Trends in the eight years before offshore transfer, 2001

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Trends in water quality in
Boston Harbor during the
8 years before offshore transfer
of Deer Island flows
Massachusetts Water Resources Authority
Environmental Quality Department
Report ENQUAD 2001-05

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Trends in water quality in Boston Harbor during the 8 years
before offshore transfer of Deer Island flows 
prepared by 
David I. Taylor
MASSACHUSETTS WATER RESOURCES AUTHORITY
Environmental Quality Department
100 First Avenue
Charlestown Navy Yard
Boston, MA 02129
(617) 242-6000
February 2001
Report No: 2001 - 05

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Citation
Taylor D. 2001. Trends in water quality in Boston Harbor during the 8 years before offshore
transfer of Deer Island flows. Boston: Massachusetts Water Resources Authority. Report
ENQUAD 2001-05. 54 p.

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TABLE OF CONTENTS 
Page 
Executive Summary………………………………………………. 5 
Introduction……………………………………………………… 7 
Justification for the water quality issues addressed……… 9 
Materials and methods 
Approach………………………………………………… 10 
Sampling, analytical procedures and data storage…………. 11 
Computations…………………………………………….. 14 
Statistical analyses………………………………………. 18 
Results 
Patterns of nitrogen……………………………………… 18 
Phosphorus………………………………………………. 24 
Molar N:P ratios…………………………………………. 27 
Phytoplankton biomass (chlorophyll-a)………………….. 30 
Water clarity and TSS…………………………………… 34 
Dissolved oxygen………………………………………… 37 
Sewerage-indicator bacteria………………………………. 41 
Temperature and salinity…………………………………. 44 
Summary of trends……………………………………….. 49 
Discussion 
Wastewater loadings…………………………………….. 51 
Correspondence between water quality 
and wastewater loadings………………………………… 51 
Acknowledgements………………………………………………. 54 
References……………………………………………………… 55

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EXECUTIVE SUMMARY 
In September 2000, the wastewater from Deer Island wastewater treatment facility
discharged to Boston Harbor was transferred 16-km offshore for diffusion into the bottom
waters of Massachusetts Bay. This transfer was important because it was one of the final
milestones of the Boston Harbor Project (BHP), the overall objective of which was to
better treat and dispose of the wastewater discharged to Boston Harbor. 
Of the various milestones of the BHP, this offshore transfer was predicted to lead to the
greatest improvements in eutrophication-related, Harbor water-quality. The future effects
of this offshore transfer will be reported elsewhere. The purpose of this particular report
was to document the baseline water quality and trends in water quality during the 8 years
before transfer. This documentation will serve as a baseline with which to assess the
future changes. 
The Massachusetts Water Resources Authority collected all data presented in the report.
Measurements of water quality in the Harbor were conducted from August 1993 (or 1996
depending on variable), through September 2000. Measurements were conducted at 10
sampling stations, 6 in the North Harbor, and 4 in the South Harbor. Measurements were
conducted weekly from May through October, and every two weeks from November
through April of each year. 
Much of the current public interest in Boston Harbor has focused on the improvements
following the September 2000 transfer. The analysis of data conducted in this report
indicates that significant changes in water quality were already occurring in the Harbor
during the 8 years before transfer. Of the 14 water quality variables monitored in this
study, 7 showed significant trends for the data averaged for the Harbor as a whole. 
A significant negative trend was observed for concentrations of total nitrogen (TN), and a
significant positive trend for concentrations of total phosphorus (TP). The Harbor
showed a significant decrease in average molar ratios of TN:TP, and a significant

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increase in average concentrations of total suspended solids (TSS). During the 8 years,
the Harbor also showed significant negative trends for percent saturation of dissolved
oxygen (DO), and counts of fecal coliform and Enterococcus bacteria. 
For 4 additional variables, trends were not observed for the Harbor as a whole, but were
observed for one or both of the individual North or South Harbor regions. The South
Harbor showed significant negative trends for dissolved inorganic nitrogen (DIN) and
dissolved inorganic phosphorus (DIP). In the North Harbor, significant positive trends
were observed for DIN, DIN as %TN, and DIP, and a significant negative trend for
secchi depth. 
Comparison of the trends in water quality with trends in loadings from the two
wastewater treatment facilities, indicated that for the Harbor as whole, many of the trends
were unrelated to changes in wastewater loadings, but were the result of natural,
background environmental trends. Trends in river inputs, ocean-Harbor exchanges, and
sediment-water fluxes within the Harbor may have contributed to these background
trends. 
At the level of the two individual regions, the correspondence between the trends in water
quality and wastewater loadings was closer than for the Harbor as a whole. For at least
certain variables, like dissolved inorganic nutrients, the changes in the two regions were
apparently correlated with inter-island transfer of flows in 1998, and upgrade to
secondary treatment at Deer Island in 1997 through 1998. 
Further changes in water quality are expected to follow the transfer of wastewater
discharges offshore in September 2000. The general nature of the future changes have
been predicted by others using numerical models. The exact nature of these changes will
likely also depend on background environmental trends like those identified in this study.

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INTRODUCTION 
In September 2000, the wastewater treated by the Deer Island wastewater treatment
facility, and previously discharged to Boston Harbor, was transferred offshore for
diffusion into the bottom-waters of Massachusetts Bay. This transfer was one of the final
milestones of a large construction and engineering project, termed the Boston Harbor
Project (BHP), designed to better collect and treat wastewater discharged to the Harbor
from the City of Boston and surrounding communities (Breen et al. 1994). 
Table 1 summarizes some of the major milestones of the BHP. Milestones completed
have included: termination of sludge dumping (1991); improved delivery of wastewater
to the Deer Island and Nut Island facilities; construction of a new primary treatment
facility at Deer Island (1995); upgrade to secondary treatment at Deer Island (1997
through1998); transfer of Nut Island flows through Deer Island (1998); and reductions
and improved treatment of combined sewer overflows (CSO). 
Of the major milestones of the BHP, the offshore transfer was predicted to lead to the
greatest improvements in eutrophication-related, Harbor water quality (HydroQual 1995).
The changes in the Harbor following the September-2000 transfer will be addressed in
future reports. The objective of this particular report was to document water quality in
the Harbor during approx. 8-years before the transfer, to provide a baseline with which to
assess these future changes. 
This report focuses on 3 water quality issues: (1) water column indices of eutrophication,
(2) water clarity, and (3) contamination of the Harbor water column with sewerage
bacteria. The report supplements other recent studies of trends in Harbor water quality.
Gong et al. (1998) documented trends in sewerage indicator bacteria from 1989 through
1996, following improvements to the combined sewer overflow (CSO) system
discharging to the Harbor and its tributaries. Taylor (2000, 2001) reported changes

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Table 1. Summary of some of the major milestones in the Boston Harbor Project. 
Milestone in 
BHP 
Date
completed 
Impacts on wastewater loadings to Harbor 
Sludge dumping
terminated 
Dec 1991 Decrease of 40 dry tons per day of solids loadings
to the Harbor. Also decrease in BOD, nutrient (N
and P) and pathogen indicator loadings to the
Harbor 
Pumping capacity at
Deer Island increased 
1989 through
1998 
Pumping capacity increased from 700 million
gallons per day (MGD) in 1989 to ca. 900 MGD in
1998, increasing volumes of wastewater treated,
and reducing CSO discharges 
New primary
treatment and
disinfection facility
completed at Deer
Island WWTF 
1995 Decreased loadings especially of TSS, but also of
pathogen indicators, BOD, N and P 
Treatment at Deer
Island upgraded to
secondary treatment 
Started in
1997, and
completed in
1998 
Decreased loadings especially of BOD, but also of
TSS, N, P and pathogen indicators 
Inter-island transfer mid-1998 Wastewater discharges from Nut Island to Central
Harbor decreased. Flows from Deer Island
increased, but total proportion of wastewater flows
subjected to secondary treatment increased.
Reduction in especially total loadings of BOD, but
also of total loadings of TSS, N, P and pathogen
indicators to the Harbor 
Offshore transfer Sept. 2000 Wastewater discharges from Deer Island WWTF to
the Harbor ended. Loadings especially of N and P
decreased further, but also of TSS, BOD and
pathogen indicators. Reductions in CSO to Harbor
and tributary rivers projected.

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in Harbor water quality following ‘inter-island transfer’ of Nut Island flows through Deer
Island in 1998. 
Others have reported changes to other components of the Boston Harbor ecosystem.
Kropp et al. (2001) documented long-term changes in the benthic invertebrate
communities of the Harbor, and Lefkowitz et al. (2000) reported trends in the health of
the Harbor lobster and flounder populations. Trends in Harbor benthic metabolism and
sediment-water nutrient fluxes were reported by Tucker et al. (2001). 
Justification for the water quality issues addressed 
The 3 issues addressed in this report (eutrophication, water clarity, and bacterial
contamination) were addressed because of their relevance to the health of the Harbor
ecosystem, the health of the public using the Harbor, and to the economic use of the
Harbor. The same 3 issues were also the focus of Taylor (2000) and Taylor (2001). 
Eutrophication, defined as organic enrichment of aquatic ecosystems (Nixon 1995), was
addressed because it is one of the major effects of elevated inputs of wastewater to
coastal systems such as Boston Harbor. Numerous symptoms of eutrophication have also
been documented in the Harbor, and loadings of nitrogen to the Harbor, one of the
components of wastewater responsible for eutrophication, have been estimated to be
among the highest reported for bays or estuaries in the USA (Kelly 1998). 
The bulk of the high N loadings were in turn contributed by the two wastewater treatment
facilities, that were in turn the focus of much of the BHP (Alber and Chan 1994). Harbor
symptoms of eutrophication have included elevated concentrations of N and chlorophyll
(HydroQual 1995), and lowered concentrations of dissolved oxygen (HydroQual 1995).
Other symptoms have included shallow depths of DO penetration into the sediments
(Kropp et al. 2000), and (at least at certain sites) elevated rates of benthic metabolism
(Tucker et al. 2001).

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The extensive mats of drift macroalgae that have developed in embayments in the Harbor
in the past (Sawyer 1965), and the almost complete demise of the once extensive seagrass
habitats of the Harbor (P. Colarusso US EPA, pers. communication), might also be
considered symptoms of eutrophication. The benthic infaunal communities of the Harbor
have also been shown to be comparable to those of eutrophied coastal bays or estuaries
(Kropp et al. 2000). 
The second issue, water clarity, was addressed because of the extensive use of the Harbor
for recreation, and the impact that water clarity can have on the aesthetics of especially
recreational beaches. Discharges of wastewater, such as those from Deer Island and Nut
Island, can affect water clarity, either directly by contributing solids to the water column,
or indirectly through stimulation of phytoplankton growth. Reductions in clarity can in
turn alter the structure and productivity of plant (Taylor et al. 1999) and animal
communities of the system. 
The third issue, contamination of the Harbor water-column with sewerage-related
bacteria, was addressed because this has perhaps been the major factor limiting public use
of the Harbor over the past 50 years. All beaches (Rex 2000) and most of the shellfish
beds of the Harbor have over the past 10 years been closed to public use for at least part
of each year, because of this contamination. At certain beaches and shellfish beds
contamination has been sufficient to require permanent closure of the beaches/beds. 
MATERIALS AND METHODS 
Approach 
This report examines trends in water quality at two levels. At the one level, trends were
examined for the Harbor as a whole. To detect such trends, volume-weighted averages
were computed for the Harbor as whole. These were averages, volume-weighted by the
volumes of the four regions of the Harbor - the Inner Harbor, North West Harbor, Central

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Harbor, and South East Harbor. Volume-weighting was required to account for the
different numbers of stations sampled per region. 
At the second level, trends were examined separately for the North Harbor (Inner Harbor
plus North West Harbor) and South Harbor (Central Harbor and South East Harbor)
regions. These were the two regions that received direct discharges of wastewater from
the two WWTF, that were in turn the focus of much of the BHP. Trends in the two
regions were examined to better identify the effects that upgrade to secondary treatment
at Deer Island, and then the transfer of Nut Island flows through Deer Island, had on
trends in water quality in the Harbor as a whole. 
Sampling, analytical procedures and data storage 
The Massachusetts Water Resources Authority (MWRA) collected all the water quality
data presented in this report. The data were collected as part of a monitoring project
called the Boston Harbor Water Quality Monitoring Project (BHWQM). The project
involved collection of water quality data from between August 1993 (or 1996, depending
on variable), through the date of transfer of Deer Island wastewater offshore on
September 6, 2000. Sampling was conducted once per week from May through October,
and then every two weeks through the remainder of the year. 
Water quality measurements were conducted at 10 stations (Fig. 1). Six of the stations
were located in the North Harbor, 2 of these in the Inner Harbor (Stns. 138 and 024) and
4 in the North West Harbor (Stns. 140, 106, 142, and 130). Four stations were located in
the South Harbor, with 3 of these in the Central Harbor (Stns. 077, 139, and 141), and 1
in the South East Harbor (Stn. 124). The regions were as defined in Sung 1991. The
coordinates of the 11 stations are listed in Table 2. 
At each station, samples were taken or measurements conducted at near-surface (0.5 m
from the water surface) or near-bottom (0.5 m above the sediment surface). The
variables monitored at each of the stations, and the sites at which the variables were

Inner Z
Harbor
NORTH
HARBOR
« Outfalls

@ Sampling stations

af proad S0ung
y Deer Island
oo wwir
North e° :
& West . . ad
Harbor @ nN . SOUTH
q > “eee HARBOR
JS Le
Ve“ >" eo. rCZ
Central @ A ooutn Eas
Harbor ° Harbor.
2s “9 G

Nut Island Rot
WWTF

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Fig. 1. Water-quality sampling stations, and major regions of Boston Harbor

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Table 2. Coordinates of the 10 stations monitored to characterize baseline water quality
in Boston Harbor. 
Station Station ID Latitude (N) Longitude (W) 
NORTH HARBOR 
Inner Harbor 
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 
President Roads 142 42 o 20.35 70 o 55.89 
Winthrop Bay 130 42 o 21.80 70 o 59.4 
Dorchester Bay/ 140 42 o 18.35 71 o 02.43 
Neponset River 
SOUTH HARBOR 
Central Harbor 
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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monitored within the water column, are summarized in Table 3. Table 4 summarizes the
field and analytical methods (for further details see Rex and Taylor, 2000). Trends in
water clarity in the Harbor were tracked using measurements of secchi depth, diffuse
attenuation coefficients (k), and concentrations of total suspended solids (TSS). 
Symptoms of eutrophication were tracked using concentrations of nitrogen (N) and
phosphorus (P), chlorophyll-a (chl-a), and dissolved oxygen (DO). Measurements were
conducted both of the ‘total’ and the ‘dissolved inorganic’ fractions of the two nutrients,
to account for the large seasonal transformations among the different fractions of the
nutrients that have been show to occur in the Harbor (Kelly 1997). Standing stocks of
phytoplankton were tracked using concentrations of chl-a. Counts of Enterococcus and
fecal coliform bacteria were used to track water-column contamination by sewage-related
pathogens. 
Concentrations of total nitrogen (TN) and total phosphorus (TP) were measured
depending on date, either directly or indirectly. Before 8/23/95, TN was estimated by
summing total Kjeldahl nitrogen (TKN) and nitrate + nitrite, and TP was estimated
directly. After 8/23/95, the concentrations of both TN and TP were estimated by
summing the concentrations of the total dissolved (TDN or TDP) and particulate fractions
of the two nutrients (PN or PP). Dissolved inorganic nitrogen (DIN) was estimated by
summing ammonium and nitrate + nitrite. 
Computations 
For the Harbor as a whole, two sets of averages are presented in the report –
instantaneous volume-weighted averages, and annual averages. For each sampling date,
instantaneous volume-weighted averages for the Harbor as a whole were computed as
follows (after Sung 1991): 
Volume-weighted average = (a*0.119) + (b*0.418) + (c*0.342) + (d*0.12)

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Table 3. Variables monitored at the 11 stations. S = surface only, S & B =
surface and bottom, P = profile. 
Variable Sample location 
Total N and P 
Dissolved inorganic N and P 
Chlorophyll-a 
Secchidepth 
Attenuation coefficient (k) 
TSS 
Dissolved oxygen (% 
saturation) 
Fecal coliform 
Enterococcus 
S 
S & B 
S & B 
S 
P 
S & B 
P 
S & B 
S & B

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Table 4. Summary of field and analytical methods. 
VARIABLE METHOD 
Total P 
TDN and TDP 
PN 
PP 
Ammonium 
Nitrate + nitrite 
Phosphate 
Chlorophyll-a 
Secchi depth 
k 
TSS 
Dissolved oxygen 
Fecal coliform 
Solarzano and Sharp (1980a) 
Solarzano and Sharp (1980b) 
Perkin Elmer CHN analyzer 
Solarzano and Sharp (1980a) 
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 
acid-corrected, (Holm Hansen 1965) as described 
in EPA (1992). Sequioa Turner Model 450 
fluorometer, 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, then Hydrolab 
Datasonde 4 
Clesceri et al. (1998, Method 9222D) 
Clesceri et al. (1998, Method 9230C)

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Enterococcus 
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 are the volumes of each of the regions expressed as a proportion of 1
(volumes from Sung 1991, citing Ketchum 1951). The volume of the Inner Harbor was
94 x 10 6 m 3 (or 11.9 % of the total Harbor volume). The volume of the North West
Harbor, 330 x 10 6 m 3 (41.8 %), the volume of the Central Harbor, 270 x 10 6 m 3 (34.2 %),
and the volume of the South East Harbor, 95 x 10 6 m 3 (12.0 %). 
For all variables except Enterococcus and fecal coliform, the regional averages used to
compute the instantaneous volume-weighted averages for the Harbor as a whole were
computed as arithmetic means. For Enterococcus and fecal coliform, the regional
averages were computed as geometric means. This was necessary because of the non-
normal distribution of the Harbor Enterococcus and fecal coliform data. 
The annual averages for the Harbor as a whole were computed by averaging the average
monthly volume-weighted averages for all months in the year. The average monthly
values were computed by averaging the instantaneous volume-weighted averages for all
dates sampled in the month. Average monthly (rather than instantaneous) average values
were used to compute the annual averages, to eliminate any bias that might have been
introduced by the more intensive sampling conducted during summer months each year. 
For the individual North Harbor and South Harbor regions, only annual average values
have been presented. These were computed from average monthly values for each of the
months in the year. The instantaneous averages used to compute the monthly averages

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for each region, were computed as simple arithmetic means of the values for all stations
sampled within the region on a particular date. 
Statistical analyses 
As recommended by Hirsch et al (1981), the non-parametric Kendall tau-b test was used
to check for the existences of monotonic trends in the data. This particular test was
employed because it considers data that are not normally distributed, exhibit seasonality,
possess missing values, or have values reported as ‘less than’. SPSS 8.0 was used to
conduct the tests (SPSS 1995). Trends were significant when the tests yielded p values =
0.05 or less, and highly significant when p = 0.01 or less. 
The test was applied to average monthly data. All the average monthly data were de-
seasonalized and the residual data ranked before application of the test. The additive de-
seasonalization model was employed, and both the de-seasonalization and ranking
procedures were conducted using SPSS 8.0. The two-tailed Kendall tau-b test was
employed in preference to the one-tailed test, because for many of the variables the
directions of the trends were not evident from simple time-series plots of the data. The
two-tailed test also tended to be more conservative than the one-tailed test. 
RESULTS 
Patterns of nitrogen 
Total Nitrogen (TN). Application of the Kendall tau-b test, showed a significant negative
trend in Harbor-wide average concentrations of TN during the study period (p = 0.05,
Table 5). Note, negative correlation coefficients indicate negative trends, and positive
coefficients, positive trends. The Kendall tau-b tests also indicated a highly significant
negative trend in TN in the South Harbor (p < 0.001), but no significant trend for TN in
the North Harbor (p = 0.83).

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Time-series plots of Harbor-wide volume-weighted averages indicated that the decrease
in TN observed Harbor-wide was not large, and was driven by a decrease in the seasonal
build up of TN during the winters in 1998/99 and 1999/00 (Fig. 2). The decrease

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Table 5. Nitrogen . Significance of trends in nitrogen concentrations averaged Harbor-
wide (Harbor), and for the North Harbor (North) and South Harbor (South) regions.
Significance tested using Kendall tau-b test. * = significant at p < 0.05 but > 0.01, ** =
significant at p < 0.01. Negative correlation coefficient values indicate decreases,
positive values, increases. 
_______________________________________________________________________ 
Variable Region Correlation Significance n (months) 
Coefficient 
_______________________________________________________________________ 
TN Harbor -0.14 0.05 62 * 
North -0.02 0.83 62 
South -0.45 <0.001 62 ** 
DIN Harbor -0.09 0.29 73 
North 0.18 0.03 73 * 
South -0.37 <0.001 73 ** 
DIN Harbor 0.13 0.11 76 
as % TN 
North 0.30 <0.001 64 ** 
South -0.05 0.55 64 
________________________________________________________________________

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1994 1995 1996 1997 1998 1999 2000
10
20
30
40
50
60
1994 1995 1996 1997 1998 1999 2000
10
20
30
40
50
60
TN (UMOL L -1 )
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 2. Total nitrogen (TN) . Top: Time-series plot of volume-weighted, Harbor-wide
average concentrations of TN. Bottom: Annual average concentrations in the North Harbor
(5 stations) and South Harbor (4 stations). Error bars are + 1 x SD.
NORTH
SOUTH

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during winter 1998/99 was manifested as a narrowing of the period of winter build up,
and in winter 1999/00, by a lowering of the extent of the build up. 
Time series plots of the annual averages for the North Harbor and South Harbor regions
showed that the decrease seen Harbor-wide was driven by a decrease in TN in the South
Harbor. The decrease in the South Harbor occurred from 1998 on. Its timing, and the
fact that it was confined to the South Harbor, suggested it followed inter-island transfer in
1998. No increase in TN after transfer was detected in the North Harbor. 
Dissolved inorganic nitrogen (DIN). Unlike for TN, which showed a significant negative
trend for the data averaged Harbor-wide, no significant trend could be detected for
concentrations of DIN averaged Harbor-wide (p = 0.29, Table 5). Significant trends for
DIN were however observed in both the individual regions. In the South Harbor, DIN
concentrations showed a highly significant decrease (p < 0.001). In the North Harbor,
concentrations showed a significant increase (p = 0.03). 
The time-series plot of Harbor-wide average DIN concentrations also revealed no
monotonic trend (Fig. 3). DIN concentrations in the Harbor showed a strong seasonal
cycle during each of the years during the study. The amplitude and timing of the
seasonal cycles were similar among all years, except in winter 1998/99 and summer 2000
when concentrations were higher than in equivalent seasons during other years. 
The absence of a trend in DIN Harbor-wide, was at least partly the result of a canceling
out of opposing trends in the North and South Harbor regions. From 1994 through 1997,
annual average concentrations in the North Harbor and South Harbor regions tracked one
another. After 1998, and probably as a result of inter-island transfer, the difference in
concentrations between the two regions increased. Concentrations in the South Harbor
decreased, while concentrations in the North Harbor increased. 
DIN as % TN. As for DIN, but unlike for TN, no significant trend could be detected for
the percent contribution of DIN to TN for the Harbor as a whole (p = 0.11, Table 5). A

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1994 1995 1996 1997 1998 1999 2000
0
10
20
30
40
1994 1995 1996 1997 1998 1999 2000
0
10
20
30
40
DIN (UMOL L -1 )
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 3. Dissolved inorganic nitrogen (DIN) . Top: Time-series plot of
volume-weighted, Harbor-wide average concentrations. Bottom: Annual average
concentrations in the North Harbor (5 stations) and South Harbor (4 stations).
Error bars are + 1 x SD.
NORTH
SOUTH

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1994 1995 1996 1997 1998 1999 2000
0
20
40
60
80
100
1994 1995 1996 1997 1998 1999 2000
10
20
30
40
50
60
DIN AS % TN
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 4. DIN as % TN . Top: Time-series plot of volume-weighted, Harbor-wide
DIN as % TN values. Bottom: Annual average concentrations in the North Harbor
(5 stations) and South Harbor (4 stations). Error bars are + 1 x SD.
NORTH
SOUTH

25 
highly significant positive trend was observed for percent contribution of DIN to TN in
the North Harbor (p < 0.001), but in the South Harbor, the data showed no trend (p =
0.55). 
No trend was also discernable from the time series plot of DIN as %TN for the Harbor as
a whole (Fig. 4). Elevated peaks in the percent contribution of DIN to TN were observed
during winters 1998/99 and 1999/00, and during summer 2000, but these peaks were
apparently not sufficient to generate a trend for the entire study period, detectable by the
Kendall tau-b test. 
The positive trend in DIN as % TN in the North Harbor was generated by an increase in
the percent contribution from 1997 or 1998 through the end of the study. The timing of
the increase, and the absence of a simultaneous decrease in the South Harbor, indicates
the increase in the North Harbor was mainly the result of the upgrade to secondary
treatment at Deer Island in 1997. 
Phosphorus 
Total P (TP). As for TN, a significant trend was observed for Harbor-wide average
concentrations of TP (Table 6). Unlike for TN, which showed a significant negative
trend, for TP, the Harbor showed a highly significant increase (p = 0.02). The increase
was confined to the North Harbor, where the increase was also highly significant (p<
0.001). TP in the South Harbor showed no detectable trend (p = 0.08). 
The time series plot of TP averaged for the Harbor as a whole, showed the trend Harbor-
wide was small (Fig. 5). The plot also indicated the increase was driven by an increase in
TP in the Harbor from approx. 1998 on. Plots of the changes in the individual regions
indicated that unlike for TN, where the decrease observed for the Harbor as a whole was
driven by a decrease in the South Harbor, for TP, the increase Harbor-wide was driven by
an increase in the North Harbor.

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Table 6. Phosphorus . Significance of trends in phosphorus concentrations averaged
Harbor-wide (Harbor), and for the North Harbor (North) and South Harbor (South)
regions. Significance tested using Kendall tau-b test. * = significant at p < 0.05 but >
0.01, ** = significant at p < 0.01. Negative correlation coefficient values indicate
decreases, positive values, increases. 
_______________________________________________________________________ 
Variable Region Correlation Significance n (months) 
Coefficient 
_______________________________________________________________________ 
TP Harbor 0.19 0.02 69 ** 
North 0.35 <0.001 66 ** 
South -0.15 0.08 66 
DIP Harbor -0.06 0.51 67 
North 0.22 0.01 66 ** 
South -0.34 <0.001 66 ** 
_____________________________________________________________

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1994 1995 1996 1997 1998 1999 2000
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
4.0
1994 1995 1996 1997 1998 1999 2000
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
4.0
TP (UMOL L -1 )
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 5. Total phosphorus (TP) . Top: Time-series plot of volume-weighted, Harbor-wide
average concentrations of TP. Bottom: Annual average concentrations in the North Harbor
(5 stations) and South Harbor (4 stations). Error bars are + 1 x SD.
NORTH
SOUTH

28 
The increase in TP in the North Harbor was observed from 1998 on. While the timing of
the increase followed inter-island transfer, the absence of a simultaneous decrease in TP
in the South Harbor, suggested the increase in the North Harbor was not simply the result
of the addition of flows from Nut Island. Had the increase in TP in the North Harbor
been the result of inter-island transfer, an increase in TN, a much larger constituent of
wastewater, might also have been expected in the region. 
Dissolved inorganic phosphorus (DIP). Unlike for TP, but as for DIN, no significant
trend could be detected for DIP for the Harbor as a whole (p = 0.51). Again as for DIN,
significant opposing trends were observed for DIP in both the North Harbor and South
Harbor regions (Table 6). As for DIN, a highly significant decrease was observed in the
South Harbor (p < 0.001), and in the North Harbor, DIP showed a significant increase (p
= 0.01). 
For the Harbor as a whole, no trend was also discernable for DIP from the time series plot
of Harbor-wide average concentrations (Fig. 6). As for DIN, the trends in DIP, the
decrease in the South Harbor, and the increase in the North Harbor, were driven by
changes from 1998 on. The timing and nature of the changes in the two regions suggested
a causal link with inter-island transfer. 
As for DIN, the significance of the decrease in DIP in the South Harbor was greater than
the significance of the increase in the North Harbor. This suggests that the impacts of
inter-island transfer were greater in the South Harbor than the North Harbor. The greater
exportation from the Harbor of wastewater discharged from Deer Island to the North
Harbor than from Nut Island to the South Harbor might account for this difference. 
Molar N:P ratios. 
TN:TP . The Kendall tau-b test indicated highly significant trends in average molar ratios
of TN:TP, for the Harbor as a whole, and for both the North and the South Harbor
regions (p = 0.002 for all 3 areas) (Table 7). The decrease observed for the Harbor as a

29 
1994 1995 1996 1997 1998 1999 2000
0
1
2
3
1994 1995 1996 1997 1998 1999 2000
0
1
2
3
DIP ( UMOL L -1 )
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 6. DIP . Top: Time-series plot of volume-weighted, Harbor-wide average concentrations
of DIP. Bottom: Annual average concentrations in the North Harbor (5 stations) and South Harbor
(4 stations). Error bars are + 1 x SD.
NORTH
SOUTH

30 
Table 7. N:P ratios . Significance of trends in N:P ratios averaged Harbor-wide
(Harbor), and for the North Harbor (North) and South Harbor (South) regions.
Significance tested using Kendall tau-b test. * = significant at p < 0.05 but > 0.01, ** =
significant at p < 0.01. Negative correlation coefficient values indicate decreases,
positive values, increases. 
_______________________________________________________________________ 
Variable Region Correlation Significance n (months) 
Coefficient 
_______________________________________________________________________ 
TN:TP Harbor -0.26 0.002 67 ** 
North -0.26 0.002 67 ** 
South -0.26 0.002 67 ** 
DIN:DIP Harbor -0.07 0.13 65 
North 0.09 0.28 65 
South -0.14 0.10 65 
________________________________________________________________________

31 
whole was clearly discernable from the time-series plot of Harbor-wide average TN:TP
ratios (Fig. 7). The decrease was evident as lowered ratios from mid-1998 on. Before
1998, TN:TP ratios exceeded the Redfield ratios of 16:1 during much of each year. After
1998, the ratios fell below 16:1, except for short periods during winters. 
The patterns of the decreases in TN:TP ere similar in the two regions. In both regions,
annual average TN:TP ratios showed a progressive decrease from 1998 on. The
mechanisms responsible for the decreases were different in the two regions. The
decrease in TN:TP in the South Harbor was driven by the decrease in TN. In the North
Harbor, the decrease was caused by an increase in TP, also after 1998. 
DIN:DIP . Unlike for TN:TP, no significant trends in molar ratios of DIN:DIP could be
detected for the Harbor as a whole, or for either the North Harbor or South Harbor
regions (Table 7). No trend could also be discernable from the time-series plot of
DIN:DIP for the Harbor as a whole (Fig. 8). DIN:DIP ratios, which tended to be lower in
the Harbor than for TN:TP, were no different at the end of the study period than at the
start. 
Unlike for concentrations of the individual DIN and DIP components, no significant
trend in annual average ratios of DIN:DIP could be detected for either of the two regions.
DIN:DIP ratios tended to be higher in the North than the South Harbor, but the difference
in ratios between the two regions remained consistent through the study. While
concentrations of the individual DIN and DIP components in both region were altered by
inter-island transfer, the relative proportions of DIN:DIP before and after inter-island
transfer were not different. 
Phytoplankton biomass (chlorophyll-a) 
Unlike for concentrations of the various N and P nutrients, no significant trends were
detected for concentrations of chlorophyll-a (chl-a), for the Harbor as a whole (p = 0.26),
or for the North Harbor (p = 0.83) or South Harbor regions (p = 0.20) (Table 8). The

32 
1994 1995 1996 1997 1998 1999 2000
0
5
10
15
20
25
30
35
1994 1995 1996 1997 1998 1999 2000
0
5
10
15
20
25
30
35
Redfield
ratio =
16:1
Redfield
ratio =
16:1
TN : TP
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 7. TN : TP . Top: Time-series plot of volume-weighted, Harbor-wide average
TN:TP ratios. Bottom: Annual average ratios in the North Harbor (5 stations) and South Harbor
(4 stations). Error bars are + 1 x SD.
NORTH
SOUTH

33 
1994 1995 1996 1997 1998 1999 2000
0
5
10
15
20
25
30
1994 1995 1996 1997 1998 1999 2000
0
5
10
15
20
25
30
Redfield
ratio =
16:1
Redfield
ratio =
16:1
DIN : DIP
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 8. DIN : DIP . Top: Time-series plot of volume-weighted, Harbor-wide average
DIN:DIP ratios. Bottom: Annual average ratios in the North Harbor (5 stations) and South Harbor
(4 stations). Error bars are + 1 x SD.
NORTH
SOUTH

34 
Table 8. Chlorophyll, clarity and TSS . Significance of trends tested using Kendall tau-
b test. Trends tested for data averaged Harbor-wide (Harbor), and for North Harbor
(North) and South Harbor (South) regions. 
_______________________________________________________________________ 
Variable Region Correlation Significance n (months) 
Coefficient 
_______________________________________________________________________ 
Chl-a Harbor -0.09 0.26 61 
North -0.02 0.83 61 
South -0.11 0.20 61 
Secchi Harbor -0.01 0.85 92 
North -0.21 0.005 83 ** 
South -0.08 0.27 83 
k Harbor 0.05 0.53 83 
North 0.07 0.37 83 
South -0.09 0.23 83 
TSS Harbor 0.40 <0.001 53 ** 
North 0.43 <0.001 53 ** 
South 0.36 <0.001 53 **

35 
seasonal pattern of chl-a seen during each of the years was basically the same during all
years during the study (Fig. 9). 
In most years (including 1997, 1998 and 1999), concentrations peaked in summer. In
other years, the peaks were observed either in spring (as in 1996 and 2000), or in fall
(1995). In the individual regions, the annual averages were similar among all years.
Unlike for concentrations of N and P, which tended to be higher in the North Harbor than
the South Harbor, chl-a concentrations in the two regions were similar. 
Water clarity and TSS 
Secchi depth. Unlike for the total forms of N and P, but as for the dissolved inorganic
forms, no significant trend could be detected for the secchi depth data averaged for the
Harbor as a whole (p = 0.85, Table 8). For the data separated by region, a highly
significant negative trend was observed for the North Harbor (p = 0.005), but no trend
was detected for the South Harbor (p = 0.27). The time series plot of average secchi
depth also revealed no trend for the Harbor as a whole (Fig. 10). 
In the North Harbor, the region that showed a significant negative trend, annual average
secchi depths showed a progressive decrease from 1995 through 2000. In the South
Harbor, the region that showed no significant monotonic trend, annual average secchi
depths showed a sinusoidal pattern, with elevated secchi depths towards the start and end,
and lowered secchi depths mid-way through the study period. 
Early in the study period, from 1993 through 1997, annual average secchi depths in the
two regions tracked one another. Later, from 1998 through 2000, the average secchi
depths in the North Harbor were consistently lower than in the South Harbor. The timing
of the separation of the values in the two regions, suggested the changes from 1998 on
were related to inter-island transfer.

36 
1994 1995 1996 1997 1998 1999 2000
0
5
10
15
20
25
1994 1995 1996 1997 1998 1999 2000
0
5
10
15
CHL-A ( UG L -1 )
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 9. Chlorophyll-a . Top: Time-series plot of volume-weighted, Harbor-wide
average concentrations of chl-a. Bottom: Annual average concentrations in the North Harbor
(5 stations) and South Harbor (4 stations). Error bars are + 1 x SD.
NORTH
SOUTH

37 
1993 1994 1995 1996 1997 1998 1999 2000
0
1
2
3
4
5
6
1993 1994 1995 1996 1997 1998 1999 2000
1
2
3
4
SECCHI DEPTH (M)
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 10. Secchi depth . Top: Time-series plot of volume-weighted, Harbor-wide
average secchi depths. Bottom: Annual average secchi depths in the North Harbor
(5 stations) and South Harbor (4 stations). Error bars are + 1 x SD.
NORTH
SOUTH

38 
Attenuation coefficient (k). As for secchi depth, no significant trend was detectable for
attenuation coefficients (k) averaged for the Harbor as a whole (p = 0.53, Table 8). No
significant trends were also detectable for k for the South Harbor (p = 0.23) or North
Harbor regions (p = 0.37). The time-series plot of Harbor-wide average k values
confirmed the absence of a trend in k values for the Harbor as a whole (Fig. 11). 
In both individual regions of the Harbor, annual average k values showed some evidence
of a progressive increase through the study. Had the progressive increase in the North
Harbor been significant, it would have agreed with the significant decrease in secchi
depth observed in the same region. In the South Harbor, the annual average k data did
not mirror the sinusoidal pattern shown by the secchi depth data. 
Total suspended solids (TSS). The Kendall tau-b test indicated highly significant
positive trends for TSS concentrations in the Harbor as a whole, and in both the North
Harbor and the South Harbor regions (p < 0.001 in all areas, Table 8). The increase in
TSS concentrations observed for the Harbor as a whole was clearly evident from the
time-series plot of average TSS concentrations (Fig. 12). 
The increase observed for the Harbor-wide averages was driven by increases in TSS in
both the North Harbor and South Harbor regions. In both regions, the patterns of
increase were similar. Annual average TSS concentrations in both regions increased
progressively from 1996 through 2000. In agreement with the secchi depth and k data,
TSS concentrations in the North Harbor were consistently greater than in the South
Harbor. 
Dissolved oxygen (DO) 
DO percent saturation (DO % sat.) . The Kendall tau-b test detected a significant
negative trend for bottom-water DO % saturation values for the Harbor as a whole (p =
0.03) (Table 9). Highly significant decreases were observed in the individual North
Harbor and South Harbor regions (p < 0.01).

39 
1993 1994 1995 1996 1997 1998 1999 2000
0.0
0.2
0.4
0.6
0.8
1.0
1.2
1993 1994 1995 1996 1997 1998 1999 2000
0.0
0.2
0.4
0.6
0.8
1.0
k (m -1 )
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 11. Attenuation coefficient . Top: Time-series plot of volume-weighted, Harbor-wide
average k values. Bottom: Annual average k values in the North Harbor (5 stations)
and South Harbor (4 stations). Error bars are + 1 x SD.
NORTH
SOUTH

40 
1994 1995 1996 1997 1998 1999 2000
0
2
4
6
8
10
1994 1995 1996 1997 1998 1999 2000
0
2
4
6
8
TSS ( MG L -1 )
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 12. Total suspended solids (TSS) . Top: Time-series plot of volume-weighted, Harbor-wide
average concentrations of TSS. Bottom: Annual average concentrations in the North Harbor
(5 stations) and South Harbor (4 stations). Error bars are + 1 x SD.
NORTH
SOUTH

41 
Table 9. Dissolved oxygen and sewerage-indicator bacteria . Significance of trends
tested using Kendall tau-b test for data averaged Harbor-wide (Harbor) and for the North
Harbor (North) and South Harbor (South) regions. 
_______________________________________________________________________ 
Variable Region Correlation Significance n (months) 
coefficient 
_______________________________________________________________________ 
DO (% sat.) Harbor -0.17 0.03 78 * 
North -0.25 0.001 78 ** 
South -0.21 0.007 78 ** 
Fecal Harbor -1.55 0.05 73 * 
coliform 
North -0.05 0.57 73 
South -0.20 0.05 73 * 
Enterococcus Harbor -0.24 0.002 73 ** 
North -0.16 0.04 73 * 
South -0.39 <0.001 73 ** 
_____________________________________________________________

42 
No clear negative trend was discernable from the time-series plot of bottom-water DO %
saturation values averaged Harbor-wide (Fig. 13). Note: the Kendall tau-b tests were
applied to de-seasonalized data. In both regions, annual average DO % saturation values
decreased through the study. The patterns of the decreases were similar in both regions.
Except for an increase in 1996, in both regions average DO % saturation values showed a
progressive decrease from 1994 through 2000. 
Sewerage-indicator bacteria 
Fecal coliform. A significant negative trend was also observed in the Harbor for counts
of fecal coliform bacteria averaged for the Harbor as a whole (p = 0.05, Table 9). The
decrease Harbor-wide was driven by a decrease in the South Harbor (p = 0.05). In the
North Harbor, counts showed no trend (p = 0.57). The negative trend for the Harbor as a
whole, was confirmed by the time-series plot of counts averaged Harbor-wide (Fig. 14).
During the second half of the study, counts tended to be lower than during the first half. 
In the South Harbor, where counts tended to be lower than in the North Harbor, annual
average counts showed a decrease from 1998 on. The timing of the decrease, and its
focus in the South Harbor, together suggested the decrease was related to the ending of
Nut Island discharges to the region in mid-1998. In the North Harbor, annual average
counts were no higher after inter-island transfer than before. 
Enterococcus . As for fecal coliform, a negative trend was observed for average counts of
Enterococcus for the Harbor as a whole (Table 9). The significance of the trend was
greater for Enterococcus (p = 0.002) than fecal coliform (p = 0.05). Unlike for fecal
coliform, where the trend was observed only in the South Harbor, for Enterococcus, the
negative trend was observed in both regions (p = 0.04 in North Harbor, and p < 0.001 in
South Harbor). 
The negative trend detected by the Kendall tau-b test, was clearly evident from the time
series plot of instantaneous average Enterococcus counts for the Harbor as a whole

43 
1994 1995 1996 1997 1998 1999 2000
60
80
100
120
140
160
1994 1995 1996 1997 1998 1999 2000
60
80
100
120
140
160
DO % SATURATION
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 13. Bottom-water DO % saturation . Top: Time-series plot of volume-weighted, Harbor-wide
average percent saturation values. Bottom: Annual average values in the North Harbor
(5 stations) and South Harbor (4 stations). Error bars are + 1 x SD.
NORTH
SOUTH

44 
1994 1995 1996 1997 1998 1999 2000
1
10
100
1000
1994 1995 1996 1997 1998 1999 2000
0.1
1
10
100
1000
FECAL COLIFORM COUNTS ( # CFU 100 ML -1 )
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 14. Fecal coliform . Top: Time-series plot of volume-weighted, Harbor-wide
average counts of fecal coliform bacteria. Bottom: Annual average counts in the North Harbor
(5 stations) and South Harbor (4 stations). Error bars are + 1 x SD.
NORTH
SOUTH

45 
(Fig. 15). Annual average counts in both regions decreased through the study. In the
South Harbor, where the decrease was larger than in the North Harbor, counts showed a
progressive decrease from 1995 on. In the North Harbor, the pattern was less consistent
among successive years, but counts too showed an overall downward trend. 
Temperature and salinity 
Water temperature. No significant trends were detected for water temperatures averaged
for the Harbor as whole (p = 0.77), or for the North (p = 0.48) or South (p = 0.88)
Harbors (Table 10). The maximum temperatures achieved each summer showed little
variation between the different years (Fig. 16). The data did however show some
evidence of a long-term increase in the minimum winter temperatures, from winter
1993/94 to winter 1998/99. 
No trends in water temperatures were also discernable from the time-series plots of
annual average temperatures for the two regions. During the earlier part of the study,
annual average water temperatures were approximately 1 o C greater in the North Harbor
than the South Harbor, but later in the study, the annual average temperatures in the two
regions were almost identical. 
Salinity . As for temperature, no significant trends could be detected for salinity for the
Harbor as a whole (p = 0.35), or for the North Harbor (p = 0.66), or South Harbor regions
(p = 0.39)(Table 31). The absence of a monotonic trend was confirmed by the time-
series plot of average salinities computed for the Harbor as a whole (Fig. 17). Variability
within each year was considerable. 
In the North Harbor, annual average salinities were consistently lower than in the South
Harbor. The pattern of annual average salinities was almost identical in each region, and
in neither of the regions, did the annual average salinities show a consistent trend through
the study period.

46 
1994 1995 1996 1997 1998 1999 2000
1
10
100
1000
1994 1995 1996 1997 1998 1999 2000
0.1
1
10
100
1000
ENTEROCOCCUS COUNTS ( # CFU 100 ML -1 )
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 15. Enterococcus . Top: Time-series plot of volume-weighted, Harbor-wide
average counts of Enterococcus bacteria. Bottom: Annual average counts in the North Harbor
(5 stations) and South Harbor (4 stations). Error bars are + 1 x SD.
NORTH
SOUTH

47 
Table 10. Temperature and salinity . Significance of trends tested using Kendall tau-b
test for data averaged Harbor-wide (Harbor) and for the North Harbor (North) and South
Harbor (South) regions. 
_______________________________________________________________________ 
Variable Region Correlation Significance n (months) 
coefficient 
_______________________________________________________________________ 
Temperature Harbor 0.01 0.77 92 
North -0.05 0.48 84 
South 0.01 0.88 84 
Salinity Harbor 0.08 0.35 73 
North 0.04 0.66 75 
South 0.07 0.39 75 
________________________________________________________________________

48 
1993 1994 1995 1996 1997 1998 1999 2000
-5
0
5
10
15
20
25
1993 1994 1995 1996 1997 1998 1999 2000
4
6
8
10
12
14
16
TEMPERATURE ( o C )
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 16. Water temperature . Top: Time-series plot of volume-weighted, Harbor-wide
average temperatures. Bottom: Annual average temperatures in the North Harbor
(5 stations) and South Harbor (4 stations). Error bars are + 1 x SD.
NORTH
SOUTH

49 
1994 1995 1996 1997 1998 1999 2000
22
24
26
28
30
32
34
36
1994 1995 1996 1997 1998 1999 2000
26
28
30
32
34
36
SALINITY (PPT)
Offshore
transfer
Inter-
island
transfer
Secondary
treatment
at Deer Is.
New primary
facility at
Deer Is.
Figure 17. Salinity . Top: Time-series plot of volume-weighted, Harbor-wide average salinity.
Bottom: Annual average salinities in the North Harbor (5 stations) and South Harbor (4 stations).
Error bars are + 1 x SD.
NORTH
SOUTH

50 
Summary of trends 
The data analysis conducted in this report indicates that water quality in the Harbor
showed significant trends during the 8-years before transfer of wastewater offshore.
Table 11 provides a summary of some of these trends. For 7 of the 14 variables
monitored (temperature and salinity excluded from this total), significant trends were
detected for the Harbor as a whole. For 4 of these variables, specifically TN:TP,
DIN:DIP, TSS and Enterococcus, the trends were highly significant (p <0.01). For the
other 3 variables (TN, TP and fecal coliform), the trends were significant (p < 0.05, but >
0.01). 
For 4 of the variables, significant trends were not observed for the Harbor as a whole, but
they showed significant (and in certain cases highly significant trends) in one or both of
the individual regions of the Harbor. These variables included DIN, DIN as %TN, DIP
and secchi depth. For only 3 variables (plus temperature and salinity) were no trends
observed, for either the Harbor as a whole or for the individual regions. These 3
variables included chl-a, DIN:DIP, and k. 
DISCUSSION 
The following section compares the trends in Harbor water quality observed in this study
with the trends in loadings from the two wastewater treatment facilities over the same
period. The purpose of this comparison was to better identify the contribution changes in
loadings might have made to the observed Harbor trends. The fact that no trends were
observed for water temperature or salinity (for the Harbor as a whole or for the individual
regions), together suggested the trends were not the result of long-term trends in water
temperatures or freshwater inflows.

51 
Table 11. Summary of trends in data averaged region-wide in the North Harbor and
South Harbor regions, 1993 to Sept. 2000. ** denotes p = 0.01, * denotes p = 0.05, and –
denotes no trend. Significance of trends determined using Kendall tau-b test. 
________________________________________________________________________ 
Variable Whole Harbor North Harbor South Harbor 
________________________________________________________________________ 
Nutrient concentrations 
Total nitrogen Decrease * - Decrease * 
DIN - Increase * Decrease ** 
DIN as % TN - Increase ** - 
Total phosphorus Increase * Increase ** - 
DIP - Increase ** Decrease ** 
TN:TP Decrease ** Decrease ** Decrease ** 
DIN:DIP - - - 
Phytoplankton biomass 
Chlorophyll-a - - - 
Water clarity 
Secchi - Decrease ** - 
k - - - 
TSS Increase ** Increase ** Increase ** 
Dissolved oxygen 
Percent saturation Decrease ** Decrease ** Decrease ** 
Pathogen indicators 
Fecal coliform Decrease * - Decrease * 
Enterococcus Decrease ** Decrease * Decrease ** 
Physical parameters 
Temperature - - - 
Salinity - - -

52 
Wastewater loadings 
Table 12 summarizes the changes in loadings from the Deer Island and Nut Island
wastewater treatment facilities combined, from 1993 through 2000. Note: the loading
estimates for 1993 and 1994 are less reliable than for later years. For the purposes of this
report, changes in loadings of 20% or more have been considered significant. Based on
this 20% criterion, loadings of DIN, DIN as %TN, TSS and BOD showed significant
changes, but loadings of TN, TP and TN:TP did not. 
Average daily loadings of DIN, and DIN as percent TN, increased by + 38% and + 33%.
This relative enrichment with DIN was likely the result of the upgrade to secondary
treatment of first Deer Island, and then of combined Deer Island plus Nut Island flows.
Loadings of solids and BOD decreased by -76% and -80%, respectively. Construction of
the new primary treatment facility at Deer Island was responsible for the bulk of the
solids decrease. The bulk of the BOD decrease was caused by the upgrade to secondary
treatment. 
Correspondence between water quality and wastewater loadings 
At the level of the Harbor as a whole, the correspondence between the trends in water
quality and the trends in loadings was poor. For TN, TP and TN:TP, no significant trends
were observed for loadings, but significant trends were observed in the Harbor as a
whole. Conversely, no significant trends were observed for DIN or DIN as %TN Harbor-
wide, but loadings of both these variables showed significant increases. Similarly, the
Harbor showed a significant decrease in percent DO saturation, despite a decrease in
BOD loadings from the treatment facilities, and an increase in TSS, despite a decrease in
solids loadings. 
The poor correspondence between the trends in water quality and loadings, suggested that
at the level of the Harbor as a whole, the trends in water quality were driven more by

53 
Table 12. Changes in loadings of various components of wastewater during the baseline
period. Loadings are for the Deer Island and Nut Island facilities combined. 
AVERAGE DAILY LOADINGS (X 10 3 KG D -1 ) a 
TN DIN DIN as 
% TN 
TP Molar 
TN:TP 
TSS BOD 
1993 30.43 17.66 58.1 4.59 14.7 107.40 178.2 
1994 30.45 17.67 58.0 3.81 17.7 117.20 177.1 
1995 31.09 20.44 65.7 4.25 16.2 87.50 146.7 
1996 34.75 21.43 61.7 4.13 18.6 99.40 143.3 
1997 32.39 21.56 66.6 4.45 16.1 86.10 114.1 
1998 29.66 23.21 78.2 3.60 18.3 42.00 49.8 
1999 30.58 23.91 78.2 3.88 17.5 32.10 42.3 
2000 31.71 24.43 77.0 3.85 18.2 27.30 36.3 
b CHANGE +1.3 +6.8 +19.0 -0.4 +2.1 -85.0 -141.4 
% c +4 +38 +33 -8 +13 -76 -80 
a Loadings for 1993 and 1994 are less accurate than for subsequent years, b Difference between 2000
loadings and the average of the 1993 and 1994 loadings combined, c Change expressed as % of the average
of the combined 1993 plus 1994 loadings.

54 
background trends in water quality than by changes in wastewater loadings. The Harbor
as a whole showed background decreases in TN and percent DO saturation, and
background increases in TSS and TP, unrelated to changes in wastewater loadings. 
Processes that likely contributed to these background trends might have included long-
term changes in Harbor-ocean exchanges, river loadings to the Harbor, and sediment-
water fluxes within the Harbor. At this time, the long-term trend that would be necessary
to assess the contributions of these processes to the trends in water quality, are not
available. This applies to loadings of TN, TP, TSS or BOD, for any of the processes. 
At the level of the individual regions, the correspondence between trends in water quality
and wastewater loadings, were closer than for the Harbor as a whole. In the South
Harbor, the decreases in concentrations of DIN and DIP all followed the ending of
discharges from Nut Island WWTF to the region in 1998. In the North Harbor, the
increases in concentrations of DIN, DIN as % TN, and DIP all followed the combination
of inter-island transfer plus upgrade of treatment at Deer Island in 1997/1998. 
The fact that average concentrations of chl-a for the Harbor as a whole showed no trend
during the study agrees with the fact that loadings of TN from the two treatment facilities
also showed no change during the study period. The absence of a chl-a response for the
Harbor as a whole and for the individual regions, is however perhaps surprising in view
of the increase in DIN loadings to the Harbor as a whole, and the changes in loadings of
both TN and DIN to both the individual regions. 
It is also surprising in view of other studies that have demonstrated positive relationships
between annual chl-a concentrations and N loadings for a variety of coastal bays and
estuaries (Nixon et al. 1986, Monbet 1992). Likely explanations for the dampened chl-a
responses might have included limitation of phytoplankton growth in the Harbor by
factors other than nutrients, perhaps by light or hydraulic residence time (Kelly 1997).

55 
The significant increases in TSS observed Harbor-wide, and the significant decrease in
secchi depth observed in the North Harbor, might together have enhanced light limitation
of phytoplankton growth during the study. The increase in TSS (and possibly also of TP)
may have been caused by increased re-suspension of bottom sediments into the Harbor
water column, in turn brought about by long-term changes in the epibenthic faunal
communities of the Harbor. 
The areal coverage of the soft-bottom sediments of the Harbor by tube-mats of the
amphipod, Ampelisca, have declined since 1996 and 1997 (Kropp et al. 2001). The
decline of these mats, that likely served to consolidate the surface sediments of the
Harbor, might have facilitated re-suspension of these sediments by waves and currents.
The reduction in the filter-feeding action of the amphipods might also have decreased
biodeposition of suspended sediments onto the Harbor bottom. 
ACKNOWLEDGEMENTS 
Grateful thanks are extended to Kelly Coughlin for help in almost all phases of this work.
Her contribution to setting up and maintaining the Harbor sampling program, and to
management and QC/QC of the data are greatly appreciated. Thanks are also due to
Nicole O’Neill for management of the field sampling in recent years, and to Ken Keay
for reviewing a draft of this report. Rob Rabideau, Keary Berger and others operated the
sampling vessels. T. Smirnova, N. O’Neill, C. Blodget, M. Gofsteyn, R. Warot and
others conducted analyses in the lab. J. Lobuglio, D. Hersh and P. Ralston provided
management of the data base.

56 
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