stations in the Inner Harbor, b = average
concentration for all stations in North West Harbor, c = average concentration for all
stations in Central Harbor, and d = average concentration for all stations in South East
Harbor. The constants, 0.119, 0.418, 0.342 and 0.12, were the volumes of the respective
regions, expressed as a proportion of 1 (volumes from Sung 1991, citing Ketchum 1951).
For all variables (except mid-summer DO), the Mann-Whitney U test was applied to
monthly, rather than survey, averages. This was required to eliminate biasing caused by
the different numbers of surveys conducted per month, at different times of the year. For

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all variables (except for mid-summer DO), all monthly averages were de-seasonalized
before the Mann-Whitney U test was applied.
For all variables, except for fecal coliform and Enterococcus, all means, for the Harbor as
a whole and for the individual stations, were computed as arithmetic means. For fecal
coliform and Enterococcus, the average monthly means were computed as geometric
means, and then arithmetic means computed from the geometric monthly means.
Monthly means were computed as geometric means, because of the non-normal
distribution of these bacteria data.
Four levels of significance were differentiated in the report. When the Mann-Whitney U
test yielded p values between 0.011 and 0.05 (95% CL), the differences in average values
between the periods before and after transfer were considered ‘significant’. When the p
values were = or < 0.01 (99% CL), the differences were ‘highly significant’, and when p
fell between 0.051 and 0.10, the differences were ‘almost significant’ (90%). For p
values > 0.05, the average values before and after transfer were considered ‘not
significantly’ different. 
RESULTS
Nitrogen concentrations 
Total nitrogen (TN). One of the improvements we observed in the Harbor over the 24-
months, was a decrease in average concentrations of TN in its water column (Table 4).
Harbor-wide average concentrations of TN decreased from 31.1 + 6.4  mol l -1 for the
baseline as a whole, to 20.4 + 3.0  mol l -1 for the 24-months. The decrease of -10.7 
 mol l -1 was equivalent to -34% of average baseline values, and was highly significant (p
< 0.01).
We were also able to detect highly significant decreases for Harbor-wide average
concentrations of TN, for each of the 12-months making up the 24-months. During the

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Table 4. Nitrogen concentrations . Comparison of volume-weighted, Harbor-wide average concentrations during the ‘baseline’
period, the first 12-months, second 12-months and 24-months after offshore transfer. Values are averages of monthly averages + 1 x
SD (n = number of months). ** denotes difference highly significant at p < 0.01, * denotes significant at p < 0.05 but > 0.011, ‘ ? ’
denotes difference possibly significant (p < 0.10 but >0.051). 
________________________________________________________________________________________________________________________________________________
Variable Average values during Difference between:
Baseline 1 st 12-months 2 nd 12-months 24-months Baseline Baseline 1 st 12-months Baseline
and and and and
1 st 12-months 2 nd 12-months 2 nd 12-months 24-months
________________________________________________________________________________________________________________________________________________
TN 31.1 + 6.4 21.0 + 3.5 19.8 + 2.4 20.4 + 3.0 -10.1 (-32%)** -11.3 (-36%)** -1.2 (-6%) -10.7 (-34%) **
(  mol l -1 ) (61) (12) (12) (24) 
DIN 11.8 + 6.4 5.5 + 3.0 3.7 + 2.1 4.6 + 2.7 -6.4 (-54%)** -8.1 (-69%)** -1.7 (-37%) -7.3 (-63%) **
(  mol l -1 ) (75) (12) (12) (24) 
DON 13.0 + 3.7 12.0 + 1.9 11.5 + 2.3 11.8 + 2.1 -1.0 (-8%) -1.5 (-11%) -0.5 (-4%) -1.2 (-9%)
(  mol l -1 ) (61) (12) (12) (24) 
NH4 6.3 + 3.4 1.1 + 0.7 0.9 + 0.45 1.0 + 1.1 -5.2 (-83%)** -5.4 (-86%)** -0.2 (-18%) -5.3 (-84%) **
(  mol l -1 ) (75) (12) (12) (24) 
NO 3+2 5.5 + 3.8 4.4 + 2.8 2.8 + 1.9 3.6 + 2.5 -1.0 (-18%)* -2.6 (-48%)** -1.6 (-36%) ? -1.8 (-33%) **
(  mol l -1 ) (77) (12) (12) (24) 
PN 6.1 + 2.4 3.6 + 1.2 4.5 + 1.7 4.1 + 1.5 -2.5 (-41%)** -1.6 (-26%)** +0.9 (+25%)** -2.1 (-34%) **
(  mol l -1 ) (60) (12) (12) (24) 
DIN as %TN 39 + 17 27 + 13 21 + 11 23 + 12 -12 (-32%)** -18 (-46%)** -6 (-22%) -16 (-41%) **
(68) (12) (12) (24) 
NH 4 as %DIN 56 + 14 23 + 11 32 + 19 27 + 3 -33 (-59%)** -25 (-44%)** +9 (+39%) -29 (-51%) **
(75) (12) (12) (24)
________________________________________________________________________________________________________________________________________________

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first 12-months, concentrations decreased by -10.1  mol l -1 (or -32%), and during the
second, by -11.3  mol l -1 (or -36%). The sizes of the decreases during the two 12-months
were not significantly different (p > 0.05).
Thus, the Harbor showed a decrease in Harbor-wide average of TN for the 24-months,
and the decrease was driven by similar-size decreases during both of 12-months making
up the 24-months. The decrease in TN during the two 12-months, and the fact that the
decreases during the two 12-months were similar in size are all confirmed in the time-
series plot of Harbor-wide average TN in Figure 3.
We were also able to detect decreases in TN for the 24-months, at all 10 of the stations
we sampled in the Harbor (Fig. 4). Subtraction of average values after transfer from
average values before transfer yielded negative values at all 10 stations, and at all 10, the 
1994 1995 1996 1997 1998 1999 2000 2001 2002
0
10
20
30
40
50
60 
TOTAL NITROGEN (TN) 
Offshore
transfer
AVERAGE CONCENTRATION
(UMOL L -1 )
Figure 3. Total nitrogen partitioned into dissolved inorganic (DIN) and non-DIN components . Values
are volume-weighted, Harbor-wide averages on individual sampling dates. Vertical arrow
shows date of offshore transfer.
DIN
OTHER

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decreases were highly significant (double asterisks). For explanations of the notations
used in the Figure, see the legend to the Figure.
At the individual stations, the decreases ranged in size from -8.8  mol l -1 (at Station 124)
to -14.6  mol l -1 (at Station 142). The two stations that showed the largest decreases
were located off of Deer Island (Stations 106 and 142). During both 12-months making
up the 24-months, we were also able to detect significant (or highly significant) decreases
at all 10 stations (Fig. 5).

1st 12-months

Former outfalls
Increase
Decrease

Significart at
(P< 0.05 >0.0t1

Highly significant at
p< 0.01

Possibly significant
(B<0.10> 0.051

Fig. 5. Total nitrogen (TN). Differences in the changes in average concentrations ( umol )

during the first (top) and second (bottom) 12-month periods after offshore transfer.

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Constituents of TN. We were also able to detect improvements during the 24-months,
for 4 of the 5 constituents of TN that we monitored - dissolved inorganic nitrogen (DIN),
ammonium (NH 4), nitrate + nitrite (NO 3+2) and particulate nitrogen (PN) (Table 4). For
the 4 constituents, as for TN, Harbor-wide averages for the 24-months were all highly
significantly lower than baseline. (For the fifth constituent, dissolved organic nitrogen
(DON), Harbor-wide averages before and after transfer, were not significantly different).
The bulk, about 68%, of the decrease in TN was contributed by the DIN fraction (solid
shaded area in Fig. 3). Harbor-wide average concentrations of DIN decreased from 11.8
+ 6.4  mol l -1 to 4.6 + 2.7  mol l -1 , or by -7.3  mol l -1 (or -63% of baseline). DIN, in
turn contributed most (ca. 71%) of the TN in the wastewater discharged to the Harbor
before transfer (table 1).
Most (ca. 73 %) of the decrease in DIN was, in turn, contributed by NH 4 (solid shaded
area, Fig. 6). Again, NH 4 contributed most of the DIN in the wastewater that the Harbor
received before transfer (MWRA, unpublished data). Harbor-wide average
concentrations of NH 4 decreased by -5.3  mol l -1 (or -84%) after transfer, and NO 3+2, by
-1.8  mol l -1 (or -33%).
For all four constituents that showed decreases for the data averaged Harbor-wide, we
were also able to detect significant (or highly significant) decreases during both of the 12-
months making up the 24-months (Table 4). For DIN, NH 4 and NO 3+2 (as for TN), the
decreases were similar in size during the two 12-months. For PN, the decrease during
the second 12-months was smaller than during the first (p < 0.01).
For the 4 constituents that showed decreases (DIN, NH 4, NO 3+2 and PN), the decreases
during the 24-months were significant (and in most cases, highly significant) at all 10
stations (Fig. 7 for DIN and PN; Fig. 8 for NH 4 and NO 3+2). Thus, not only did the
Harbor show a decrease in TN at all 10 stations, but at all 10 stations, the 4constituents
were responsible for the decreases.

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.
For 3 of the 4 constituents, specifically DIN, NH 4 and PN, we were also able to detect
decreases at all 10 stations, during both 12-months making up the 24-months (Fig. A-1 in
Appendix, DIN; Fig. A-2, PN; Fig. A-3, NH 4). For the fourth constituent, NO 3+2, five
stations showed decreases during the first 12-months, and 10 stations, during the second
twelve (Fig. A-4).
As a result of the different size changes for the different constituents, the nature of the N-
pool of the Harbor was also different after transfer (Fig. 9). The largest difference was a
decrease in the percent contribution of DIN to TN, from 39% to 23%. Percent DON
increased from 42% to 57%, and % PN, remained unchanged at ca. 20%. 
1994 1995 1996 1997 1998 1999 2000 2001 2002
0
5
10
15
20
25
30
35
Fig. 6. DIN concentrations partitioned into ammonium and nitrate+nitrite fractions. Values are volume-weighted
Harbor-wide average concentrations on individual sampling dates. Vertical arrow shows date of offshore transfer..
Offshore
transfer 
DISSOLVED INORGANIC NITROGEN (DIN) 
AVERAGE CONCENTRATION
(UMOL L -1 )
NH4
NO32

Figure 7.

ap

z

Former outfalls

Increase

Decrease
Significant at
£<0.05 > O.0tt

Highly significant at
p<0.01

Possibly significant
B <0.10> 0.051

Dissolved inorganic nitrogen (DIN) and particulate nitrogen(PN). Comparison of

the spatial patterns of changes in concentrations (,umol | -') for DIN (top) and
PN (bottom) during the 24-months after transfer. Other details as in Figure 4.

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Figure 8.

AMMONIUM

Former outfalls
Increase
Decrease

Significant at
p<0.05>001

Highly significant at
p< 0.01

Possibly significant
(BP <0.10 >0.051

Ammonium (NH » and nitrate + nitrite (NO,,,). Comparison of the spatial changes

in average concentrations ( umol |-!) of ammonium (top) and nitrate + nitrite (bottom)

during the 24-months after offshore transfer.

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The nature of the DIN-pool in the Harbor water-column was also changed. Before
transfer, NH 4 contributed most (ca. 56%) of the DIN. After transfer, it contributed 22%
of DIN. Conversely, the percent contribution of NO 3+2 to DIN increased from 44% (and
less than one-half before transfer), to 78% (and well above one-half), after transfer. 
Concentrations of phosphorus 
Total phosphorus (TP). As for TN, we were also able to detect an improvement in
concentrations of TP in the Harbor (Table 5, Fig. 10)). Harbor-wide average
concentrations of TP decreased from 1.78 + 0.32  mol l -1 during the baseline, to 
0
5
10
15
20
25
30
35
40 
NITROGEN POOL
NO 2+3
NH 4
DON
PN 
Figure 9. Nitrogen pool . Differences in the nature of the N pool of the Harbor water column,
before and 24-months after offshore transfer. Values in bars are percent contributions of
the different constituents to the total pool. 
PN
NO 2+3
NH 4
DON 
24-MONTHS
POST-TRANSFER
BASELINE 
5%
18%
20%
57%
18%
22%
20%
42% 
42
AVERAGE CONC. ( UMOL L -1 )

27 
Table 5. Phosphorus concentrations . Comparison of volume-weighted, Harbor-wide average concentrations during the
‘baseline’ period, the first 12-months, second 12-months and 24-months after offshore transfer. Details as in Table 4. 
________________________________________________________________________________________________________________________________________________
Variable Average values during Difference between:
Baseline 1 st 12-months 2 nd 12-months 24-months Baseline Baseline 1 st 12-months Baseline
and and and and
1 st 12-months 2 nd 12-months 2 nd 12-months 24-months
________________________________________________________________________________________________________________________________________________
TP 1.78 + 0.32 1.56 + 0.32 1.47 + 0.22 1.51 + 0.27 -0.23 (-13%)** -0.31 (-17%)** -1.2 (-6%) -0.27 (-15%)**
(  mol l -1 ) (61) (12) (12) (24) 
DIP 1.05 + 0.37 0.73 + 0.28 0.71 + 0.24 0.72 + 0.26 -0.32 (-31%)** -0.34 (-33%)** -0.03 (-3%) -0.33 (-31%) **
(  mol l -1 ) (68) (12) (12) (24) 
DOP 0.15 + 0.24 0.42 + 0.10 0.30 + 0.16 0.36 + 0.14 +0.27 (+175%)** +0.14 (+95%)** -0.12 (-29%) ? +0.21 (+140%)**
(  mol l -1 ) (61) (12) (12) (24) 
PP 0.58 + 0.18 0.42 + 0.12 0.47 + 0.14 0.44 + 0.13 -0.16 (-27%)** -0.10 (-18%)** +0.05 (+12%)* -0.14 (-24%)**
(  mol l -1 ) (61) (12) (12) (24) 
DIP as % TP 59 + 18 46 + 12 48 + 15 47 + 13 -13 (-22%)** -11 (-19%)** +2 (+15%) -12 (-20%)**
(61) (12) (12) (24)
________________________________________________________________________________________________________________________________________________

28
1.51 + 0.27  mol l -1 for the 24-months. The decrease of -0.27  mol l -1 (or -15%) was
smaller than for TN, but was, as for TN, highly significant (p < 0.01).
Harbor-wide average concentrations of TP were also highly significant lowered during
both 12-months making up the 24-months (Fig. 10). As for TN, the sizes of the decreases
were similar during the two 12-months; -0.23  mol l -1 (or -13%) for the first 12-months
and -0.31  mol l -1 (or -17%) for the second.
Average concentrations of TP were also significantly (or highly significantly) lowered at
all 10 stations for the 24-months (Fig. 11). This was as for TN. The decreases in TP at
the individual stations ranged in size from -0.2  mol l -1 to -0.5  mol l -1 , with the largest
decreases off of Deer Island and in the mid- Central Harbor. 
1994 1995 1996 1997 1998 1999 2000 2001 2002
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
4.0 
TOTAL PHOSPHORUS (TP) 
Figure 10. Total phosphorus (TP) partitioned into the dissolved inorganic phosphorus (DIP) and 
non-DIP fractions . Other details as in Figure 3.
Offshore
transfer
AVERAGE CONCENTRATION
( UMOL L -1 )
DIP
NONDIP

29
TP showed decreases at 9 stations during both 12-months making up the 24-months; 1
less than the 10 stations for the 24-months (Fig. 12). During the first 12-months, TP
decreased at all 10 stations except Station137. During the second 12-months, Station 124
was the only station that showed no decrease. The two stations that showed no decreases
were two of the stations located furthest from the former discharge sites off of Deer
Island.

1st 12-months

Former outfalls

a Increase
Decrease

” Significant at

2nd 12-months B<0.05> 0.011

ee Highly significant at
ps0.o1

? Possibly significant
p<0.10>0.051

Fig. 12. Total phosphorus (TP). Comparison of the spatial patterns of changes during

the first (top) and second (bottom) 12-month periods after offshore transfer.

30

31 
Constituents of TP. We were also able to detect improvements during the 24-months for
2 of the 3 constituents of TP that we monitored - dissolved inorganic phosphorus (DIP)
and particulate phosphorus (PP) (Table 5). For both fractions, Harbor-wide average
concentrations for the 24-months were highly significantly lower than baseline. DIP
decreased by -0.33  mol l -1 (or -31%), and PP, by -0.14  mol l -1 (or -24%).
For the third constituent, dissolved organic phosphorus (DOP), Harbor-wide average
concentrations after transfer were highly significantly greater than baseline. The fact that
the DIP and PP, and especially the DIP, fractions contributed to the decrease in TP was as
for N. The increase in the DOP fraction was unlike for DON, and likely dampened the
decrease in TP that followed transfer.
For the two constituents that showed decreases, DIP and PP, the decreases during the 24-
months were significant (or highly significant) at all 10 stations (Fig. 13). Again, this
was as for the equivalent N-fractions. Thus, the Harbor showed a decrease in TP at all 10
stations, driven at all 10 stations by decreases in both DIP and PP.
During both of the 12-months making up the 24-months, we were able to detect decreases
in DIP at all 10 stations (Fig. A-5). Again, this was as for DIN. For PP, we were able to
detect decreases at 9 stations for the first 12-months, and at 4 stations during the second.
As a result of the different size changes for the different P constituents, the nature of the
P-pool of the Harbor was also changed after transfer (Fig. 14). The percent contribution
of DIP to TP, which tended to be higher than for N, decreased from 59% to 47%. The
percent contribution of DOP increased from 8% to 24% of TP. Percent PP remained
unchanged, at ca. 30% of TP.

Former outfalts

a nerease

v Decrease

* Significant at
B< 0.05 >0.011

- Highly significant at
ps aot

? Possibly significant
p<0.10>0.051

Fig. 13. Dissolved inorganic phosphorus (DIP) and particulate phosphorus (PP). Changes in
concentrations ( umol |-1) during the 24-months after offshore transfer. Other details as in
Figure 4.

32

33 
Molar ratios of N:P 
Molar TN:TP . During the 24-months, we were also able to detect a decrease in average
molar ratios of TN:TP in the Harbor water-column (Table 6, Fig. 15). Harbor-wide
average ratios decreased from 17.6 + 4.4:1 during baseline, to 13.4 + 2.5:1 for the 24-
months. The decrease of -4.2:1 (or-24%) was highly significant. Thus, the Harbor,
showed highly significant decreases for both TN and TP, and also for TN relative to TP
(or TN:TP). 
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
4.0
Figure 14. Phosphorus pool . Differences in the nature of the P pool of the Harbor water column,
before and 24-months after offshore transfer. Values in bars are percent contributions of
the different constituents to the total pool. 
PP
DIP
DOP
PP
DIP 
24-MONTHS
POST-TRANSFER
BASELINE
AVERAGE CONC. ( UMOL L -1 ) 
DOP 24%
8%
48%
59%
29%
33%
PHOSPHORUS POOL

34 
Table 6. Molar ratios of N:P . Comparison of volume-weighted, Harbor-wide average ratios during the ‘baseline’ period, the
first 12-months, second 12-months and 24-months after offshore transfer. Details as in Table 4. 
________________________________________________________________________________________________________________________________________________
Variable Average values during Difference between:
Baseline 1 st 12-months 2 nd 12-months 24-months Baseline Baseline 1 st 12-months Baseline
and and and and
1 st 12-months 2 nd 12-months 2 nd 12-months 24-months
________________________________________________________________________________________________________________________________________________
TN:TP 17.6 + 4.4 12.9 + 2.8 14.0 + 2.2 13.4 + 2.5 -4.7 (-27%)** -3.7 (-21%)** -1.0 (-21%)** -4.2 (-24%)**
(61) (12) (12) (24) 
DIN:DIP 11.4 + 5.2 7.0 + 3.2 4.6 + 2.0 5.8 + 3.2 -4.4 (-39%)** -6.8 (-60%)** +2.4 (+55%)* -5.6 (-49%) **
(68) (12) (12) (24) 
DON:DOP 83 + 57 30 + 6 41 + 13 35 + 11 -54 (-64%)** -42 (-51%)** -11 (-37%) ** -48 (-58%)**
(61) (12) (12) (24) 
PN:PP 10.0 + 2.3 8.9 + 0.9 9.5 + 1.3 9.2 + 1.1 -1.2 (-11%) ? -0.6 (-6%) +0.05 (+12%) -0.8 (-8%) ?
(61) (12) (12) (24)
________________________________________________________________________________________________________________________________________________

35
Decreases in Harbor-wide average ratios of TN:TP were also highly significant during
both of the 12-months making up the 24-months. During the first 12-months, average
ratios decreased by -4.7:1 (or -27%), and during the second, by -3.7:1 (or -21%). Unlike
for TN and TP, the decrease was highly significantly smaller during the second 12-
months than during the first.
For the data averaged for the entire periods before and after transfer, Harbor-wide
average ratios decreased from above the Redfield Ratio of 16:1 before transfer, to below
the Redfield Ratio after transfer. This applied for data for both the 24-months, and the
individual 12-months. Harbor-wide average ratios decreased from 17.6:1 before transfer,
to 13.4:1 for the 24-months, 12.9:1 for the first 12-months, and 14.0:1 for the second.
The decreases that we observed for TN:TP in the Harbor can be interpreted as an
improvement in water quality, because temperate coastal systems such as Boston Harbor
are known to be more sensitive to elevated inputs (and hence concentrations) of TN than
TP (Howarth 1988). The decrease from above to below the Redfield Ratio can also be
viewed as an improvement, because it indicates a shift to potential N (relative to P)
limitation of phytoplankton production (and hence of eutrophication) of the Harbor.
During the 24-months, we were also able to detect significant (or highly significant)
decreases in TN:TP at all 10 stations (Fig. 16). The decreases in at the individual stations
ranged in size from -3.1:1 to -5.7:1; with the largest decreases observed off of Deer
Island and in the mid-Central Harbor. Thus, not only did all 10 stations show decreases
in both TN and TP, but all 10 also showed decreases in TN relative to TP.
During both of the individual12-months making up the 24-months, decreases in average
ratios of TN:TP were observed at 9 stations, 1 less than for the 24-months (Fig. 17). At 2
stations (Stations 137 and 124), the decreases during one of the two 12-months were not
significant. Both stations were among the stations located furthest from the former Deer
Island discharge sites.

Figure 16.

Former outfalis
nerease
Decrease
Significant at
B<005>0.011

Highly significant at
p< 0.01

Possibly significant
B<0.10 > 0.051

Molar TN: TP (top) and DIN:DIP (bottom). Spatial patterns of the changes in average

ratios during the 24-months after offshore transfer. Other details as in Figure 4.

36

Fig. 17.

1st 12-months

Former outtalls
Increase
Decrease
Significant at
(P< 0.05>0.011

Highly significant at
peao

Possibly significant
p<0.10> 0.051

Molar TN:TP. Comparison of the spatial patterns of changes in ratios during the
first (top) and second (bottom) 12-month periods after offshore transfer.

37

38 
DIN:DIP, DON:DOP and PN:PP . We were also able to detect improvements during the
24-months for 2 of the 3 constituent N:P ratios that we monitored – DIN:DIP and
DON:DOP (Table 6). For both ratios, Harbor-wide averages for the 24-months were
highly significantly lower than baseline; average DIN:DIP decreased by -5.6:1 (or -49%),
and DON:DOP, by -48:1 (or -58%). For the third ratio (PN:PP), the difference of -0.8:1
(or -8%), was ‘almost’ significant.
For both DIN:DIP and DON:DOP, the decreases were also highly significant during both
of the individual 12-months. For DIN:DIP, the decrease during the second 12-months
was greater than during the first twelve. For DON:DOP, as for TN:TP, the opposite
applied, and the decrease during the first 12-months was larger than during the second.
For the 24-months, we were able to detect significant (or highly significant) decreases for
DIN:DIP at all 10 stations (Fig. 16). This was again as for concentrations of the
individual components. The decreases at the stations ranged in size from -1.2:1 to -6.7:1;
the largest decreases were observed off of Deer Island. During the individual 12-months,
9 stations showed decreases in DIN:DIP during the first 12-months, and 10, during the
second twelve (Fig. A-6) 
Phytoplankton biomass (chlorophyll-a) 
One of the other improvements we observed in the Harbor over the 24-months was a
decrease in concentrations of chl-a (Table 7). We monitored three fractions of chl-a -
‘total’ chl-a, acid-corrected (or ‘active’) chl-a, and phaeophytin (or degraded) chl-a, and
for all three, Harbor-wide averages for the 24-months were significantly (or highly
significantly) lower than baseline. (Total chl-a, as used here, refers to the sum of acid-
corrected chl-a plus phaeophytin).
For total chl-a, Harbor-wide averages decreased from 6.5 + 4.1  g l -1 for baseline to 5.0 +
3.0  g l -1 for the 24-months. The decrease of -1.5  g l -1 was equivalent to -24% of

39 
Table 7. Chlorophyll-a and phaeophytin . Comparison of volume-weighted, Harbor-wide average concentrations during the
‘baseline’ period, the first 12-months, second 12-months, and 24-months after offshore transfer. Details as in Table 4. 
________________________________________________________________________________________________________________________________________________
Variable Average values during Difference between:
Baseline 1 st 12-months 2 nd 12-months 24-months Baseline Baseline 1 st 12-months Baseline
and and and and
1 st 12-months 2 nd 12-months 2 nd 12-months 24-months
________________________________________________________________________________________________________________________________________________
Total chl-a 6.5 + 4.1 3.6 + 1.7 6.4 + 3.4 5.0 + 3.0 -2.9 (-45%)** -0.1 (-2%) +2.8 (+78%)** -1.5 (-24%)*
(  g l -1 ) (61) (12) (12) (24) 
Acid-corrected 4.7 + 3.1 2.3 + 1.1 4.9 + 3.4 3.8 + 2.8 -2.3 (-50%)** +0.3 (+6%) +2.6 (+113%)** -0.9 (-19%) * 
chl-a (  g l -1 ) (61) (12) (12) (24) 
Phaeophytin 1.9 + 1.3 1.3 + 0.6 1.4 + 0.5 1.4 + 0.5 -0.6 (-32%)** -0.5 (-25%)** +0.1 (+8%) -0.5 (-29%)**
(  g l -1 ) (61) (12) (12) (24)
________________________________________________________________________________________________________________________________________________

40
baseline, and was significant (c.f. highly significant for most total and dissolved
inorganic nutrients). Most (ca. 60%) of the decrease in total chl-a was contributed by
the acid-corrected fraction (dark shaded area in Fig. 18).
Harbor-wide average concentrations of acid-corrected chl-a decreased from 4.7 + 3.1  g
l -1 to 3.8 + 2.8  g l -1 . The decrease of -0.9  g l -1 was equivalent to -19% of baseline, and
was, as for the total fraction, significant. For phaeophytin, Harbor-wide average
concentrations decreased by -0.5  g l -1 (or -29%), and the decrease was, as for most
nutrients, highly significant.
During the individual 12-months, we were able to detect decreases during one of the two
12-months for total and acid-corrected chl-a, and for both 12-months, for phaeophytin.
For both total and acid-corrected chl-a, Harbor-wide average concentrations during the
first 12-months were highly significantly lower than baseline. During the second 12-
months, the averages were not significantly different from baseline. 
1995 1996 1997 1998 1999 2000 2001 2002
0
5
10
15
20
25
30
Figure 18. Total chl-a partitioned into the acid-corrected chl-a and phaeophytin fractions. ) Values are
volume-weighted, Harbor-wide averages, Vertical arrow shows date of offshore transfer.
Offshore
transfer 
CHLOROPHYLL-A 
AVERAGE CONCENTRATIONS
(UG L -1 )
CHLA
PHAEO

41
For the 24-months as a whole, for all three chl-a fractions, the number of stations that
showed significant (or highly significant) decreases was less than for most nutrients (Fig.
19). For total chl-a, we were able to detect decreases at 4 stations; two in the Inner
Harbor, and 2 in the Central Harbor. The decreases at the 4 stations ranged in size from
1.5  g l -1 to -2.8  g l -1 .
For acid-corrected chl-a, 2 stations showed decreases; the 2 stations were the same 2 in
the Central Harbor that showed decreases for total chl-a. The decreases at the two
stations were -1.0  g l -1 and -2.1  g l -1 . Thus, the Harbor showed decreases for chl-a, as
it did for most nutrients, but the decreases were focussed in specific areas of the Harbor;
in the Inner Harbor and Central Harbor for total chl-a, and the Central Harbor alone, for
acid-corrected chl-a.
During the individual 12-months, for both total (Fig. A-7) and acid-corrected chl-a (Fig.
20), we were able to detect decreases at individual stations during only the first of the two
12-months. For acid-corrected chl-a, concentrations during the first 12-months were
lower than baseline at 7 stations. At the other 3 stations, subtraction of averages after
transfer from averages before transfer also yielded negative values, but the decreases
were not significant.
During the second 12-months, subtraction yielded positive values at 6 of the 7 stations in
the Outer Harbor, and at 2, one in outer President Roads and the other in outer Nantasket
Roads, the increases were significant (or highly significant). The increases at the two
stations that showed significant increases were +1.5  g l -1 to +1.8  g l -1 .
Thus, the Harbor showed decreases in N, P and N:P over both 12-months, and during
both 12-months, the decreases were observed over most of the area of the Harbor. For
chl-a, concentrations were also decreased over most of the area over the first 12-months,
but during the second 12-months, the Harbor showed a localized increase in chl-a,
focused in the outer, Outer Harbor.

Figure 19.

TOTAL CHL-A

Former outfalls
nerease
Decrease
Significant at

(P< 0.05>0.011

Highly significant at
Ps 0.01

Possibly significant
B<010> 0.051

Total chl-a (top) and acid-corrected chl-a(bottom). Spatial patterns of
changes in concentrations during the 24-months after offshore transfer.
Units are ug |''. Other details as in Figure 4.

42

Fig. 20.

1ST 12-MONTHS

2ND 12-MONTHS

Former outfalls
increase
Decrease
Significant at

2 <0.05 > 0.011

Highly significant at
p<0.01

Possibly significant
1B <0.10 > 0.051

Acid-corrected chl-a. Differences in the changes in average concentrations ( ug!"')
between the first (top) and second (bottom) 12-month periods after offshore transfer.

43

44 
Suspended particulate material 
Total suspended solids (TSS). Unlike for N, P and chl-a, we were unable to detect
significant improvements for concentrations of TSS in the Harbor water column over the
24-months (Table 8, Fig. 21). Harbor-wide average concentrations of TSS averaged 3.6
+ 1.2 mg l -1 during the baseline, and 3.8 + 1.2 mg l -1 for the 24-months. The difference
of +0.2 mg l -1 (or + 7%) was not significant.
We were also unable to detect significant decreases for TSS, for the two 12-months
making up the 24-months. During the first 12-months, Harbor-wide average
concentrations were not significantly different from baseline; during the second 12-
months, concentrations were +0.6 mg l -1 (or +15%), and significantly greater than
baseline.
The absence of a decrease during the first 12-months and increase during the second, are
both evident in the time-series plot of Harbor-wide average TSS in Fig. 21. The Figure 
1995 1996 1997 1998 1999 2000 2001 2002
0
1
2
3
4
5
6
7
8
Figure 21. Total suspended solids (TSS) partitioned into the particulate carbon (PC) and non-PC fractions. 
Values are volume-weighted, Harbor-wide averages. Vertical arrow shows date of offshore transfer.
Offshore
transfer 
TOTAL SUSPENDED SOLIDS (TSS) 
AVERAGE CONCENTRATIONS
(MG L -1 )
PC
NONPC

45 
Table 8. Solids, particulate carbon, and water clarity . Comparison of volume-weighted, Harbor-wide average values during
the ‘baseline’ period, the first 12-months, second 12-months, and 24-months after offshore transfer. Details as in Table 4. 
________________________________________________________________________________________________________________________________________________
Variable Average values during Difference between:
Baseline 1 st 12-months 2 nd 12-months 24-months Baseline Baseline 1 st 12-months Baseline
and and and and
1 st 12-months 2 nd 12-months 2 nd 12-months 24-mths
________________________________________________________________________________________________________________________________________________
SOLIDS
TSS 3.6 + 1.2 3.5 + 1.1 4.1 + 1.3 3.8 + 1.2 -0.1 (-1%) +0.6 (+15%)* -0.3 (-7%) ? +0.2 (+7%)
(mg l -1 ) (55) (12) (12) (24) 
PC 42.9 + 16.1 26.6 + 7.6 34.4 + 13.6 30.5 + 11.5 -16.3 (-38%)** -8.4 (-20%)** -7.9 (-48%)* -12.3 (-29%)**
(  mol l -1 ) (61) (12) (12) (24) 
PC as %TSS 15 + 5 10 + 3 11 + 4 10 + 4 -5 (-32%)** -4 (-29%)** -1 (-10%) -4.5 (-30%)**
(by weight) (48) (12) (12) (24) 
WATER CLARITY
k 0.53 + 0.12 0.45 + 0.08 0.55 + 0.13 0.50 + 0.12 -0.8 (-15%)** +0.03 (+5%) +0.11 (-138%)** -0.03 (-5%) ?
(m -1 ) (73) (12) (12) (24) 
Secchi depth 2.6 + 0.6 2.9 + 0.6 2.7 + 0.8 2.8 + 0.7 +0.3 (+10%)* +0.1 (+3%) +0.4 (-133%) +0.2 (+7%) ?
(m) (85) (12) (12) (24)
________________________________________________________________________________________________________________________________________________

46
also shows that the Harbor experienced a background increase in TSS that started well
before transfer, and that might have compensated for any decrease in TSS that followed
transfer. The material responsible for the background increase, and in turn, the
‘dampened’ TSS response, was largely inorganic in nature (light shaded area in Fig. 21).
For the 24-months, we were also unable to detect decreases in TSS that we could relate to
transfer, at any of the 10 stations (Fig. 22). At 1 station, concentrations were lower than
baseline, and at 3 stations, higher. The location of the 1 station in the upper Inner
Harbor, suggested its decrease was unrelated to transfer. The 3 stations that showed the
increases were all located in the outer, Outer Harbor, suggesting that the background
increase in TSS was focused in this area.
We were also unable to detect decreases in TSS that we could relate to transfer, at the
individual stations, during the individual 12-months. During the first 12-months, at none
of the stations were average concentrations different from baseline. During the second
12-months, concentrations were lowered at 1 station (the same station that showed the
decrease for the 24-months), and 5 stations, showed elevated concentrations.
Thus, unlike for N, P and chl-a, we were unable to detect a transfer-related decrease in
TSS in the Harbor during the 24-months. During the first 12-months, when the Harbor
showed a decrease in chl-a, we could detect no change for TSS. During the second 12-
months, when the Harbor showed a localized increase in chl-a, it also showed an increase
in TSS focused in the Outer Harbor. 
Particulate carbon (PC). We were however able to detect significant (and in many
cases, highly significant) decreases in PC in the Harbor during the 24-months (Fig. 24,
Table 8). Harbor-wide average concentrations of PC decreased from 42.9 + 16.1  mol l -1
for the baseline, to 30.5 + 11.5  mol l -1 for the 24-months. The decrease of -12.3  mol l -
1 (or-29%), was highly significant.

Figure 22.

TSS

Former outfalls
ncrease
Decrease

Significant at
p< 0.05>0011

ge =

- Highly significant at
p< 0.01

? Possibly significant
B<010> 0,051

Total suspended solids (TSS) and particulate carbon (PC).

Spatial

patterns of changes in concentrations during the 24-months after offshore

transfer. Units are mg | “Other details are as in Figure 4.

47

1ST 12-MONTHS

Former outfalls

a increase
v Decrease
bad Significant at
2ND 12-MONTHS 2< 0.05 > 0.011
x Highly significant at
ps oot

? Possibly significant
B<0.10 > 0.051

Fig. 23. Total suspended solids (TSS). Differences in the changes in average concentrations

(mg I"') between the first (top) and second (bottom) 12-month periods after offshore
transfer.

48

49
The decreases were also highly significant for Harbor-wide average concentrations of PC,
during both of the 12-months making up the 24-months. During the first 12-months,
Harbor-wide average concentrations decreased by -16.3  mol l -1 (or -38%); and during
the second 12-months, by -8.4  mol l -1 (or -20%). The decrease during the second 12-
months was significantly smaller during the first.
At the individual stations, the decreases in PC were significant (or highly significant) at
all 10 stations during the 24-months (Fig. 21). At the individual stations, the decreases
ranged in size from -7.0  mol l -1 to -14.7  mol l -1 . During the individual 12-months, 9
stations showed decreases during the first 12-months, and 7 during the second twelve
(Fig. A-8).
Thus, as for most of the N and P nutrients, the Harbor showed decreases in PC during
both the first and second 12-months. Unlike for most of the total and dissolved inorganic
N and P fractions, the sizes of the decreases during the two 12-months were different. As 
1995 1996 1997 1998 1999 2000 2001 2002
0
20
40
60
80
Fig. 24. Particulate carbon (PC) . Time-series plot of volume-weighted, Harbor-wide average concentrations
Vertical arrow shows date of completion of offshore transfer.
Offshore
transfer 
PARTICULATE CARBON 
AVERAGE CONCENTRATION
( UMOL L -1 )

50
for particulate N and P, and also for chl-a, the decrease during the second 12-months was
smaller and more localized than during the first.
As a result of the absence of a decrease for TSS and highly significant decrease for PC,
the Harbor also showed a decrease in the percent contribution of PC to TSS after transfer
(Table 8). Before transfer, PC contributed 15% of TSS; after transfer, its percent
contribution was 10% (p < 0.01). Thus, we were not able to detect a decrease in
concentrations of TSS, but we were for the organic content of the TSS. 
Water clarity 
We conducted two measures of water clarity in the Harbor – vertical attenuation
coefficient (k) and secchi depth (Table 8). For both variables, as for TSS, Harbor-wide
averages for the 24-months were not significantly different from baseline. For both
variables, however, and unlike for TSS, the differences were ‘almost significant’. (Note:
the k values are reported as reciprocal values, therefore decreases in k represent increases
in clarity).
For both variables, for the data averaged Harbor-wide, we were able to detect significant
improvements during the first 12-months, but not the second (see time-series plot for k in
Fig. 25). During the first 12-months, Harbor-wide average k values decreased by -0.8 m -1
(or -15%), and the decrease was highly significant. During the same 12-months, average
secchi depth were +0.3 m (or +10%), and significantly greater than baseline.
During the second 12-months, the same 12-months the Harbor showed the localized
increase in chl-a and Harbor-wide increase in TSS, Harbor-wide average k and secchi
depth values were not significantly different from baseline. During the second 12-
months, the increase in clarity that was observed during the first 12-months, was
apparently ‘dampened’ by the increase in TSS and chl-a also observed during the second
12-months.

51
For the 24-months as a whole, and for both k and secchi depth, we were, however, able to
detect significant (or highly significant) increases in clarity at individual stations (Fig.
26). For k, significant (or highly significant) improvements were observed at 2 stations
(both in the mid- to upper Inner Harbor). For secchi depth, improvements were observed
at 6 stations; 5 of them in the North Harbor and 1 in the Central Harbor.
For both variables, subtraction yielded differences suggestive of an increase in clarity at
all stations except the 2 or 3 in the outer, Outer Harbor that showed increases for TSS for
the 24-months. The different numbers of stations that showed improvements for k and
secchi depth probably reflects the different optical properties measured by the two
variables.
During the individual 12-months, for k, the number of stations that showed improvements
was 5 during the first 12-months, and zero during the second (Fig. 27). The 5 stations
that showed improvements during the first 12-months were all located in the North
Harbor, and extended from the area off of Deer Island up into the Inner Harbor. During 
1994 1995 1996 1997 1998 1999 2000 2001 2002
0.0
0.2
0.4
0.6
0.8
1.0
1.2 
ATTENUATION COEFFICIENT (k) 
Fig. 25. Vertical attenuation coefficients (k) . Time-series plot of volume-weighted, Harbor-wide average values.
Date of offshore transfer shown by vertical arrow.
Offshore
transfer
AVERAGE k ( M -1 )

Figure 26.

Former outfals
a Incranse

v Decrease

. Signticant a
B< 0.06 > O00

se Highiy significant
ps 001

? Possibly signticare
p<010> 0.061

Former cutfals
a Increa:
Decrease

= Signticart at
B<0G »aon

™* Highly sign@icart at
ps0.08

? Possibly significant
p<O.10>0.01

Attenuation coefficient (k) and secchi depth. Spatial pattern
of changes in average k and secchi depth values during the
24-months after offshore transfer. Units are nr‘ for k, and 'm’
for secchi depth. Other details as in Figure 4.

52

1ST 12-MONTHS

Former cutfalls
&  incease
Y — Decease
* ‘Significant a
2ND 12-MONTHS B<0.05 +0011
+ Highly signticart at
psoo1
2 Possibly signiticart
PxO10> 0.051

Fig. 27. Attenuation coefficients (k). Differences in the changes in average values

(m-1) between the first (top) and second (bottom) 12-month periods after offshore
transfer.

53

54
the second 12-months, k showed significant increases (decreases) in clarity at 4 stations,
3 in the outer, Outer Harbor and 1 in Quincy Bay.
For secchi depth, during the first 12-months, 4 stations showed significant (or highly
significant) increases (Fig. A-9). The 4 stations were located in the outer North Harbor
and outer Central Harbor. During the second 12-months, increases were significant (or
highly significant) at 5 stations. During this particular 12-months, the increase in secchi
depth seen in the outer, outer Harbor during the first 12-months, was apparently
dampened by the increase in TSS that occurred in this area during the same 12-months. 
Bottom-water dissolved oxygen (DO) 
One of the other improvements we saw over the 24-months was a small but significant
increase in bottom-water dissolved oxygen (DO) (Table 9). We monitored two measures
of dissolved oxygen; DO concentrations (Fig. 28) and DO percent saturation. For neither
variable, were we able to detect significant changes for the data averaged Harbor-wide,
using year-round data.
We were, however, able to detect changes using data from ‘mid-summer’ alone; ‘mid-
summer’, as used here, refers to August + September. For both DO variables, Harbor-
wide average, mid-summer values for the 24-months, were significantly greater than
baseline. The increases in DO concentrations, and their focus during summers, are both
evident in the time-series plot of DO concentrations in Figure 28.
Harbor-wide average, mid-summer DO concentrations increased from 7.0 + 0.7 mg l -1 to
7.4 + 0.6 mg l -1 . The increase of +0.4 mg l -1 (or +6%) was small, but significant.
Likewise, Harbor-wide average, mid-summer DO % saturation values increased from
87.3 + 7.4% to 91.8 + 7.5 %. The increase of +4.5 % was equivalent to +5%, and was (as
for DO concentrations), significant.

55 
Table 9. Bottom-water dissolved oxygen (DO) . Comparison of volume-weighted, Harbor-wide average values during the
‘baseline’ period, the first 12-months, second 12-months and 24-months after offshore transfer. Details as in Table 4. 
________________________________________________________________________________________________________________________________________________
Variable Average values during Difference between:
a Baseline 1 st 12-months 2 nd 12-months 24-months Baseline Baseline 1 st 12-months Baseline
and and and and
1 st 12-months 2 nd 12-months 2 nd 12-months 24-months
________________________________________________________________________________________________________________________________________________
YEAR-ROUND
DO 8.6 + 1.2 8.7 + 1.1 9.0 + 1.6 8.8 + 1.3 +0.1 (+1%) +0.4 (+5%) +0.3 (-7%) +0.2 (+3%)
(mg l -1 ) (40) (12) (12) (24) 
DO 94.0 + 6.3 91.0 + 5.4 95.5 + 5.3 93.3 + 5.7 -3 (-3%) ? +1.4 (+2%) +4.4 (+147%) ? -0.8 (-1%)
(% saturation) (40) (12) (12) (24) 
b MID-SUMMER
DO 7.0 + 0.7 7.4 + 0.7 7.4 + 0.3 7.4 + 0.6 +0.4 (+6%) +0.4 (+6%)* 0 (0%) +0.4 (+6%)*
(mg l -1 ) (33) (10) (6) (16) 
DO 87.3 + 7.4 92.1 + 10.6 91.4 + 3.4 91.8 + 7.5 +4.9 (+6%) +4.1 (+5%) -0.8 (-16%) +4.5 (+5%)*
(% saturation) (34) (8) (7) (15)
________________________________________________________________________________________________________________________________________________

56
For the two 12-months making up the 24-months, we were able to detect significant
differences for the mid-summer DO data averaged Harbor-wide, for one or none of the
12-months, depending on variable. For DO concentrations, a significant increase was
observed during the second 12-months but not the first. For DO % saturation, we could
not detect an increase for either of the 12-months.
For both variables, for the 24-months, we were also able to detect significant (or highly
significant) improvements in DO at individual stations (Fig. 29). For mid-summer DO
concentrations, significant (or highly significant) increases were observed at 5 stations,
and at 2 others, the increases were almost significant. Four of the 5 stations that showed
increases were located in the North West Harbor up into the Inner Harbor, and 1 in the
mid- Central Harbor.
For DO % saturation, the spatial patterns of changes were basically as for concentrations
of DO. Significant (or highly significant) increases were observed at 3 stations, two in 
1993 1994 1995 1996 1997 1998 1999 2000 2001 2002
6
8
10
12
14 
DISSOLVED OXYGEN 
Figure 28. Bottom-water dissolved oxygen concentrations . Time-series plot of volume-weighted, Harbor-wide
average concentrations. Dashed line prior to May 1997 indicates earlier data obtained using different
instrumentation. Only data collected after (and including) May 1997 have been used to compute
averages and compare values before andafter transfer.
YSI
Hydrolab Offshore
transfer
AVERAGE CONCENTRATION
( MG L -1 )

57
the Inner Harbor and one in the mid- Central Harbor. The 3 stations that showed the
increases were 3 of 5 that showed increases for the concentrations of DO. At 3 other
stations, the increases in DO % saturation were almost significant.
For the individual 12-months, the number of stations that showed increases in DO were
similar or different between the two 12-months, depending on variable. For DO
concentrations, 1 station showed an increase during the first 12-months, and 5 stations
during the second (Fig. 30). For DO % saturation, 2 stations showed increases during the
first 12-months, and 2 (one of them different) during the second (Fig. A-10).
Thus, the Harbor showed increases in bottom-water DO. Unlike for most nutrients and
for chl-a and PC, the increases were confined to the mid-summer period alone. Unlike
for most nutrients and PC, but as for chl-a, the increases were confined to specific areas
of the Harbor. Unlike for chl-a, where the decreases were confined to the first of the two
12-months, for DO, the increases were observed during both 12-months. 
Sewerage indicator bacteria 
One of the other improvements we were able to detect in the Harbor during the 24-
months was a decrease in counts of two types of sewerage-indicator bacteria that we
monitored – Enterococcus and fecal coliform (Table 10). Note, for Enterococcus, data
were available for the full 24-months post- transfer; for fecal coliform, data were
available only for the first of the two 12-months. 
Enterococcus. Harbor-wide average counts of Enterococcus decreased from 10 + 12 cfu
100 ml -1 , to 5 + 4 cfu 100 ml -1 . The difference of -5 cfu 100 ml -1 was equivalent to -
50% of baseline, and was (as for most nutrients) highly significant. Again as for most

DO CONC. (mid-summer)

Former outtalts
Increase

Decrease

» ap:

Significant at
B<005>0.011

™ Highly significant at
pe 0.01

? Possibly significant
p<0.10>0.051

Fig. 29. Mid-summer, bottom-water DO concentrations and percent saturation. Comparison
of the changes in average concentrations (mg |‘) and saturation values (%) during the
24-months after transfer.

58

Fig. 30.

1st 12-months

2nd 12-months

Former outfalls

Decrease

Significant at
P< 0.05 > 0.011

Highly significart at
pe 0.01

Possibly significant
p<0.10> 0.051

Bottom-water DO concentrations. Comparison of the changes in average mid-summer
concentrations (mg |‘) during the first (top) and second 12-months after offshore transfer.

59

60 
Table 10. Sewerage-indicator bacteria, salinity and temperature . Comparison of volume-weighted, Harbor-wide average
values during the ‘baseline’ period, the first 12-months, the second 12-month, and the 24-months after offshore transfer. Details as in
Table 4, except that for the two bacterial indicators, the averages are arithmetic averages of geometric monthly means. 
________________________________________________________________________________________________________________________________________________
Variable Average values during Difference between:
Baseline 1 st 12-months 2 nd 12-months 24-months Baseline Baseline 1 st 12-months Baseline
and and and and
1 st 12-months 2 nd 12-months 2 nd 12-months 24-months
________________________________________________________________________________________________________________________________________________
SEWERAGE-INDICATOR BACTERIA
Enterococcus 26 + 30 6 + 4 5 + 5 5 + 4 -20 (-77%)** -21 (81%)** -1 (-13%) -21 (-80%)**
(cfu 100 ml -1 ) (72) (12) (12) (24) 
Fecal coliform 18 + 27 13 + 19 nm nm -5 (-28%) ? nm nm nm
(cfu 100 ml -1 ) (72) (12) 
SALINITY AND WATER TEMPERATURE
Salinity 30.5 + 1.2 a 31.0 + 0.9 31.4 + 0.9 31.2 + 0.9 +0.5 (+2%) +0.9 (+3%)** +0.4 (+80%)* +0.6 (+2%)**
(ppt) (55) (12) (12) (24) 
Water 9.9 + 5.8 a 9.5 + 6.1 9.8 + 6.0 9.7 + 6.0 -0.4 (-4%) -<0.1 (-<1%) -0.3 (-48%) -0.2 (-2%) 
temperature (61) (12) (12) (24)
( o C)
________________________________________________________________________________________________________________________________________________

61
nutrients, the decreases were also highly significant and similar in size during both 12-
months. During the first 12-months, average counts decreased by -5 cfu 100 ml -1 (or -
45%), and during the second twelve, by -6 cfu 100 ml -1 (or -55%).
The decrease in counts of Enterococcus in the Harbor is evident in the time-series plot of
Enterococcus counts in Fig. 31. Before transfer, average counts often peaked, and when
they did so, often exceeding the State Swimming Standard for Enterococcus of 33 cfu
100 ml -1 . During the 24-months after transfer, the size and frequency of the peaks were
lowered, and the Standard was exceeded on only two occasions; once during the first
month after transfer, and then once during June 2002.
For the 24-months, we were also able to detect significant decreases in counts of
Enterococcus at individual stations (Fig. 32). At 5 stations, all in the Outer Harbor,
average counts after transfer were significantly (or highly significantly) lower than
baseline. At the 5 stations, the decreases ranged in size from -1 cfu 100 ml -1 to -3 cfu 100
ml -1 . 
1994 1995 1996 1997 1998 1999 2000 2001 2002
100
200
300
400
500
600
700
800 
ENTEROCOCCUS 
State
swimming
std. 
Fig. 31. Enterococcus . Time-series plot of volume-weighted, Harbor-wide average counts. Vertical
indicates date of completion of offshore transfer.
Offshore
transfer
AVERAGE COUNTS
(# CFU 100 ML -1 )

62
During the individual 12-months, more stations showed decreases during the second 12-
months than during the first Fig. 33). During the first 12-months, 2 stations (both in the
outer North West Harbor), showed significantly (or highly significantly) lowered counts.
During the second 12-months, 5 stations showed significant (or highly significant)
decreases; two of them were two that showed decreases during the first 12-months. 
Fecal coliform . For the first 12-months, the 12-months for which we had data, we were
unable to detect a decrease in Harbor-wide average counts of fecal coliform bacteria
(Table 10). During the baseline, Harbor-wide average counts averaged 18 + 27 cfu 100
ml -1 . During the first 12-months, the average was 13 + 19 cfu 100 ml -1 . The differences
was ‘almost’ significant; c.f. highly significant for Enterococcus.
While the decrease for the data averaged Harbor-wide was not significant, we were able
to detect significant decreases for fecal coliform at individual stations (Fig. 32). At 3 of
the 10 stations, all in the Outer Harbor, average counts after transfer were highly
significantly lower than baseline (this was 1 more than showed decreases for
Enterococcus for the same 12-months, Fig. 33).
Thus, the Harbor showed lowered counts of both Enterococcus and fecal coliform
bacteria. For Enterococcus, for the 24-months and both 12-months, the decreases were
highly significant, and focused in the Outer Harbor. For fecal coliform, the decrease for
the Harbor-wide average counts, for the 12-months, was less significant than for
Enterococcus. Significant decreases were, however, observed in the Outer Harbor. 
Salinity and water temperature 
Salinity. One of the other changes we observed for the 24-months was an increase in the
average salinity of the Harbor (Table 10). Harbor-wide average salinity increased from
30.5 + 1.2 ppt during baseline, to 31.2 + 0.9 ppt for the 24-months. The increase of +0.6
ppt (or +2%) was small, and not discernable from the times-series plot of Harbor-wide
average salinity (Fig. 34). It was, however, highly significant (p < 0.01).

ENTEROCOCCUS

Former outfalls
ncrease

Decrease

sae.

Significant at
B<0.05>0.011

** Highly significant at
pe0.0t

? Possibly significant
P<0.10>0.05t

Figure 32. Enterococcus and fecal coliform bacteria. Spatial patterns of changes in average
counts during the 24-months for Enterococcus, and the first 12-months for fecal
coliform, after offshore transfer. Units are cfu 100 ml’. Other details as in
Figure 4.

63

1st 12-months

«ap

Former outfalls

Decrease

Significant at
BP <0.05>0011

Highly significant at
p<0.01

Possibly significant
Bp <0.10 >0.051

Fig. 33. Enterococcus. Comparison of the changes in average counts (cfu 100 mi ) during
the first (top) and second (bottom) 12-months after transfer.

64

65
Separation of the data into the first and second 12-months, indicated the increase for
salinity averaged Harbor-wide was driven by an increase during the second of the two 12-
months alone. During the first 12-months, Harbor-wide average salinity was not
significantly different from baseline. During the second 12-months, Harbor-wide average
salinity was highly significantly greater than baseline.
For the 24-months as a whole, we were also able to detect significant (or highly
significant) increases in salinity at individual stations (Fig. 35). At 8 of the 10 stations,
averages during the 24-months were significantly (or highly significantly) greater than
baseline. The increases at these 8 stations ranged in size from +0.7 ppt to +1.7 ppt.
During the individual 12-months, the number of stations that showed increases in salinity
was greater during the second 12-months than first (Fig. 36). During the first 12-months,
salinity increased at 5 stations, focused in the outer, Outer Harbor, down into the South
East Harbor. During the second 12-months, 9 stations showed increases. Increases were 
1993 1994 1995 1996 1997 1998 1999 2000 2001 2002
24
26
28
30
32
34 
SALINITY Offshore
transfer
Fig. 34. Salinity . Time series plot of volume-weighted Harbor-wide average values. Vertical arrow
shows date of offshore flow transfer. Only data from after May 1997 have been used in the
computations of means and to test for differences in values between periods before
and after transfer.
AVERAGE SALINITY
(PPT)
YSI
HYDROLAB

Figure 35.

SALINITY

Former outfalls

A Inc

bad Significant at
B<0.05>0001

ee Highly significant at
p<0.01

? Possibly significant
Bp <0.10 > 0.051

Salinity (top) and water temperature (bottom). Spatial patterns of changes during
the 24-months after offshore transfer. Units are ppt. for salinity, and °C for temperature.
Other details as in Figure 4, except that colors have not been ascribed to symbols and
area of shading, because for temperature and salinity, the changes cannot at this time
be assessed as ‘improvements’ or ‘decreases’ in water quality.

66

1ST 12-MONTHS

Former outfalls
a In

D
* Significant at

p<0.05>0.011

” Highly significart at
ps 001

? Possibly significant
p<010>0.051

Fig. 36. Salinity. Comparison of the spatial patterns of changes in salinity (ppt) during
the first (top) and second (bottom) 12-months after offshore transfer.

67

68
observed at all stations except Station 140 in the Neponset River region of the North
West Harbor. 
Water temperature . Unlike for salinity, and as expected, we were unable to detect a
change in water temperature related to transfer, for either the Harbor as a whole (Table
10), or for individual stations (Fig. 35). Harbor-wide water temperature averaged 9.9 +
5.8 o C for the baseline, and 9.7 + 6.0 o C for the 24-months. The difference of -0.2 o C (or
-2%) was not significant.
At the individual stations, temperature during the 24-months was significantly different
from baseline at only 1 station. At this station (Station 137), average water temperature
was very slightly lower (-0.9 o C) than baseline. Based on the location of the station in the
upper Inner Harbor, this decrease was unlikely related to transfer. 
DISCUSSION
Changes during the 24-months versus first 12-months 
Harbor-wide average values . The objective of this section was to compare the changes
we observed for the 24-months with the changes we observed for the first 12-months (and
reported in Taylor 2002). Table 11 compares the changes between the two periods, for
the data averaged Harbor-wide. For interpretation of the symbols used in this Table, see
the footnote to the Table.
For 16 of the 19 variables listed in Table 11 we detected significant (or highly
significant) changes for the data averaged Harbor-wide, for the 24-months as a whole
(solid arrows, Table 11). For 13 of the 16 (including most of the N and P variables, chl-a,
PC and Enterococcus), the directions of the changes, and the fact that they were
significant, were as we saw for the first 12-months.

Table 11. Comparison of the changes during the 24-months with those observed
during the first 12-months (and reported in Taylor 2002). Only changes that were
statistically significant at p = or <0.05 have been included in the Table.

VARIABLE CHANGE DURING CHANGE DURING
FIRST 12-MONTHS 24-MONTH
TN (mol!) 4 -10.1 (-32%) ¥ 10.7 (-34%)
DIN (umol I~) + 6.4 (-54%) ty -7.3(-62%)
DIN as % TN & ~12 (-22%) ¥ -16 (-41%)
TP(umol!“) ¥ -0.23 (-13%) aa -0.27 (-15%)
DIP (umol |“) G -0.32 (-31%) 4 -0.33 (-31%)
DIP as % TP uy ~13 (-22%) ¥ ~12 (-20%)
TN:TP 4 -5 (-27%) ty ~4 (-24%)

: ~4 (-39%) ~6 (-49%!
DIN:DIP ¥ (-39%) S (-49%)
TOTAL CHL-A (ug I~) ¥ -2.9 (-45%) 4¥ ~1.5 (-24%)
"ACTIVE' CHL-A (ug I') + -2.3 (-50%) vy -0.9 (-19%)
PHAEOPHYTIN (1g I~? ) o -0.6 (-32%) wy -0.5 (-29%)
PC (umol I-*) g -16.3 (-28%) ¥ ~12.3 (-29%)
TSS (mg!) _ raze 15-405
k(m- -0.8 (-15%) -0.04 - -0.12
kim") Ly b
SECCHI DEPTH (m) YY +0.3 (410%) 4 40.2 - 40.4
DO CONC. (mid-summer) (mg 1‘) 4 7 r’ 40.4 (46%)
DO % SAT. (mid-summer) 4y +8.6 - 415.5 4 +4.5 (45%)
ENTEROCOCCUS (cfu 100 m!-') ¥ -24 (-74%) ¥ -21 (-80%)
SALINITY (ppt) 4) 40.7 -41.2 * +0.6

69

70
For 3 of the 16 variables that showed significant changes for the data averaged Harbor-
wide for the 24-months, the significance of the change was greater than for the first 12-
months. For these, variables, which included mid-summer DOC concentration, mid-
summer DO % saturation and salinity, the changes for the 24-months were significant for
the data averaged Harbor-wide, but during the first 12-months, the changes were
significant only at individual stations.
For 3 of the 19 variables listed in Table11, including TSS, k and secchi depth, differences
were significant only at certain stations during the 24-months. For one of them (TSS),
changes were observed at none of the stations during the first 12-months, and for the
other two (k and secchi depth), the decreases were significant for the data averaged
Harbor-wide for the 24-months. 
Spatial patterns . Differences could also been seen in the spatial extents of changes
between the 24-months and first 12-months (Figures 31 through 35). For certain
variables, including most of the nutrients (TN, DIN, NH 4, DIP, PC), the changes during
the 24-months occurred over most of the area of the Harbor, and this was as we saw
during the first 12-months.
For others, the area that showed changes was larger during the 24-months than first 12-
months – this applied for example to TP, TN:TP, DIN:DIP, secchi depth, mid-summer
bottom-water DO concentration, Enterococcus and salinity. For these, the changes
during the first 12-months were enhanced during the second twelve.
For other variables, the area that showed the improvements for the 24-months was more
localized than for the first 12-months – these included total chl-a, acid-corrected chl-a,
and k. For these variables, changes seen during the first 12-months, were dampened
during the second, by processes apparently occurring in the outer, Outer Harbor.

TOTAL NITROGEN

TOTAL PHOSPHORUS

12-MONTH

NOT POSSIBLE TO
'MPROVEMENT' ‘DEGRADATION’ CLASSIFY AS
: IMPROVEMENT OR
DEGRADATION

Fig. 31. Total nitrogen (TN), total phosphorus (TP) and molar TN: TP. Comparison of the
changes during the first 12-months and the 24-month after offshore transfer. Red crosses show
sampling stations. Other details as in Figure 4.

71

DISSOLVED INORGANIC NITROGEN

DISSOLVED INORGANIC PHOSPHORUS

MOLAR DIN:DIP

NOT POSSIBLE TO
'MPROVEMENT' ‘DEGRADATION’ CLASSIFY AS
. IMPROVEMENT OR
DEGRADATION

Fig. 32. Dissolved inorganic nitrogen (DIN), dissolved inorganic phosphorus (DIP) and
molar DIN:DIP. Comparison of the changes during the 12-month and 24-month periods. Red
crosses show sampling stations.

72

ACID-CORRECTED CHL-A

TSS

24-MONTH

NOT POSSIBLE TO
'IMPROVEMENT' NO: ' CLASSIFY AS
DEGRADATION IMPROVEMENT OR
DEGRADATION

Figure 33. Acid-corrected chl-a, TSS and PC. Comparison of the changes during the first
12-months and the 24-months after offshore transfer. Red crosses show sampling stations.
Other details as in Figure 4.

73

SECCHI DEPTH

12-MONTH

24-MONTH

NOT POSSIBLE TO
'IMPROVEMENT' N ' CLASSIFY AS
DEGRADATION IMPROVEMENT OR
DEGRADATION

Fig. 34. Attenuation coefficient (k), secchi depth and mid-summer DO concentrations
Comparison of the changes during the first 12-months and the 24-months after
offshore transfer. Red crosses show sampling stations. Other details as in Figure 4.

74

75
For one variable, TSS, improvements related to transfer could not be detected at stations,
during both the 24-months and first 12-months. For this variable, increased
concentrations were observed in the outer, Outer Harbor over the 24-months, c.f. during
the first 12-months, when changes (increases or decreases) were observed at none of the
stations.

76
Thus, for many of the nutrients and PC, the large Harbor-wide improvements observed
during the first 12-months were repeated for the 24-months. For many of the particulate
(chl-a and TSS) or particulate-related variables (k and secchi depth), the improvements
were ‘dampened’ during the second of the two 12-months. For other variables, DO and
Enterococcus, the improvements were enhanced during the second 12-months.
Three factors might have contributed to the different responses of the different variables,
between the 24-months and first 12-months. The first factor might have been a natural
change in the response of the Harbor ecosystem with time. The second factor might have
been inter-annual environmental variability, especially in river inflows to the Harbor (the
second 12-months was dry). Third, background trends in water quality unrelated to
transfer could have ‘dampened’ (or ‘enhanced’, depending on variable) the changes in
water quality that followed transfer. 
Observed versus predicted changes 
The changes observed after transfer can be compared with two sets of predicted changes:
predictions made by us using simple mass balance calculations (see below); and
predictions made by others using more complex numerical models (hydrodynamic
modeling by R. Signell, USGS Woods Hole, and ecosystem modeling by HydroQual
1995). 
Simple mass balance calculations . Table 12 compares for seven variables, the changes
observed for the 24-months (and each of the 12-months), with those predicted from using
simple mass balance calculations. The calculations, which used estimated changes in
wastewater loadings, a hydraulic residence-time factor, and estimates of re-entry of
wastewater back into the Harbor from Massachusetts Bay, are shown in the footnote to
the Table.

77
Table 12. Observed versus predicted changes. Comparison of changes in Harbor-wide
average concentrations of nutrients, chl-a and TSS observed during the 24-months (and
two 12-month periods) with the changes predicted from simple mass balance
calculations.
______________________________________________________________________________________
Variable Observed changes Predicted 24-mth observed
change as proportion of
1 st 12-mth 2 nd 12-mth 24-months predicted
______________________________________________________________________________________ 
NITROGEN (  mol l -1 )
TN -10.1** -11.3 ** -10.7** -11.4 a 0.94
DIN -6.4** -8.1** -7.3** -7.4 a 0.99
NH4 -5.2** -5.4** -5.4** -7.7 a 0.70 
PHOSPHORUS (  mol l -1 )
TP -0.23** -0.31** -0.27** -0.72 a 0.38
DIP -0.32** -0.34** -0.33** -0.4 a 0.82 
CHLOROPHYLL-A (  g l -1 )
Acid-corr. -2.3** +0.3 -0.9* -1.0 b 0.82
chl-a 
SOLIDS (mg l -1 )
TSS -0.1 +0.6* +0.2 -0.5 a -0.40
______________________________________________________________________________________
a Computed using changes in loadings from Table 1, assuming mid-tide volume of Harbor was 643 x 10 6
m 3 (Stolzenbach and Adams 1998), and residence time of the Harbor was 6 d (R. Signell, USGS Woods
Hole, pers. comm.), and corrected for re-entry of transferred wastewater from Massachusetts Bay c .
Predicted change =((change in loadings x residence time)/mid-tide volume)-(concentration from re-entry
from Massachusetts Bay).
b Computed from predicted DIN changes assuming a change in DIN of 10  mol l -1 yields a change in the
same direction of acid-corrected chl-a of 1.0  gl -1 .
c Net re-entry of wastewater was estimated to contribute 3.4  mol l -1 for TN, +2.7  mol l -1 for DIN, +2.3 
 mol l -1 for ammonium, +0.18  mol l -1 for TP, +0.12  mol l -1 for DIP, and +0.1 mg l -1 for TSS. These
concentrations were computed as average concentrations in Deer Island wastewater during 24 months after
transfer/500. Average wastewater concentrations during 24-months were 1702  mol l -1 for TN, 1344.5 
 mol l -1 for DIN, 1266  mol l -1 for ammonium, 91.4  mol l -1 for TP, 59.6  mol l -1 for DIP, and mg l -1 for
TSS for 9/27/00 through 8 Aug. 01 (MWRA unpublished data). 500 = estimated 500:1 dilution of
wastewater in Harbor after offshore transfer (from dilution plot in Rex and Connor 2000, based on
hydrographic modeling by R. Signell USGS, Woods Hole). a Computed using changes in loadings from
Table 1, assuming mid-tide volume of Harbor was 643 x 10 6 m 3 (Stolzenbach and Adams 1998), and
residence time of the Harbor was 6 d (R. Signell, USGS Woods Hole, pers. comm.) Predicted change
=(change in loadings x residence time)/mid-tide volume.

78
For six of the seven variables (including the five nutrients and acid-corrected chl-a), the
directions of the changes for both the 24-months and the first 12-months, were as
predicted based on the estimated decreases in loadings. For five of the six variables (chl-
a excluded), the same applied for the second of the two 12-months.
For two variables, for TSS (for the 24-months and both 12-months), and for chl-a (for the
second 12-months), the directions of the changes were not as predicted from the mass
balance calculations. TSS concentrations were predicted to show a small decrease of
-0.5 mg l -1 , and concentrations of chl-a to decrease by ca. –1.0  g l -1 .
For four of the five nutrients and for chl-a, the sizes of the observed and predicted
decreases were very similar. For the three N nutrients (TN, DIN and NH 4) and for DIP,
the sizes of the decreases for the 24-months were between 0.70 and 0.99 of the predicted
decreases. For chl-a, the observed decrease was 0.82 of predicted.
.
For the remaining nutrient, TP, the proportion was smaller, and 0.38 of predicted
decreases. For TSS, the increase was unlike the predicted decrease. For both these
variables, the decreases appear to have been dampened by a background increase that
started before offshore transfer (Taylor 2001 a). 
Numerical model predictions . The changes we observed for the 24-months were also
similar to the changes predicted by the Bays Hydrodynamic Model, BHM (R. Signell
USGS Woods Hole) and Bays Eutrophication Model, BEM (HydroQual 1995). For
instance, the increase in Harbor-wide average salinity of +0.6 ppt for the 24-months was
similar to the +1-ppt increase predicted by the BHM.
Also, the size and pattern of the decreases we observed for DIN were also as predicted by
the BEM model. The BEM predicted average concentrations of DIN would decrease by
about one-half, and that the decrease would occur over most of the Harbor (HydroQual
1995). This size and the decrease over most of the Harbor was as we saw during both the
24-months and first 12-months.

79
For acid-corrected chl-a, the 30% decrease for the data averaged Harbor-wide, and the
focus of the decrease in the Central Harbor alone, were smaller and more localized than
predicted by the BEM. During the first 12-months, the 50% decrease over most of the
Harbor, was similar to the changes predicted by the BEM.
During the second of the two 12-month periods, the decreases in chl-a were apparently
dampened by background increases in chl-a in the Outer Harbor that were not predicted
by the BEM. The predictions made earlier by the BEM were made using 1993/1994
boundary conditions, and these likely differed from the boundary conditions during the
24-months after transfer.
For bottom-water DO, the opposite applied. During the 24-months, the increase in mid-
summer DO of <+1.0 mg l -1 for the data averaged Harbor-wide, and the focus of this in
the Inner Harbor and North West Harbor regions, were both as predicted by the BEM.
During the first 12-months, the increases were smaller and more localized than predicted. 
ACKNOWLEDGEMENTS 
Grateful thanks are extended to Drs Andrea Rex and Mike Delaney for providing the
administrative and logistic support necessary to conduct this work. Thanks are due to Maury Hall
for reviewing drafts of this report. Kelly Coughlin assisted in almost all aspects of this work, and
considerable thanks are due to her. She contributed especially to setting up and maintaining the
field-sampling program, and managing the data. Thanks are also due to Nicole O’Neill and
Keary Berger for oversight of the field-sampling program, and for data QA/QC. Rob Rabideau,
Keary Berger and others operated the sampling vessels. T. Smirnova, C. Blodget, M. Gofsteyn,
R. Warot, and numerous others conducted laboratory analyses. Thanks are also due to N.
McSweeney and L. Wong for QA/QC of analytical results. D. Hersh, J. Lobuglio, P. Ralston,
S.Y. Liang and others provided management of the data.

80 
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Kelly, J. R. 1997. Nitrogen flow and the interaction of Boston Harbor with
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Rex, A. C. and Taylor, D. I. 2000. Combined Work/Quality Assurance Project Plan for
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84 
APPENDIX A
COMPARISON OF SPATIAL PATTERNS OF CHANGES DURING THE
1 ST AND 2 ND 12-MONTHS AFTER TRANSFER

1st 12-months

Former outfalls

a ncrease
Decrease
* Significant at
B<0.05>0.011

- Highly significant at
Bs 0.01

2 Possibly significant
B<0.10>0.05t

Fig. A-1. Dissolved inorganic nitrogen (DIN). | Comparison of the changes in average
concentrations ( umol I**) during the first (top) and second (bottom) 12-months
after offshore transfer.

85

Fig. A-2.

1st 12-months

Former outfalls
Increase
Decrease
Significant at
p< 0.05>0.011

Highly significant at
p< 0.01

Possibly significant
Bp <0.10 >0.051

Particulate nitrogen (PN). Comparison of the spatial patterns of changes in
concentrations ( umol I"') during the first (top) and second (bottom) 12-month

periods after transfer.

86

Fig. A-3.

1st 12-months

Former outfalts
nerease
Decrease
Significant at

B<005>0011

Highly significant at
ps0.

Possibly significant
p<0.10 > 0.051

Ammonium (NH 4). Comparison of the spatial patterns of changes in concentrations

(umol-t) during the first (top) and second (bottom) 12-months after transfer.

87

Fig. A-4.

1st 12-months

Former outfalls
Increase
Decrease

Significant at
p<0.05>0.011

Highly significant at
p< 0.01

Possibly significant
p<0.10 > 0.051

Nitrate + nitrite (NO 3.2). | Comparison of the changes in average concentrations

(.urmol |-!) during the first (top) and second (bottom) 12-month periods after
offshore transfer.

88

1st 12-months

Former outfalls
Increase
Decrease
Significart at
p<0.05>0.011

Highly significart at
p< 0.01

Possibly significant
Pp <0.10 > 0.051

Fig. A-5. Dissolved inorganic phosphorus (DIP). Comparison of the changes in average
concentrations ( umol I**) during the first (top) and second (bottom) 12-month periods
after offshore transfer.

89

1st 12-months

Former outfalls

a Increase

Decrease

bd Significant at
B<0.05> 0.011

oe Highly significant at
p< 0.01

? Possibly significant
p<0.10>0051

Fig. A-6. Molar DIN:DIP._ Comparison of the spatial patterns of changes
during the first (top) and second (bottom) 12-month periods after
transfer.

90

1ST 12-MONTHS

increase
v Decrease

” p<005>0.01
-* p< 0.01

2ND 12-MONTHS

Fig. A-7. Total chl-a. Comparison of the spatial patterns of changes in concentrations
(yg | -") during the first (top) and second (bottom) 12-month periods after
offshore transfer.

91

Fig. A-8.

1st 12-months

2nd 12-months on

Former outfalls
increase
Decrease
Significant at

P< 0.05 >0.011

Highly significant at
ps 001

Possibly significant
p<0.10> 0.051

Particulate carbon(PC). Differences in the changes in average concentrations
(urmol *) between the first (top) and second (bottom) 12-months after transfer.

92

1ST 12-MONTHS

2ND 12-MONTHS

Former outfalls
Decrease

Significant at
P< 0.05>0.011

Highly significant at
p< 0.0t

Possibly significant
p<010> 0.051

Fig. A-9. Secchi depth. Differences in the changes in average secchi depths (m)
between the first (top) and second (bottom) 12-month periods after offshore

transfer.

93

Fig. A-10.

Ist 12-months

2nd 12-months

»=<@pPpe

Former outfalts

Decrease

Significant at
B<005>0,01t

Highly significant at
p<0.01

Possibly significant
(B<0.10 > 0051

Bottom-water DO % saturation. Comparison of the changes in average percent saturation values

during the first (top) and second 12-month periods after transfer.

94

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