November 28, 2023 - Daniel L. Codiga, PhD

U.S. Environmental Protection Agency · from the EPA · 5 pages · 235 KB
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Michele Barden 
U.S. Environmental Protection Agency – Region 1 
5 Post Office Square, Suite 100 (06-1) 
Boston, MA 02109-3912 
Claire Golden 
MassDEP - Surface Water Discharge Program 
150 Presidential Way 
Woburn, MA 01801 
RE: Comments on MWRA Deer Island 2023 Draft Permit for Massachusetts Bay outfall 
I am an oceanographer with many years of experience researching processes related to water quality in
several coastal New England waterbodies including Massachusetts Bay. I worked as full-time staff at
MWRA, where the environmental quality department and its contracted consultants run a high-quality
monitoring program, for more than 8 years until early 2023. One of my roles there was to help analyze
and interpret various Mass Bay datasets with respect to the monitoring goals. Although I wasn’t involved
in the 1990s and 2000s, I have become very familiar with the history of the monitoring program
development and resulting 2000 permit; I am appreciative that EPA and MassDEP based them on good
science, and that the Outfall Monitoring Science Advisory Panel has continued to give informed guidance
through the years. My academic affiliation is the University of Rhode Island but the views expressed here
are my own, as a scientist with knowledge of the Mass Bay ecosystem and MWRA monitoring programs,
and as a Boston resident and MWRA ratepayer. 
Background context relevant to below comments. As is reflected in the Fact Sheet and references it
cites, the single most identifiable effect of the outfall on Mass Bay and its most serious potential cause of
harm is nutrients in the effluent, particularly ammonium. The influence of effluent ammonium on the
bay has been the subject of intense monitoring and analysis and is well understood. It results in water
column concentrations increased above natural background levels persistently within about 5-10 km of
the outfall, lesser increases that occur intermittently out to about 10-15 km away, and, rarely, more
minor increases as far as 20-25 km away. Furthermore, it also is well understood that the only
mechanism by which nutrients could potentially affect other aspects of the bay ecosystem is through
their uptake by phytoplankton, and that studies seeking to identify modified phytoplankton conditions
have found none. This includes phytoplankton species responsible for harmful algal blooms (HABs). The
new permit should update the water column monitoring accordingly, in line with the recommendations
from Hagy et al (2022) as cited in the Fact Sheet, for “reducing effort to monitor issues that have been
resolved significantly via decades of monitoring” and to “focus on the most pertinent and prospective
environmental concerns and their potential relationship to the discharge”. 
Requiring zooplankton monitoring by MWRA is not justified. 
The water column monitoring spans hydrographic conditions, nutrients, phytoplankton, and
zooplankton. Hydrography, nutrients, and phytoplankton are all closely relevant to potential effects of
effluent and merit sustained bay monitoring—at least under the approach taken by the Draft Permit,
which is cautious as noted by Hagy et al (2022) which the Fact Sheet cites as its supporting rationale.

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In contrast, potential effects of effluent nutrients on zooplankton would have to result from impacts on
phytoplankton. As noted in the Fact Sheet and documents it cites, such effects on phytoplankton are so
far absent, and not anticipated to be likely even under the potential regime shifts raised by the Fact
Sheet. While it is cautious to continue monitoring phytoplankton, continuing to monitor zooplankton is
sufficiently beyond cautious to be unwarranted. Zooplankton are a trophic level further removed from
potential influence of the outfall. Furthermore, in Mass Bay the relationship between zooplankton
whales feed on and phytoplankton is not a tight coupling, in contrast to top-down systems strongly
influenced by grazing, in part because the most important prey for some key zooplankton may not be
phytoplankton. 
Zooplankton are prey for endangered North Atlantic Right whales, and as such, monitoring and research
to expand our understanding of them is important and necessary. However, the link between
zooplankton and the MWRA outfall is too weak to reasonably justify continuation of MWRA zooplankton
monitoring, until and unless more conclusive links between phytoplankton and effluent are documented. 
Requiring Cape Cod Bay monitoring by MWRA is not justified. 
The three Cape Cod Bay stations are so distant from the outfall, well beyond any intermittent minor
influence of increased ammonium from the outfall, that they should be dropped from MWRA
monitoring. In recent years there have been occurrences of hypoxia in Cape Cod Bay, but as noted by the
Fact Sheet and documents it cites, extensive analysis has concluded that the factors responsible (e.g.
regional trends for warming and shifts in wind patterns, unusual regional dinoflagellate blooms) do not
include the outfall. This is consistent with knowledge of effluent ammonium dispersal in Mass Bay (as
noted above) and the fact that dilution is very high by the time it reaches Cape Cod Bay, at least 37 km
away. 
Monitoring and understanding hypoxia in Cape Cod Bay is of course a high priority in general, but the
link to the MWRA outfall influence is too weak to reasonably justify continuation of MWRA monitoring
there. The only document considered by the Fact Sheet that indicates Cape Cod Bay monitoring by
MWRA should continue is Hagy et al (2022), which does not provide supporting information for its
assertion specific to the relationship between outfall influences and Cape Cod Bay. 
Harmful algal bloom monitoring required of MWRA by the permit needs to (1) be oriented around a
specific monitoring question focused on the potential role of effluent nutrients; and (2) improve its
effectiveness through use of more modern technologies to the fullest extent justified. 
HABs are a serious concern and carry potential threats to public health through shellfish consumption.
They merit oceanographic research and rapid response monitoring. 
However, the Fact Sheet and documents it cites make clear that the potential relationship between HABs
and the outfall is unproven and largely speculative. The Draft Permit requirement for MWRA to continue
the existing HAB component of its water column monitoring, and expand its rapid response sampling for
additional HAB species, is a very cautious approach. 
HAB monitoring and research are specialized and expensive endeavors. In addition to the public at large,
the main beneficiaries are the shellfishing industry, related public health agencies, and scientific
researchers. The scope and expense of the HAB monitoring in the Draft Permit is large, and it does not

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include a sufficient focus on potential links to the outfall to justify it being funded wholly by MWRA
ratepayers. 
The HAB monitoring required by the Draft Permit consists mainly of weekly Rapid Response vessel-based
surveys, during years when they bloom to an extent that they are observed during routine surveys above
certain levels and/or their toxins are observed in shellfish above certain levels. The weekly surveys are
necessary to achieve field sampling of nutrients and certain HAB species ( Alexandrium , Pseudo-nitzschia )
more frequently than occurs during routine monitoring surveys, which are each 3-5 weeks. While this
weekly monitoring will improve tracking of HABs, and is of general interest, it is not designed with
emphasis on improving understanding of the role of outfall nutrients on HABs. 
As an example of this last point, there are extensive data from more than two decades of Rapid
Response vessel-based surveys for Alexandrium , which have occurred in roughly half of the years. These
data have improved our general understanding of bloom characteristics and variability. But they have not
enabled advances toward better understanding of the potential role of effluent nutrients. This is evident
from the statements in the Draft Permit and the documents it cites, which highlight a persistent lack of
knowledge on the possible linkage between HABs and the outfall. 
The Draft Permit and Fact Sheet do not provide a clear monitoring question that needs to be answered
by the continued and expanded HAB monitoring. Such a question needs to be formulated, must be
focused on potential effluent nutrient effects, and should be noted in the new permit so that there is an
end game for the monitoring. At present it appears that the continued and expanded HAB monitoring in
the Draft Permit is targeted on general understanding of HAB occurrence and variability, but not on links
between effluent nutrients and HABs, and insufficient guidance is provided on the desired outcome or
end goal. 
A better approach would be for the new permit to require MWRA to carry out a Special Study to: 
1. More definitively probe the existing phytoplankton monitoring datasets for potential relationships
between effluent nitrogen and phytoplankton community structure, including HAB species. 
2. Research available technologies and methods for HAB monitoring and do cost-benefit analyses
comparing them to the Rapid Response survey approach of the Draft Permit with emphasis on cost-
effectiveness and ability to identify potential roles of effluent nutrients. 
MWRA has proven effective with Special Studies in the past, including through engagement of outside
consultants in the process, and there is considerable oceanographic expertise available to them in
Massachusetts and nearby states. 
Examples of technologies for #2 include phytoplankton imaging systems, automated water sample
collection devices, in situ ammonium sensors, autonomous surface vessels as sampling platforms, and
many others. The potential advantages of equipping the A01 mooring (operated by NERACOOS) and the
44013 Boston Buoy (operated by NDBC) with HAB-relevant sensors, through suitable partnerships with
these operators, should also be prioritized. 
The Special Study should culminate in a report summarizing scientific understanding of links between
effluent and phytoplankton, with guidance to define a monitoring question focused on the role of
effluent ammonium, and recommendations to improve on the HAB monitoring approach described by

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the Draft Permit through application of updated technology if justified in light of the cost-benefit
analysis. 
Note that the results of the technologies and methods part of the Special Study should be informative to
improve not only the HAB component of the monitoring but also all the other components of the water
column monitoring; in fact, if there is no Special Study focused on HABs there should be one focused on
technologies and methods to improve the rest of the water column monitoring. In need of particular
attention is that the 3-5 week gaps between the routine vessel-based surveys, as noted in the Fact Sheet,
severely limit the understanding of oceanographic variability and events in bay conditions that occur
during them. This makes continuous time series measurements extremely valuable. The Draft Permit
requirement for MWRA to sustain its continuous sampling on the A01 mooring helps in this regard
(though the Draft Permit should be clearer as to what parameters it requires for this sampling, and what
depths each parameter should be sampled at). Additional timeseries sampling would bring many
advantages to the monitoring, including possibly cost-effectiveness, and should be thoroughly explored. 
The Mass Bay bacteria monitoring program should consist only of the “adverse” surveys component,
with the routine monthly (“conditional”) surveys discontinued. 
Based on the extensive dataset for bacteria in Mass Bay, the monitoring of bacteria in effluent at the
treatment plant is fully protective except potentially under unusual plant operating conditions or plant
upset beyond the scale of those experienced during prior monitoring. The potential environmental
impacts of such upsets are addressed by the adverse surveys, as triggered based on plant conditions, so
continuing them will protect public health. 
In contrast, the routine monthly surveys in Mass Bay should be ended. As shown by documents the Fact
Sheet cites, nearly all results from the routine surveys have 90% or higher proportion of non-detects.
Continuing to collect these data would not be informative nor useful. This is especially true because
effluent will continue to be sampled for bacteria routinely at the treatment plant, with adverse surveys
triggered and executed as appropriate. 
Also: In the Draft Permit, the second sentence of item #3 on page 8 states “For reporting an average
based on a mix of values detected and not detected, assign a value of “0” to all non-detects for that
reporting period and report the average of all the results.” While this approach is expedient, and has
been used in past analyses, it is contrary to best practices for statistical methods (e.g., Helsel et al.,
2020). The permit should either (a) provide justification for this requirement, despite that it does not
follow best practices, or (b) instead require use of statistical methods appropriate for analysis of datasets
with censored values (e.g., Helsel et al., 2020). 
In the Draft Permit the elimination of several components of the MWRA Mass Bay monitoring
programs—including the Contingency Plan, the benthic/sediment monitoring, the fish and shellfish
monitoring, and the water quality modeling—is strongly supported by the scientific results from 30+
years of completed monitoring. 
Contingency Plan. The Contingency Plan (CP) was valuable and useful during the first several years of
operations of the Mass Bay outfall and served its intended purpose. However, after several years it was
clear that the outfall operated as planned, without causing harmful changes. Since then, the CP has been
ineffective because its thresholds were defined to detects changes relative to the 1990s baseline period,

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and not necessarily changes that are harmful. This means that in recent years some of its thresholds
have been exceeded due to climate change, unrelated to the outfall; for example, oxygen declines due to
regional changes have caused CP exceedances over the past few years. The 30 years of baseline and
post-diversion monitoring mean that we now understand much more about the bay, and potential
outfall effects, such that requiring MWRA to continue to carry out the CP threshold checks and
associated reporting would have effectively no benefit (and be an unjustified expense). 
Benthic/sediment monitoring; Fish and shellfish monitoring. The monitoring questions these programs
were designed to address have been thoroughly answered. MWRA has documented this in detail, in the
reports cited by the Fact Sheet. For at least the most recent 5 years this monitoring has provided limited
information useful to further address the questions. The programs were successful but they do not merit
continuation and would not be an effective use of resources; this will remain true even under the
influence of the potentially emerging regime changes the Fact Sheet cites as rationale for continued
water column monitoring. 
Water quality modeling. The investigations done using the Bays Eutrophication Model, in the late 1990s
prior to the permit and as required by the permit since 2000, have served their purpose and led to
improved understanding of potential effects of the outfall on Massachusetts Bay water quality. However,
our current knowledge of processes by which the outfall influences bay conditions is quite mature. The
recent update to the BEM showed that state-of-the-art modern modeling methods lead to results that
confirm findings from earlier modeling. This includes scenario simulations that explicitly evaluate water
quality with and without inputs from wastewater effluent. (Hagy et al 2022 commented that the recently
updated model was not applied to such scenarios, but this is because they prepared their report a short
time earlier than when MWRA published results of these particular simulations.) The benefits of
modeling, as a complement to the observational monitoring program, have reached or passed a point of
diminishing returns. Discontinuing the modeling requirement is justified, and will help MWRA to succeed
more effectively with other goals. 
Daniel L. Codiga, PhD 
November 28, 2023 
References cited 
Hagy, J., Gleason, T., Oczkowski, A., Tatters, A., and Wan, Y., 2022. Technical Memorandum: Review of
MWRA Water Quality Monitoring Results to Address Potential for Harmful Effects of the Deer Island
Discharge on Threatened and Endangered Species in Massachusetts Bay. U.S. Environmental Protection
Agency, Washington, DC, EPA/600/R-22/063. 
Helsel, D.R., Hirsch, R.M., Ryberg, K.R., Archfield, S.A., and Gilroy, E.J., 2020. Statistical Methods in Water
Resources: U.S. Geological Survey Techniques and Methods, book 4, chapter A3, 458 p.