Peconic
Estuary
Program
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C
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THREE
NUTRIENTS
MANAGEMENT
PLAN
To
facilitate
viewing
the
many
figures
that
accompany
this
chapter,
all
figures
have
been
placed
at
the
end
of
this
chapter.

OBJECTIVES
1)
No
net
increase
in
western
estuary.
Immediately
prevent
net
increases
in
nitrogen
loading
to
the
surface
waters
of
the
western
estuary
(
Peconic
River
and
Flanders
Bay)
to
prevent
worsening
of
current
dissolved
oxygen
(
DO)
stresses
in
the
marine
surface
waters
of
the
area.

2)
Long­
term
reductions
in
western
estuary.
Develop
and
implement
a
long­
term
nitrogen
load
reduction
strategy
to
the
western
estuary,
to
optimize
surface
water
conditions
for
dissolved
oxygen,
with
ancillary
consideration
of
potential
benefits
to
submerged
aquatic
vegetation
(
especially
eelgrass)
habitat.

3)
Eelgrass
habitat
optimization
in
shallow
water.
Maintain
and,
where
cost­
effective,
improve
conditions
with
respect
to
nitrogen
(
and
related
chlorophyll­
a,
light
extinction,
and
possibly
other
parameters)
in
shallow
waters
(
less
than
three
meters)
to
optimize
eelgrass
habitat.

4)
Water
quality
preservation
in
eastern
waters.
Implement
a
"
water
quality
preservation"
policy
in
eastern
estuary
waters
(
east
of
Flanders
Bay)
to
prevent
degradation
which
could
adversely
impact
the
high
quality
of
those
surface
waters.

5)
Subwatershed
management.
Focus
on
characterization
of
peripheral
creeks
and
embayments
and
management
of
their
subwatersheds;
optimize
surface
water
quality
in
these
areas,
which
are
often
highly
productive
but
poorly
flushed
and
subject
to
environmental
stresses.

6)
Load
allocation
in
the
entire
watershed.
Develop
and
implement
a
load
allocation
strategy
for
point
and
nonpoint
sources
in
the
entire
estuary,
which
accomplishes
the
above
objectives.
Peconic
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Program
CCMP
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MEASURABLE
GOALS
The
PEP's
measurable
goals
with
respect
to
nutrients
include:

 
Decrease
the
total
nitrogen
concentrations
in
the
western
estuary
to
a
summer
mean
of
no
more
than
0.45
mg/
l
(
based
on
1994­
96
model
verification
conditions,
and
measured
by
surface
water
nitrogen
concentrations
as
compared
to
the
PEP
nitrogen
guidelines).
[
See
Actions
N­
4,
N­
5,
N­
10]

 
Improve
the
dissolved
oxygen
concentrations
in
the
western
estuary
to
ensure
that
the
New
York
State
dissolved
oxygen
standard
(
currently
5.0
mg/
l)
is
not
violated
(
measured
by
surface
and
bottom
dissolved
oxygen
levels
as
compared
to
the
New
York
State
dissolved
oxygen
standard).
[
See
Actions
N­
1,
N­
10]

 
Ensure
that
the
total
nitrogen
levels
in
shallow
waters
remain
at
or
below
0.4
mg/
l
to
help
optimize
water
clarity,
maintaining
and
potentially
improving
conditions
for
eelgrass
beds,
a
critical
habitat
(
based
on
1994­
96
model
verification
conditions,
and
measured
by
light
extinction
coefficients
as
compared
to
the
recommended
eelgrass
habitat
optimization
goal
of
at
or
below
0.75
±
0.05
m­
1).
[
See
Actions
N­
1,
N­
4,
N­
5,
N­
10]

 
Ensure
that
the
existing
total
nitrogen
and
dissolved
oxygen
levels
are
maintained
or
improved
in
waters
east
of
Flanders
Bay
(
i.
e.,
do
not
increase
TN
nor
decrease
DO)
(
measured
by
surface
water
total
nitrogen
concentrations
as
compared
to
the
PEP
nitrogen
guidelines
and
surface
and
bottom
dissolved
oxygen
levels
as
compared
to
the
New
York
State
dissolved
oxygen
standard).
[
See
Actions
N­
1,
N­
2,
N­
4,
N­
5,
N­
10]

 
Develop
a
quantitative
total
nitrogen
load
allocation
strategy
for
the
entire
estuary
(
measured
by
development
of
a
strategy
and
timely
endorsement
by
local
and
State
agencies).
Preliminary
work
group
estimates,
and
work
performed
by
other
programs,
indicate
that
a
10­
25
percent
fertilizer
reduction
goal
is
a
reasonable
first
order
target
for
existing
residential
and
agricultural
fertilizing
programs.
[
See
Action
N­
3]

 
Implement
a
quantitative
nitrogen
load
allocation
strategy
for
the
entire
estuary
(
measured
by
attaining
the
PEP
recommendations
including
the
implementation
of
the
recommended
Agricultural
Environmental
Management
(
AEM)
program
as
well
as
other
recommendations
which
may
include
fertilizer
reduction
programs,
sanitary
system
upgrade
programs,
point
source
controls,
etc.,
as
well
as
monitoring
for
the
impacts
on
measurable
groundwater
quality
parameters).
[
See
Actions
N­
3,
N­
4,
N­
5,
N­
10]

 
Ensure
that
there
is
no
substantial
net
increase
in
nitrogen
loading
to
areas
east
of
Flanders
Bay
and
reductions
in
the
Peconic
River/
Flanders
Bay
region
so
that
an
increase
in
new
development
would
be
offset
by
reductions
in
loads
from
pre­
existing
uses.
The
nitrogen
work
groups
will
develop
means
of
attaining
this
goal,
which
may
include
groundwater
performance
standards
(
e.
g.,
nitrogen
concentrations
in
groundwater
resulting
from
postdevelopment
discharge/
recharge),
implementing
fertilizer
and
clearing
restrictions,
and
zoning.
[
See
Actions
N­
3,
N­
4,
N­
5,
N­
6,
N­
10]

 
Continue
sponsoring
and
coordinating
research
and
information
gathering
(
measured
by
funding
appropriated
and
research
conducted,
relative
to
PEP
recommendations).
[
See
Actions
N­
7,
N­
8,
N­
9]

 
Continue
and
expand
open
space
acquisition
programs
(
measured
by
funding
appropriated
and
acres
acquired
in
target
areas).
[
See
Action
N­
6]
Peconic
Estuary
Program
CCMP
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INTRODUCTION
Nutrients
are
critical
for
sustaining
the
marine
ecosystem,
but
can
be
harmful
to
an
estuary
at
excessive
levels.
"
Cultural
eutrophication"
is
the
process
by
which
estuaries
can
become
overenriched
with
nutrients
and
associated
organic
carbon,
due
to
human
inputs.
Nitrogen
and
phosphorus
are
the
primary
nutrients
that
can
impact
water
quality.
Micronutrients,
salts,
metals,
and
organic
solids
can
also
contribute
to
the
nutrification
of
an
estuary.
Nitrogen
is
the
primary
nutrient
of
concern
in
the
marine
waters
of
the
Peconic
Estuary
during
critical
summer
conditions
when
environmental
stresses
are
greatest.

When
nutrients
are
introduced
to
the
estuary
at
higher
than
normal
rates
from
runoff,
groundwater
inflow,
atmospheric
deposition,
or
point
source
discharges,
the
excess
nutrients
stimulate
aquatic
plant
growth,
including
production
of
microscopic
algae
(
microscopic
plants
that
live
in
surface
waters).
Algae
photosynthesize
in
the
day,
producing
oxygen,
which
is
released
into
the
water
column.
At
night,
they
undergo
respiration,
consuming
dissolved
oxygen
(
DO)
in
the
water
column.
This
respiration
can
result
in
short­
term
dissolved
oxygen
depression,
which
is
known
as
"
diurnal"
dissolved
oxygen
variation.
In
the
Peconic
Estuary,
which
is
generally
a
shallow,
well­
mixed
estuary,
chronic
dissolved
oxygen
problems
due
to
"
stratification"
(
a
deeper
layer
of
water
which
can
experience
sustained
DO
depression)
are
usually
not
a
problem,
as
they
are
in
deeper
systems
such
as
Long
Island
Sound.

Increased
aquatic
plant
productivity
adds
organic
material
to
the
system,
which
eventually
dies
and
decays.
The
decaying
organic
matter
settles
to
the
bottom
and
depletes
oxygen
levels
in
the
water
which
are
needed
by
aquatic
organisms
in
what
is
known
as
"
sediment
oxygen
demand"
(
SOD).
From
sediments,
nutrients
can
be
recycled
back
into
the
system
("
sediment
nutrient
flux"),
further
exacerbating
the
pollution
problem
with
nitrogen
contributions.

Processes
such
as
diurnal
DO
depression,
sediment
oxygen
demand,
and
sediment
nutrient
flux
can
result
in
dissolved
oxygen
levels
which
are
low
enough
to
be
harmful
to
marine
life.
Factors
and
processes
which
govern
oxygen
levels
are
complex,
and
include
temperature,
light
availability,
wind
mixing,
localized
water
column
stratification
(
such
as
the
salt
wedge
which
occurs
in
the
Peconic
River
area),
zooplankton
grazing,
submerged
aquatic
vegetation
(
SAV)
dynamics,
and
bio­
geochemical
and
bacterial
processes.
Low
DO
levels
adversely
affect
marine
life,
potentially
resulting
in
mortality
and
in
behavioral
and
physiological
effects
on
individual
species
and
communities.

The
increased
production
of
microscopic
algae
caused
by
increased
nutrient
enrichment
results
not
only
in
dissolved
oxygen
problems
but
also
discolors
the
water,
decreases
water
clarity
and
diminishes
the
amount
of
light
received
by
rooted
aquatic
plants.
Submerged
aquatic
vegetation
that
are
at
a
species'
depth
limit
for
clear
water
conditions
would
be
expected
to
decline
due
to
the
lack
of
sufficient
light
energy
in
turbid
waters.
Eutrophication
will
also
promote
the
growth
of
epiphytes
on
In
the
Peconics,
excessive
levels
of
nutrients
can
harm
eelgrass,
a
critical
habitat,
due
to
algal
light
shading,
stimulation
of
epiphytes
(
plants
which
live
on
eelgrass),
and,
possibly,
direct
adverse
metabolic
impacts.
One
theory
also
holds
that
Brown
Tide
may
be
related
to
levels
of
dissolved
organic
nitrogen
(
DON)
in
relation
to
the
supply
of
dissolved
inorganic
nitrogen
(
DIN).
This,
however,
is
one
of
several
hypotheses,
many
of
which
do
not
implicate
nutrients
as
a
causal
factor.

Sediment
Nutrient
Flux
Sediment
Flux
(
i.
e.,
exchange
of
chemicals,
such
as
nutrients,
between
the
sediment
and
water
column
due
to
geochemical
and
bacterial
processes)
is
an
internal
(
recycled)
nitrogen
source
that
reflects
current
and
historic
anthropogenic
pollution
inputs.
It
is
greater
than
any
other
individual
source
of
point
or
nonpoint
pollution.
Peconic
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eelgrass
blades,
again
shading
the
plant
itself
and
hindering
production.
Furthermore,
species
such
as
red
or
green
macroalgae,
which
adsorb
nutrients
more
quickly
than
eelgrass,
may
competitively
exclude
eelgrass
plants.

Eutrophication
may
also
impact
eelgrass
as
a
result
of
this
species'
high
nitrate
uptake
efficiency.
Eelgrass
lacks
a
mechanism
to
terminate
nitrate
uptake.
It
is
thought
that
excess
nitrate
in
eelgrass
impairs
carbohydrate
metabolism,
resulting
in
impaired
plant
health
and
a
decline
in
shoot
production
(
Cashin
Associates,
1996).

Because
SAV
beds
are
prime
habitat
for
bay
scallops
and
juvenile
fish,
the
loss
of
SAV
can
have
repercussions
throughout
the
food
chain.
SAV
beds
also
provide
numerous
other
functions
including
a
food
source,
bottom
stabilization,
and
nutrient
cycling
all
that
are
further
discussed
in
Chapter
4.

Nitrogen
levels
may
also
be
linked
to
the
Brown
Tide.
One
hypothesis
is
that
Brown
Tide
conditions
may
be
favorable
when
dissolved
organic
nitrogen
(
DON)
is
elevated
in
relation
to
dissolved
inorganic
nitrogen
(
DIN)
supply.
Brown
Tide
bloom
conditions
may
thus
be
most
favorable
in
a
dry
year
(
LaRoche,
1997;
USGS,
1998),
where
there
is
a
low
DIN
supply
as
a
result
of
low
groundwater
inputs.
This
may
be
particularly
significant
when
the
dry
year
follows
a
wet
year,
which
results
in
elevated
DON
levels.
Because
inorganic
nitrogen
levels
in
groundwater
appear
to
have
risen
substantially,
the
levels
of
DON
(
DIN
is
"
converted"
to
DON
in
the
marine
environment)
in
surface
waters
may,
too,
have
become
elevated.

Ecosystem
impacts
due
to
excessive
nutrient
inputs
are
often
long­
term
and
difficult
to
measure.
Nitrogen
may
be
having
subtle
effects
on
species
abundance
and
distribution
in
the
system.
Moreover,
nitrogen
is
often
associated
with
other
pollutants,
such
as
organic
carbon,
and
can
be
considered
as
one
"
indicator"
measurement
of
human
degradation.
Because
major,
short­
term,
nitrogen­
induced
impacts
have
not
been
demonstrated
in
the
Peconic
Estuary,
the
PEP
is
faced
with
the
difficult
task
of
establishing
rational,
cost­
effective
preservation
policies
to
prevent
impacts
which
have
generally
not
yet
occurred.

For
most
Peconic
Estuary
waters,
the
PEP
goal
is
to
establish
rational
and
implementable
preservation
targets
prior
to
degradation
and
occurrences
of
use
impairments.
In
the
absence
of
detailed
ecosystem
data,
the
PEP
was
faced
with
the
major
challenge
of
characterizing
water
segments
with
respect
to
nitrogen
and
dissolved
oxygen
quality.
As
part
of
this
characterization
process,
numerous
discrete
studies
were
performed
to
examine
issues
such
as
land
use,
groundwater,
and
sediment
nutrient
flux.

CHARACTERIZATION
OF
THE
ESTUARY
SYSTEM
Characterization
Studies
Numerous
characterization
studies
have
been
completed
and
others
are
ongoing
to
determine
the
sources,
loadings,
and
impacts
of
nutrients
to
the
estuary
system.
The
work
of
past
programs,
such
as
the
L.
I.
208
Study
(
1978)
and
BTCAMP
(
1992),
have
been
refined
and
expanded
with
a
more
comprehensive
surface
water
monitoring
program,
detailed
land
use
data,
and
improved
sediment
No
major
eelgrass
beds
exist
west
of
Shelter
Island
(
except
Bullhead
Bay),
possibly
due
in
part
to
nitrogen
enrichment
(
see
Figure
3­
1).
Also,
sediment
flux
studies
and
other
characterizations
suggest
eutrophication
pressures
on
the
"
central
estuary"
(
Great
and
Little
Peconic
Bays).
Finally,
recent
research
indicates
that
elevated
levels
of
nitrogen
in
groundwater
input
may
be
one
causal
factor
related
to
Brown
Tide
onset.
Peconic
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characterizations.
A
habitat
linkage
was
added
with
a
submerged
aquatic
vegetation
study,
and
a
state­
of­
the­
art
model
was
developed
to
integrate
and
use
the
data.

One
overall
goal
of
this
characterization
process
was
to
bring
the
amount
of
information
available
on
the
eastern
estuary
waters
(
east
of
Flanders
Bay)
and
watershed
(
see
Figure
3­
2)
to
the
level
of
the
western
estuary,
which
had
been
analyzed
in
great
detail
in
prior
studies.
The
PEP
also
committed
to
detailed
studies
of
subwatersheds
for
peripheral
creeks
and
embayments,
such
as
Meetinghouse
Creek,
Sag
Harbor,
and
West
Neck
Bay.

The
water
and
sediment
quality
technical
characterization
framework
is
illustrated,
in
simplified
schematic
form,
in
Figure
3­
3.
Within
the
watershed,
the
PEP
sought
to
characterize
not
only
direct
loads,
such
as
point
source
discharges,
but
also
land
use
and
land
cover,
which
greatly
affect
the
nature
of
nonpoint
source
loadings.
Groundwater
quality
and
quantitative
input
rates
were
also
the
subject
of
major
investigations.
Finally,
atmospheric
(
airshed)
and
direct
(
e.
g.,
point
source)
loads
to
surface
waters
were
evaluated.
In
the
estuary
itself,
surface
water
monitoring
and
modeling
were
major
initiatives.
Sediment
quality
and
dynamics
were
also
the
foci
of
major
studies,
including
sediment
toxics,
sediment
nutrient
flux,
and
sediment
accretion.

The
size
of
the
data
sets
is
tremendous.
For
example,
the
Suffolk
County
Department
of
Health
Services
(
SCDHS)
has
collected
over
8,000
surface
water
samples,
analyzed
for
a
comprehensive
array
of
physical
and
chemical
parameters
(
including
Brown
Tide
and
coliform
bacteria),
at
39
routine
surface
water
monitoring
stations
and
10
routine
point
source
monitoring
stations.
Also,
the
Suffolk
County
Planning
Department
has
developed
precise,
field­
verified
land
use
data
for
each
tax
map
parcel
in
the
110,000­
acre
watershed.
Thousands
of
SCDHS
groundwater
quality
samples
were
analyzed
in
conjunction
with
the
U.
S.
Geological
Survey's
groundwater
budgets
and
subwatershed
models.

This
characterization
process
is
discussed
in
great
detail
in
several
characterization
reports
available
from
the
Peconic
Estuary
Program
Office.
Key
findings
from
characterization
studies
have
been
used
to
formulate
the
proposed
nutrient
actions
in
this
CCMP.
Some
of
these
findings
are
shown
in
the
accompanying
text
box.

PEP
Hydrodynamic
and
Eutrophication
Model
The
PEP
Hydrodynamic
and
Eutrophication
Model
will
serve
as
a
tool
for
evaluating
main
bays
water
quality,
as
well
as
water
quality
for
embayments
such
as
Sag
Harbor,
West
Neck
Bay,
and
Meetinghouse
Creek.
The
model
is
a
three­
dimensional
hydrodynamic
and
water
quality
model
with
a
predictive
sediment
submodel.
It
is
the
only
known
model
to
be
run
for
a
continuous
eight­
year
simulation
robustly,
with
no
intermediate
forcings
or
corrections
to
the
sediment
processes.

Model
results
are
still
under
review
by
the
Peconic
Estuary
Program
Management
Conference,
and
its
advisory
panel,
the
Model
Evaluation
Group.
When
the
model
is
approved
for
evaluating
preliminary
management
alternatives,
several
realistic
best­
case,
worst­
case,
and
intermediate
management
alternatives
will
be
examined.
Economic
estimates
of
various
management
measures
will
be
developed
by
a
consultant,
and
costs
of
various
management
strategies
can
be
weighed
against
benefits
(
e.
g.,
attainment
of
guidelines
and
criteria
discussed
below).
Through
this
process,
feasible
and
quantitative
subregional
loading
targets
can
be
developed,
and
costs
and
timeframes
for
implementation
mechanisms
can
be
established.
The
goal
is
to
make
this
powerful
management
tool
Peconic
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available
in
the
near
future
(
calendar
year
2001)
and
to
develop
an
implementable
load
allocation
strategy
for
the
entire
watershed.

Specific
functions
of
the
PEP
water
quality
model
include
the
following
abilities:

 
Simulate
historic
water
quality
conditions
based
on
data
collected
since
1988;

 
Predict
future
water
quality
conditions
if
present
trends
continue;

 
Predict
future
water
quality
conditions
in
the
estuary
as
a
result
of
management
actions;

 
Simulate
responses
of
water
quality
and
sediment
processes
to
point
and
nonpoint
source
control
actions;

 
Perform
both
short­
term
(
seasonal)
and
long­
term
(
multi­
year)
simulations;

 
Determine
the
effect
of
localized
management
actions
in
peripheral
embayments;
and,

 
Determine
the
response
time
of
the
estuary
to
management
actions.
Peconic
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Program
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Key
Findings
Related
to
Nutrients
in
the
Estuary
System
 
Overall,
the
Peconic
Estuary
main
bays
and
monitored
embayments
generally
have
"
excellent"
water
quality
with
respect
to
dissolved
oxygen
(
DO),
with
less
than
three
percent
of
the
area
of
the
estuary
exceeding
the
recommended
total
nitrogen
(
TN)
guideline
for
DO
attainment
purposes
(
the
DO
standard
is
5.0
mg/
l,
at
all
times)
(
see
Figures
3­
4
and
3­
5).
Similarly,
most
of
the
estuary
attains
light
extinction
properties
optimal
to
eelgrass,
at
least
in
non­
Brown
Tide
years
(
see
Figure
3­
6).
However,
the
westernmost
estuary
(
Peconic
River
and
Flanders
Bay)
and
several
small
embayments
violate
TN
guidelines
and
exhibit
DO
stresses
(
see
Figures
3­
7
and
3­
8,
discussed
further
in
Table
3­
2).
Also,
several
studies
suggest
eutrophic
stresses
in
the
"
central
estuary"
(
Great
and
Little
Peconic
Bay);

 
Nitrogen
loadings
appear
to
be
at
an
all­
time
high
(
see
Figure
3­
9),
showing
an
increase
of
greater
than
200
percent
since
the
1950s
due
to
increasing
residential
land
use
and
more
pervasive
use
of
highly
soluble
fertilizers;

 
In
the
early
to
mid­
1900'
s,
western
estuary
(
Peconic
River
and
Flanders
Bay)
nutrient
inputs
were
dominated
by
point
source
duck
farm
discharges.
The
decline
in
duck
farming
has
been
more
than
offset
by
an
increase
in
nonpoint
source
nitrogen
loading,
primarily
attributable
to
residential
fertilizer
and
sanitary
systems,
coupled
with
agricultural
fertilizers.
Water
quality
trends
probably
reflect
these
loading
patterns:
dramatic
improvements
in
water
quality
in
western
estuary
creeks
and
embayments
once
affected
by
duck
farms,
and
gradual
increases
in
eutrophication
stresses
for
the
waters
east
of
Flanders
Bay;

 
Fully
40
percent
of
the
study
area
is
still
subject
to
development,
posing
a
substantial
potential
threat
to
water
quality
in
the
main
bays
as
well
as
in
the
embayments
(
see
Figure
3­
10);

 
On
a
regional
basis,
over
80
percent
of
the
existing
total
nitrogen
load
comes
from
developed
lands
and
farmland
(
see
Figure
3­
11).
Thus,
for
existing
land
uses,
on
a
regional
basis,
management
of
residential
and
agricultural
lands
is
an
obvious
priority.
For
medium
density
residential
lands,
sanitary
waste
and
fertilizers
contribute
comparable
amounts
of
nitrogen.
At
lower
densities,
fertilizer
loadings
become
more
prominent;

 
New
residential
development
is
the
major
concern
on
an
estuary­
wide
basis,
particularly
in
the
western
estuary
and
on
the
South
Fork.
Under
a
scenario
in
which
100
percent
of
farmland
is
preserved
and
developable
land
is
developed,
nitrogen
loading
could
increase
substantially
in
every
major
region
of
the
estuary
(
see
Figures
3­
12
and
3­
13).
This
scenario
is
considered
"
worst
case"
because
farmland
has
a
higher
nitrogen
loading
rate
than
most
other
allowable
uses
on
developable
lands.
Overall,
a
total
nitrogen
increase
for
the
estuary
study
area
would
be
near
40
percent
(
about
41
percent
in
eastern
estuary,
and
34
percent
in
western
estuary).
In
the
eastern
estuary,
the
increase
on
the
South
Fork
would
be
most
profound
(
over
60
percent);

 
New
industrial
and
commercial
development
is
an
issue
prominent
mainly
in
the
western
estuary,
particularly
in
Riverhead
Town.
Overall,
over
90
percent
of
the
developable
industrial
acreage
in
the
study
area,
and
almost
one­
half
of
the
developable
commercial
acreage,
is
in
Riverhead
Town;

 
Open
space
acquisition
and
preservation
programs
have
been
tremendously
successful
in
averting
potential
nitrogen
loading
increases
(
see
Figure
3­
14);

 
Widespread
areas
of
groundwater
are
enriched
with
total
nitrogen
on
about
an
order
of
magnitude
higher
than
native
groundwater
(
see
Figure
3­
15).
Most
of
the
groundwater
entering
the
estuary
system
is
contributed
from
the
western
estuary
and
South
Fork
(
see
Figure
3­
16);
and,

 
Low
DO
levels
can
adversely
affect
the
feeding,
growth,
and
survival
of
living
marine
resources.
DO
levels
tend
to
be
lowest
during
the
summer,
unfortunately
when
the
abundance
of
many
finfish
and
invertebrate
species,
including
eggs,
larvae,
and
juveniles
are
at
their
greatest.
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CCMP
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SOURCES
AND
LOADINGS
OF
NUTRIENTS
IN
THE
SYSTEM
Many
sources
contribute
nutrients
to
the
Peconic
Estuary
System,
including
sediments,
groundwater,
direct
rainfall
to
surface
waters,
point
source
discharges
(
such
as
discharges
from
the
Riverhead
sewage
treatment
plant),
and
stormwater
runoff.

Sediments
contribute
nutrients
to
the
estuary
system
through
a
process
called
sediment
flux.
Sediment
nutrient
flux
is
an
internal,
recycled
source
of
nitrogen
where
sediments
release
nitrogen
into
the
water
column.
Sediment
flux
is
related
to
point
and
nonpoint
source
nitrogen
inputs.
Reductions
in
human
nutrient
inputs
will
eventually
be
reflected
in
lowered
sediment
flux
rates.
The
annual
sediment
flux
to
the
estuary,
at
about
14,000
pounds
per
day,
is
overwhelmingly
the
largest
source
of
nitrogen
to
the
estuary.
This
source
comprises
51
percent
of
the
total
nitrogen
loading
to
the
estuary.

Groundwater
is
one
of
the
largest
external
sources
of
nitrogen
to
the
estuary
(
21
percent
of
total
nitrogen
load
or
about
7,560
pounds/
day).
It
integrates
nitrogen
from
fertilizer,
sanitary
system
waste,
and
other
sources.
Atmospheric
deposition
(
to
surface
waters)
contributes
substantial
nitrogen
(
26
percent
of
total
load).
The
remaining
load
to
the
estuary,
only
about
2
percent,
is
from
stormwater
runoff
and
sewage
treatment
plants.
Although
these
sources
represent
a
small
percentage
of
total
nitrogen
loading,
they
may
have
localized
effects.

In
the
early
to
mid­
1900s,
western
estuary
(
Peconic
River
and
Flanders
Bay)
nutrient
inputs
were
dominated
by
point
source
duck
farm
discharges.
The
decline
in
duck
farming
has
been
more
than
offset
by
an
increase
in
nonpoint
source
nitrogen
loading,
primarily
attributable
to
residential
fertilizer
and
sanitary
systems,
coupled
with
agricultural
fertilizers.
The
water
quality
of
the
Peconic
Estuary,
on
a
regional
basis,
is
primarily
nonpoint­
source
impacted.
However,
point
sources
such
as
the
Riverhead
Sewage
Treatment
Plant
and
Meetinghouse
Creek
(
which
integrates
the
Corwin
Duck
Farm
and
other
upstream
sources)
are
very
significant
locally
due
to
their
direct,
concentrated
discharge
to
poorly
flushed
and
stressed
areas
of
the
estuary.
The
Sag
Harbor
sewage
treatment
plant,
although
a
relatively
small
facility,
may
also
have
localized
effects
in
Sag
Harbor
Cove.

Stormwater
runoff
in
the
overall
western
study
area
is
almost
negligible
from
a
nitrogen
perspective,
but
may
still
be
significant
for
water
quality
in
specific
embayments.
In
the
far
western
portions
of
the
estuary,
total
nitrogen
loads
may
have
increased
substantially
due
to
nonpoint
source
loadings
from
fertilizers
and
sanitary
systems
(
LaRoche,
1996).
This
suggests
that
central
main
bays
water
quality
may
slowly
be
becoming
more
enriched
with
nutrients,
via
direct
contributions
from
groundwater
and
indirect
recycling
from
sediment
nutrient
flux,
although
this
is
certainly
a
"
most
probable
scenario"
assessment,
in
the
absence
of
long­
term
monitoring
data.

For
the
eastern
estuary,
sediment
flux
is,
by
far,
the
greatest
quantitative
source.
The
only
other
major,
externally
controllable
source
in
the
eastern
estuary
is
groundwater,
which
still
has
significant
degradation
potential.
Point
sources
and
stormwater
runoff
in
the
overall
eastern
study
area
are
minor
nitrogen
sources,
but
both
may
still
be
significant
for
water
quality
in
specific
embayments.

Nonpoint
source
nitrogen
loading
to
the
estuary
appears
to
be
at
an
all
time
high.
The
nature
of
nonpoint
source
management
is
complex
and
challenging,
as
it
deals
with
relatively
small
but
extremely
pervasive
contributions
from
sanitary
systems,
fertilizers,
and
other
sources.
Peconic
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Existing
nitrogen
loads
to
the
estuary
are
shown
in
Table
3­
1,
and
in
Figures
3­
17
and
3­
18.
These
estimates
are
derived
directly
from
characterization
studies
conducted
by
the
PEP
and
others
and
are
discussed
in
detail
in
the
SCDHS
report,
Point
and
Nonpoint
Source
Loading
Overview
(
1998).

ENVIRONMENTAL
CRITERIA
AND
RECOMMENDED
GUIDELINES
The
Clean
Water
Act
(
CWA)
mandates
two
types
of
approaches
to
meeting
water
quality
standards:
technology­
based
and
water
quality­
based
approaches.
Section
301
of
the
Clean
Water
Act
requires
the
application
of
technology­
based
criteria
to
point
source
discharges,
so
that
effluent
will
meet
specific
effluent
limits
for
the
given
discharge
class.
This
can
be
considered
a
"
minimum
requirement"
for
all
point
source
discharges
to
surface
waters.

However,
if
technology­
based
standards
are
not
sufficient
to
achieve
water
quality
standards,
then
additional
pollution
control
measures
may
be
required
of
point
sources
to
ensure
attainment
of
the
water
quality
standards.
The
water
quality­
based
approach
under
Section
303
of
the
Clean
Water
Act
results
in
specific
limits
applied
to
discharges
so
that
waterbodies
meet
standards.

The
Clean
Water
Act
requirements
are
reflected
in
the
New
York
Code
of
Rules
and
Regulations
(
NYCRR).
6
NYCRR
754.1(
a)(
I)
sets
forth
the
requirement
that
limitations
(
more
stringent
than
technology­
based
limitations)
shall
be
included
in
State
Pollutant
Discharge
Elimination
System
(
SPDES)
permits
where
necessary
to
meet
water
quality
standards
or
to
implement
total
maximum
daily
loads
(
TMDLs).

Dissolved
Oxygen
Low
dissolved
oxygen
(
DO)
levels
can
adversely
affect
the
feeding,
growth,
and
survival
of
the
Peconic
Estuary's
living
marine
resources.
Dissolved
oxygen
levels
tend
to
be
lowest
in
the
Peconic
Estuary
during
the
summer,
which
is
also
when
the
abundance
of
many
finfish
and
invertebrate
species
are
at
their
greatest.
Additionally,
summer­
time
is
when
the
eggs,
larvae,
and
juveniles
of
many
marine
species
are
also
at
their
greatest
concentrations
following
the
adult
spawning
events
in
the
spring
and
summer
months.
These
early
life
history
stages
are
also
known
to
have
increased
susceptibility
to
the
effects
of
low
DO
concentrations.

New
York
State
has
a
water
quality
standard
for
DO
of
no
less
than
5.0
mg/
l
for
all
class
SA,
class
SB,
and
class
SC
waters
(
see
6
NYCRR
Part
703.3).
All
of
the
waters
in
the
Peconic
River
and
Flanders
Bay
drainage
basins
fall
within
the
SA,
SB,
or
SC
classifications
(
see
6
NYCRR
921).

In
addition
to
the
5.0
mg/
l
DO
standard,
which
has
regulatory
significance,
there
are
other
technical
"
benchmarks"
which
are
used
to
evaluate
surface
water
quality
with
respect
to
DO.
This
is
because
5
mg/
l
is
considered
extremely
protective,
and
scientists
believe
that
levels
slightly
below
5
mg/
l
can
be
sustained
without
harming
marine
life.
For
example,
the
Long
Island
Sound
Study
(
LISS),
a
research
and
management
project
funded
by
the
National
Estuary
Program,
has
developed
the
following
benchmarks:
5.0
mg/
l
to
be
fully
protective;
3.5
mg/
l
(
one
day
average)
to
be
protective
of
most
species;
and
2.0
mg/
l
(
all
times)
to
prevent
major
loss.
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Table
3­
1.
Peconic
Estuary
Program
Total
Nitrogen
Loading
Estimates
(
Annual
Average).

West
1
East
OVERALL
(
of
Flanders
Bay)
(
lb/
day)
(%
West)
(
lb/
day)
(%
East)
(
lb/
day)
(%
Total)

NONPOINT
SOURCES
Sediment
Flux
2
250
12
13,600
54
13,850
51
Groundwater
3
1320
61
4,500
18
5,820
21
Atmospheric
Dep.
4
160
7
6,900
28
7,060
26
Stormwater
Runoff
5
30
1
100
0
130
0
TOTAL
NONPOINT
1,760
81
25,100
100
26,900
98
POINT
SOURCES
Peconic
River
6
140
6
­­­
­­­
140
1
Riverhead
STP
7
170
8
­­­
­­­
170
1
Meetinghouse
Creek
8
110
5
­­­
­­­
110
0
Sag
Harbor
STP
9
­­­
­­­
14
0
14
0
SI
Heights
STP
10
­­­
­­­
3
0
3
0
TOTAL
POINT
420
19
20
0
440
2
TOTAL
POINT
&
NONPOINT
2,200
25,100
27,300
1
Note:
Preliminary
analysis
of
historical
duck
farm
data
in
the
western
estuary
indicates
that
duck
farms
may
have
discharged
1,400
pounds/
day
or
more
for
decades
through
the
early
1970s.
Discharge
dropped
to
about
500
pounds/
day
in
mid­
70s,
and
400
pounds/
day
in
early­
mid
1980s.
In
1988,
the
last
duck
farm
(
Corwin
Duck
Farm
on
Meetinghouse
Creek)
stopped
surface
water
discharge.
2
Summer
sediment
flux
rates:
120
pounds/
day
west,
16,200
pounds/
day
east.
3
Groundwater
underflow
estimates:

Area
cfd
(
per
USGS)
mg/
l
N
lb/
day
N
North
Fork
3,800,000
9
2130
South
Fork
11,000,000
3
2060
Shelter
Island
1,700,000
3
320
Peconic
River
e/
o
gauge:
20.8
cfs,
6
mg/
l
N,
670
pounds/
day
N
North
Flanders:
8.8
cfs,
9
mg/
l
N,
430
pounds/
day
N
South
Flanders:
13.8
cfs,
3
mg/
l
N,
220
pounds/
day
N
4
Uses
6.06
mg/
m2/
day,
after
Tetra­
Tech.
Areas:
12.1
km2
for
west,
522
km2
for
east.
Eastern
study
area
estimates
are
for
sediment
flux
analysis
study
area,
including
part
of
Block
Island
Sound.
The
modeler
will
spread
the
loading
rate
over
the
surface
area
accordingly.
5
Load
is
taken
from
Brown
Tide
Comprehensive
Assessment
&
Management
Program
for
west;
eastern
study
area
loadings
are
rough
estimates
only.
Estimates
will
be
refined
using
land
use
data.

6
Peconic
River
based
on
37
cfs
(
mean
from
1942­
96),
0.7
mg/
l.
7
Based
on
Riverhead
STP
Discharger
Monitoring
Report
(
DMR)
data
for
Jan­
June
1997.

8
Meetinghouse
Creek:
1.4
cfs,
15
mg/
l
9
DMR
data
for
6/
96­
5/
97:
0.083
mgd,
20
mg/
l
TN.

10
DMR
data
for
6/
96­
5/
97:
0.033
mgd,
9.2
mg/
l
TN.
Peconic
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Program
CCMP
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The
results
of
the
LISS
experiments
have
shown
that
short­
term
exposure
to
DO
levels
below
2.0
mg/
l
can
have
adverse
effects
on
growth
and
survival
during
the
larval
and
juvenile
stages
of
development.
The
studies
also
demonstrated
that
short­
term
exposure
(
24
hr)
to
DO
levels
in
the
range
of
5.0
­
3.5
mg/
l
can
affect
their
growth
and
survival
in
the
larval
and
juvenile
stages.

The
LISS
studies
also
showed
that
exposure
to
DO
levels
in
the
range
of
5.0
­
3.5
mg/
l
for
24
hours
significantly
reduced
the
growth
of
larval
marsh
grass
shrimp
(
Palaemonetes
vulgaris),
larval
longnose
spider
crab
(
Libinia
dubia)
and
larval
sheepshead
minnow
(
Cyprinodon
variegatus)
by
20
percent,
10
percent,
and
10
percent,
respectively.
Additionally,
at
these
DO
levels,
larval
Atlantic
rock
crab
(
Cancer
irroraturs)
displayed
a
10
percent
decrease
in
survival.

Oxygen
levels
between
3.5
and
2.0
mg/
l
resulted
in
a
50
percent
reduction
in
the
survival
and
growth
of
larval
rock
crabs
and
grass
shrimp
and
a
30
percent
reduction
in
the
growth
of
larval
sheepshead
minnow.
Furthermore,
exposure
to
dissolved
oxygen
levels
in
this
range
reduced
the
growth
rates
of
juvenile
grass
shrimp
by
50
percent
and
juvenile
summer
flounder
(
Paralichthys
dentatus)
by
30
percent.

Short­
term
exposure
to
dissolved
oxygen
levels
below
2.0
mg/
l
resulted
in
the
greatest
effects
to
marine
finfish
and
invertebrate
survival.
The
following
species
experienced
a
50
percent
reduction
in
survival
during
the
juvenile
stage:
silverside
(
Menidia
beryllina),
winter
flounder
(
Pleuronectes
americanus),
scup
(
Stenotomus
chrysops),
Atlantic
menhaden
(
Brevoortia
tyrannus),
summer
flounder,
sand
(
Crangon
septemspinosa)
and
grass
shrimp,
tautog
(
Tautoga
onitis),
windowpane
flounder
(
Scoptalmus
aquosus),
and
fourspine
stickleback
(
Apeltes
quadracus).

While
the
organisms
tested
in
the
LISS
experiments
are
representative
of
those
found
in
the
Peconic
Estuary,
species
such
as
the
bay
scallop
(
Argopecten
irradians)
and
bay
anchovy
(
Anchoa
mitchilli)
were
not
specifically
studied.
These
species
are
known
to
be
of
significant
ecological
and
commercial
importance
to
the
Peconic
Estuary.
Nevertheless,
the
LISS
experiments
examined
a
wide
range
of
finfish
and
invertebrate
species
known
to
occur
throughout
the
Peconics
and
can,
therefore,
be
used
as
a
guideline
to
assess
the
impacts
of
low
DO
concentrations
to
the
living
resources
of
the
Peconic
Estuary.

Nitrogen
New
York
State
has
not
adopted
a
general
water
quality
standard
for
nitrogen.
However,
to
mitigate
adverse
impacts
of
dissolved
oxygen
depletion
in
marine
surface
waters,
regulatory
entities,
including
Pollutant
Loadings
Under
the
Federal
Clean
Water
Act
Section
303(
d),
states
develop
a
list
of
waterbodies
not
meeting
water
quality
standards
after
the
implementation
of
technology­
based
limitations
and
must
develop
Total
Maximum
Daily
Loads
(
TMDLs)
to
reduce
point
and
nonpoint
sources
of
pollutants
to
those
waterbodies
that
do
not
meet
their
designated
uses.
TMDLs
are
detailed
technical
water
quality
assessments
which
determine
the
maximum
amount
of
a
given
pollutant
a
waterbody
can
assimilate
while
still
meeting
water
quality
standards
and
designated
uses.

A
TMDL
with
waste
load
allocations
and
loading
allocations
prescribing
total
nitrogen
(
TN)
load
reductions
to
meet
the
0.45
mg/
l
TN
guideline
and
allow
attainment
of
the
DO
standard
of
5.0
mg/
l
is
recommended
for
the
entire
Peconic
River/
Flanders
Bay
watershed
(
including
subwatersheds
for
Meetinghouse
and
East
Creek/
Riverhead).
The
PEP
will
ultimately
develop
very
detailed,
waterbody­
specific
load
control
strategies
for
the
remainder
of
the
estuary
to
ensure
that
existing
high
water
quality
is
preserved.
Peconic
Estuary
Program
CCMP
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the
New
York
State
Department
of
Environmental
Conservation
(
NYSDEC),
control
nitrogen
discharges
from
point
sources.
This
is
based
on
the
well­
documented
relationship
between
nitrogen
loading
and
dissolved
oxygen
stresses
in
marine
surface
waters.
In
addition,
the
NYSDEC
has
adopted
a
marine
surface
water
total
nitrogen
guideline
for
the
Peconic
River/
Flanders
Bay
of
0.5
mg/
l
based
on
1988­
90
conditions.
(
See
the
Brown
Tide
Comprehensive
Assessment
and
Management
Program
and
PEP
Action
Plan.)
This
guideline
supports
the
"
no
net
increase"
discharge
policy
for
point
sources
of
nitrogen
in
the
western
estuary.

For
dissolved
oxygen
management,
this
Management
Plan
recommends
modification
of
the
NYSDEC's
total
nitrogen
guideline
to
0.45
mg/
l,
based
on
1994­
96
data.
The
SCDHS
PEP
data
analysis,
based
mainly
on
the
1994­
96
expanded
monitoring
program,
suggests
that
the
mean
TN
guideline
of
0.45
mg/
l
for
summer
conditions
(
July­
September),
as
a
benchmark
based
on
1994­
96
conditions,
may
be
a
valuable
management
tool
to
minimize
the
risk
of
DO
depression
below
the
5.0
mg/
l
New
York
State
dissolved
oxygen
standard.
This
recommendation
is
based
mainly
on
correlating
surface
water
TN
levels
with
the
frequency
of
DO
standard
violations,
using
SCDHS
data
from
daytime
(
nonworst
case)
conditions
(
see
Figures
3­
19
and
3­
20).
The
1994­
96
database
was
used
in
the
empirical
analyses
because
it
provided
the
extensive
shallow
water
and
peripheral
bays
data
necessary
to
assess
the
relationship
between
TN
and
DO,
as
well
as
light
extinction
and
chlorophylla
within
a
temporally
consistent
timeframe
of
synoptic
sampling
events.

This
proposed
guideline
will
be
used
to
empirically
assess
relative
spatial
variations
in
water
quality
in
given
waterbodies
over
a
given
time
period
and
to
establish
modeling
benchmarks
against
which
impacts
of
future
load
allocations
can
be
assessed.
Thus,
the
proposed
guideline
is
an
assessment
tool
and
a
vehicle
for
setting
rational
load
allocations,
rather
than
a
standard
in
the
regulatory
sense.

To
optimize
eelgrass
habitat
and
preserve
water
quality
in
eelgrass
habitat
areas,
a
more
stringent
total
nitrogen
criterion
of
0.4
mg/
l
is
recommended
for
shallow
estuary
waters
(
three
meters
or
less).
This
recommendation
is
based
on
the
relationships
between
mean
summer
nitrogen,
chlorophyll­
a,
and
light
extinction
(
Kd)
for
the
1994­
96
period
of
the
"
expanded"
SCDHS
monitoring
program
and
model
verification
period,
coupled
with
an
analysis
of
water
quality
in
relation
to
SAV
beds
delineated
in
a
1994
survey
(
Cashin
Associates).
Other
recommended
habitat
criteria
include
Kd
(
0.75
+/­
0.05
m­
1),
and
chlorophyll­
a
(
5.5
+/­
0.5
µ
g/
l),
which
are
modest
refinements
to
guidelines
recommended
in
the
LISS.
A
detailed
discussion
of
the
methodology
and
conclusions
of
the
SAV
Submerged
Aquatic
Vegetation
(
SAV)

SAV
provides
critical
habitat
for
shellfish
and
finfish
as
well
as
numerous
other
functions,
such
as
bottom
stabilization
and
nutrient
cycling.
In
the
Peconic
Estuary,
eelgrass
is
generally
considered
to
be
the
most
valuable
SAV
species,
due
largely
to
its
high
habitat
value.
It
is
a
rooted
plant
and
has
a
vascular
system.
Other
SAV
that
are
present
in
the
estuary
include
widgeon
grass
(
present
in
relatively
small
areas),
which
is
also
rooted
and
vascular.
The
presence
and
extent
of
rooted
aquatic
plants
is
a
quantitative
measure
of
ecosystem
health.
Rooted
aquatic
plants
generally
are
sensitive
to
conditions
of
water
clarity
and
associated
nutrient
concentrations
(
which
result
in
algal
light
shading)
and
suspended
particulate
levels.
Also,
research
suggests
that
elevated
levels
of
nutrients
may
have
direct
adverse
metabolic
impacts
on
eelgrass.

Macroalgae
are
also
considered
SAV,
but
they
are
not
rooted
or
vascular.
Rather,
they
are
algal
colonies,
visible
to
the
eye,
and
sometimes
attached
to
the
bay
bottom.
They
generally
have
lower
habitat
value
and
are,
in
some
cases,
considered
indicators
of
environmental
degradation.

Excess
nutrients
may
result
in
the
displacement
of
eelgrass
by
macroalgae
(
see
Figure
3­
21).
In
the
western
and
central
estuaries
(
Flanders
and
Great/
Little
Peconic
Bays),
with
the
exception
of
Bullhead
Bay,
there
are
no
known
significant
beds
of
eelgrass
present.
Peconic
Estuary
Program
CCMP
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evaluation
are
contained
in
the
SCDHS
Peconic
Estuary
Surface
Water
Quality
(
1998)
report.
The
SAV
analysis
also
provided
preliminary
guidance
to
PEP
natural
resources
programs,
such
as
the
SAV
Long­
Term
Monitoring
Program
(
Cornell
Cooperative
Extension)
and
the
Eelgrass
Habitat
Criteria
Study
(
EEA,
Inc.,
1999),
which
is
providing
more
detailed
guidance
on
SAV
habitat
criteria.
These
proposed
criteria
are
based
on
the
fact
that
lower
nutrient
levels
clearly
relate
to
greater
water
column
light
penetration,
an
important
factor
for
eelgrass,
which
needs
adequate
light
to
survive.

For
the
time
being,
these
criteria
are
being
proposed
as
"
interim"
criteria
because
the
scientific
community
has
not
come
to
consensus
regarding
the
causal
factors
related
to
eelgrass
decline.
Substantial
additional
data
from
ongoing
studies
will
be
available
soon.
When
coupled
with
the
expanded
SCDHS
monitoring
program,
with
additional
sites
at
eelgrass
beds
and
additional
years
of
data,
a
more
exhaustive
analysis
will
be
performed
for
developing
SAV
habitat
criteria.

OVERALL
QUALITY
AND
USE
IMPAIRMENTS
Based
on
the
recommended
total
nitrogen
guideline
of
0.45
mg/
l,
the
PEP
Management
Conference
has
developed
a
water
quality
hierarchy
to
describe
use
impairments
and
recommend
management
measures
for
waterbodies
within
the
Peconic
Estuary
System
(
see
Table
3­
2).
This
hierarchy
includes
"
mitigation
priority"
waters,
"
stressed/
threatened"
waters,
and
"
preservation
priority"
waters.
The
water
quality
hierarchy
can
be
used
to
better
channel
resources
for
best
management
practices
and
other
land
use
and
pollution
control
programs
and
can
assist
in
review
and
prioritization
of
potential
implementation
projects.
It
can
also
be
used
in
numerous
other
programs,
such
as
the
State
Environmental
Quality
Review
Act,
whereby
all
applications
to
undertake,
fund,
or
approve
an
action
must
undergo
rigorous
environmental
review
prior
to
approval.

The
PEP
Management
Conference's
adoption
of
the
hierarchy
has
important
implications.
However,
the
hierarchy
does
not
imply
prioritization
among
categories.
That
is,
funding
for
mitigation
for
Flanders
Bay
is
not
presumptively
a
higher
priority
than
preservation
efforts
in
eastern
waters.

Mitigation
Priority
Waters
In
relatively
small
areas
of
the
estuary,
particularly
the
tidal
Peconic
River
and
Flanders
Bay
(
the
"
western
estuary"),
Meetinghouse
Creek,
and
East
Creek/
Riverhead,
nitrogen
levels
need
to
be
reduced
to
optimize
DO
conditions.
These
waters
are
characterized
by
substantial
violations
of
the
proposed
total
nitrogen
guideline
for
mean
summer
conditions.
There
are
also
frequent
and
sometimes
"
serious"
DO
standard
violations
in
surface
samples.
These
are
extremely
small
areas,
making
up
far
less
than
one
percent
of
the
estuary's
surface
waters
(
see
Table
3­
2).

Management
considerations
for
these
waters
include
mitigation
to
alleviate
these
frequent
and
sometimes
serious
DO
problems.
TMDLs
are
prescribed
by
Section
303(
d)
of
the
Clean
Water
Act
for
surface
waters
not
attaining
water
quality
standards.
Based
on
the
conditions
in
mitigation
priority
waters,
a
Clean
Water
Act
Section
303(
d)
listing
based
on
not
achieving
the
state
dissolved
oxygen
standard
and
a
TMDL
should
be
considered
for
the
entire
Peconic
River/
Flanders
Bay
watershed
(
including
subwatersheds
for
Meetinghouse
Creek
and
East
Creek/
Riverhead).
Peconic
Estuary
Program
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Table
3­
2.
Surface
Water
Characterization
and
Management
Hierarchy.

Mitigation
Priority
Waters
Stressed/
Threatened
Waters
Preservation
Priority
Waters
Waterbodies
*
Tidal
Peconic
River/
western
Flanders
Bay
*
Meetinghouse
Creek
*
East
Creek/
Riverhead
*
Flanders
Bay
(
Central/
East)
*
West
Neck
Bay
*
Sag
Harbor
*
East
Creek
complex/
Southold
*
Town
Creek
complex
*
Northwest
Creek
*
Presumptively
all
other
waters
TN
Guideline
Attainment
"
Extreme"
exceedances
(>
0.6
mg/
l
TN)
Exceedances
(
not
"
extreme")
Compliance
DO
Standard
Violation
Frequency
Frequent
violations
(>
20%
of
samples)
Frequent
(>
20%)
or
occasional
(
2­
5%)
violations
for
some
stations;
depressed
mean
DO
for
all
others.
No
more
than
one
violation
DO
Standard
Violation
Severity
Several
"
serious"
violations
(
below
3.5
&
2
mg/
l)
Not
"
serious"
(
no
DO
<
3.5
mg/
l)
No
"
serious"
violations
Management
Implications**
Total
Maximum
Daily
Loads;
load
reductions***
TN
load
controls
prevent
substantial
additional
loads***
Rational
load
control
targets***

*
Based
on
nitrogen
and
DO
concerns.
**
Does
not
imply
management
prioritization
among
three
categories.
***
Based
on
total
nitrogen
guidelines,
modeling
results,
and
cost­
effectiveness
analysis.

Stressed/
Threatened
Waters
A
small
class
of
waters
exists
that
exhibit
marginally
"
stressed"
or
"
threatened"
characteristics
with
respect
to
nitrogen
and
dissolved
oxygen
concentrations.
These
waters
include:

 
West
Neck
Bay
 
Central/
Eastern
Flanders
Bay
 
East
Creek
complex/
Southold
 
Town
Creek
complex
 
Sag
Harbor
 
Northwest
Creek
These
waters
are
characterized
by
modest
violations
of
the
proposed
total
nitrogen
guideline
for
mean
summer
conditions,
and
"
occasional"
but
no
"
serious"
DO
standard
violations
for
surface
samples
for
many
of
the
stations
(
see
Table
3­
2).
Peconic
Estuary
Program
CCMP
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Management
considerations
include
mitigation
to
reduce
nitrogen
and
ensure
optimal
DO
conditions,
and
nitrogen
reduction
controls
should
be
considered
and
implemented
where
cost­
effective.
Neither
a
Clean
Water
Act
303(
d)
listing
nor
a
TMDL
establishment
is
recommended
for
these
waters
at
this
time.
However,
the
subwatersheds
to
the
waterbodies
should
be
the
particular
focus
of
load
control
strategies,
with
specific
load
targets
developed.

Preservation
Priority
Waters
Preservation
priority
waters
include
all
waters
of
the
Peconic
Estuary
System
not
listed
as
mitigation
priority
or
stressed/
threatened
waters
above.
These
waters
are
in
compliance
with
total
nitrogen
guidelines
and
exhibit
no
more
than
one
DO
violation
and
have
no
"
serious"
DO
violations.
Because
surface
water
quality
conditions
with
respect
to
DO
(
and
related
nitrogen)
are
generally
excellent
in
the
Peconic
Estuary,
much
of
the
estuary
falls
within
this
classification.
The
New
York
State
DO
standard
of
five
mg/
l
is
consistently
attained
in
greater
than
97
percent
of
the
estuary
(
see
Table
3­
2).

Recommended
management
considerations
for
these
waters
are
that
mitigation
and
nitrogen
reduction
controls
are
appropriate
where
demonstrated
to
be
cost­
effective,
especially
when
multiple
benefits
will
accrue
(
coliforms,
toxics,
habitat,
etc.).
Cost­
effective
preservation
also
is
needed
to
prevent
degradation
so
that
nitrogen
levels
are
maintained
at
their
current
levels.
In
these
"
preservation
priority"
waters,
model
results
will
be
especially
critical
in
evaluating
results
of
best­
case
and
worstcase
management
scenarios,
as
well
as
very
discrete
management
plans.

Even
though
some
of
the
estuary's
waterbody
segments
are
clearly
more
enriched
than
others
with
respect
to
nitrogen,
most
have
not
demonstrated
obvious
and
acute
impairments
with
respect
to
conventional
dissolved
oxygen,
such
as
fish
kills.
This
does
not
mean,
of
course,
that
subtle,
longterm
ecosystem
changes
have
not
occurred
due
to
nitrogen
enrichment.

MANAGEMENT
STRATEGY
An
overarching
PEP
management
principle
is
to
support
management
decisions
based
on
comprehensive,
site­
specific
studies
(
monitoring,
modeling,
land
use,
etc.)
for
the
main
bays
and
main
watershed,
as
well
as
in
subwatersheds
such
as
West
Neck
Bay,
Sag
Harbor,
and
Meetinghouse
Creek.
Increasing
emphasis
is
also
being
placed
on
linkages
with
living
resource
issues,
such
as
submerged
aquatic
vegetation.

Already,
a
point
source
total
nitrogen
freeze
has
been
implemented
for
the
western
estuary
(
Peconic
River
and
Flanders
Bay).
Major
sewage
treatment
plant
upgrades
at
Riverhead
and
Sag
Harbor
have
been
funded,
in
large
part,
by
New
York
State,
two
examples
of
numerous
demonstration
and
early
implementation
actions.

Overall,
the
PEP
management
strategy
is
based
on
three
distinct,
but
related,
approaches:

 
Optimize
pre­
existing
and
emerging
management
programs;

 
Provide
additional
local
characterizations,
applying
water
quality
and
pollutant
load
assessments;
and,

 
Utilize
the
surface
water
model
and
economic
valuation
and
financing
tools
to
develop
and
implement
a
total
nitrogen
load
allocation
strategy
for
the
entire
estuary.
Peconic
Estuary
Program
CCMP
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The
load
control
strategy
includes
a
recommendation
to
pursue
a
Clean
Water
Act
Section
303(
d)
listing
and
a
TMDL
for
the
Peconic
River
and
Flanders
Bay,
and
a
non­
regulatory
total
nitrogen
load
allocation
for
the
areas
east
of
Flanders
Bay.
The
load
reductions
targeted
for
the
western
estuary
appear
feasible
for
nonpoint
sources
(
the
primary
nitrogen
inputs),
since
only
modest
increases
in
the
western
estuary
are
likely
(
13
percent
increase
maximum)
under
full
build­
out
over
a
manageable
area.
The
need
for
"
water
quality
preservation"
in
the
eastern
estuary
is
highlighted,
since
greater
nitrogen
load
increases
are
likely
(
greater
than
20
percent
increase)
over
a
much
larger
area
at
full
build­
out.

These
approaches
are
designed
to
achieve
the
following
goals
(
based
on
1994­
96
model
calibration
conditions):

 
Attain
0.45
mg/
l
TN
guideline
in
all
waters,
to
ensure
that
the
New
York
State
DO
standard
(
5
mg/
l)
is
maintained
at
all
times,
thereby
minimizing
potential
adverse
impacts
to
marine
life;

 
Attain
0.4
mg/
l
shallow
water
TN
criterion,
where
feasible
and
cost­
effective,
to
optimize
water
clarity,
maintaining
and
potentially
improving
conditions
for
eelgrass
beds,
a
critical
habitat;
and,

 
Implement
the
"
preservation
policy"
in
waters
east
of
Flanders
Bay,
to
prevent
degradation
and
maintain
nitrogen
levels
at
their
current
concentrations,
where
water
quality
meets
or
exceeds
established
standards,
criteria,
or
guidelines.

Existing
and
Emerging
Management
Programs
In
addition
to
the
programs
noted
above,
including
sewage
treatment
plant
upgrades
and
a
point
source
nitrogen
freeze
update,
several
other
programs
are
critical
to
nitrogen
management.
As
discussed
above,
perhaps
the
most
prominent
is
open
space
preservation,
which
continues
to
protect
not
only
drinking
water,
but
also
estuarine
water
quality
(
see
Figure
3­
14).
Funding
available
for
open
space
acquisition
and
farmland
preservation
along
the
East
End
has
risen
dramatically
in
recent
years.
A
substantial
part
of
a
pool
of
funding
totaling
$
361
million
could
be
available,
largely
for
the
Suffolk
County
East
End
(
see
Chapter
9).
Aggressive
continuation
of
open
space
programs
will
be
a
critical
aspect
of
CCMP
implementation.

Important
regulatory
programs
discussed
in
this
chapter
include
the
Pine
Barrens
Program,
the
East
Hampton
Harbor
Protection
Overlay
District,
the
State
Environmental
Quality
Review
Act
(
SEQRA),
and
the
Suffolk
County
Planning
Commission
review
process.

The
Pine
Barrens
Program
has
resulted
in
ensuring
the
preservation
of
over
2,000
acres
in
the
Peconic
River
corridor
in
their
natural
state.
Were
it
not
for
this
program,
potential
additional
nitrogen
loading
to
the
estuary
would
be
substantial.

A
program
which
occurred
during
the
formative
years
of
the
PEP
is
the
Harbor
Protection
Overlay
District
in
East
Hampton
Town.
This
program
has
instituted
several
key
land
management
and
pollution
control
measures
in
areas
contributing
groundwater
and
stormwater
runoff
from
all
coastal
properties
in
the
Town
of
East
Hampton.
These
include
sanitary
system
upgrades,
clearing
restrictions,
and
stormwater
containment
requirements
for
structures
and
driveways.
Peconic
Estuary
Program
CCMP
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The
SEQRA
requires
special
environmental
assessments
prior
to
undertaking,
funding,
or
approving
certain
types
of
actions.
Most
new
development
and
pollution
control
actions
are
subject
to
SEQRA.
PEP
recommendations
and
actions
will
be
important
factors
for
State
and
local
agencies
that
undertake,
fund,
and
review
projects.

The
Suffolk
County
Planning
Commission
is
a
regional
commission
that
reviews
several
types
of
land
development
applications
and
plans,
including
those
occurring
within
500
feet
of
the
shoreline.
An
adverse
determination
by
the
Commission
can
only
be
overridden
by
a
supermajority
of
the
approving
town
board.
Thus,
consideration
of
PEP
recommendations
and
actions
by
the
Commission
is
an
excellent
mechanism
for
CCMP
implementation
for
nearshore
areas.

Several
other
programs
with
nitrogen
implications
are
ongoing.
These
include
river
and
wetlands
preservation
programs
including
the
Wild,
Scenic
and
Recreational
Rivers
statute
and
regulations
(
6
NYCRR
Part
666),
the
Freshwater
Wetlands
regulations
(
6
NYCRR
Part
663),
the
Tidal
Wetlands
Land
Use
regulations
(
6
NYCRR
Part
661),
and
the
Protection
of
Waters
regulations
(
6
NYCRR
Part
608).
These
regulations
can
mitigate
nitrogen
loads
by
minimizing
stormwater
runoff
and
improving
denitrification
and
uptake.
With
regard
to
local
government,
upzoning
efforts,
wetland
restrictions,
clearing
restrictions,
and
clustering
requirements
have
resulted
in
a
much
lower
pollutant
loading
potential.

Numerous
non­
regulatory
efforts
also
have
been
targeted
at
nitrogen
controls.
Perhaps
the
most
prominent
of
these
are
public
education
and
outreach
initiatives
directed
at
stakeholders
such
as
residential
homeowners,
tourists,
youth
groups,
and
small
business
owners.
These
efforts
are
described
in
the
Public
Education
and
Outreach
chapter
of
this
Management
Plan.
Best
management
practices
(
BMPs)
are
yet
another
important
component
of
the
PEP
approach.
With
respect
to
residences
and
commercial
and
industrial
uses,
the
PEP
has
developed
a
draft
Nonpoint
Source
Inventory
of
local
programs,
which
is
being
translated
into
management
actions.
A
large
part
of
the
process
is
review
and
implementation
of
Section
6217(
g)
management
measures
and
practices
identified
as
part
of
the
Coastal
Zone
Act
Reauthorization
Amendments
of
1990.

Additional
Planning
and
Management
Based
on
PEP
Characterizations
The
characterization­
based
management
strategies
are
discussed
in
the
preceding
sections.
These
include
a
marine
surface
water
total
nitrogen
(
TN)
"
guideline"
(
0.45
mg/
l)
for
DO
management
purposes.
Based
on
that
guideline,
this
CCMP
identifies
a
surface
water
quality
"
hierarchy"
which
can
immediately
be
used
in
resource
allocation
and
planning
efforts
and
in
other
programs
involving
environmental
review.
The
PEP
is
recommending
a
presumptively
even
split
for
funding
of
preservation
and
mitigation
efforts
(
50
percent
for
preservation,
50
percent
for
mitigation).

An
even
more
stringent
"
shallow
water
criterion"
of
0.4
mg/
l
TN
is
proposed
for
the
shallow
waters
(
waters
three
meters
deep
or
less)
of
the
estuary
to
optimize
eelgrass
habitat.
This
is
an
interim
In
addition
to
future
funding
for
proposed
and
ongoing
management
programs,
a
total
of
over
$
11
million
in
Federal
and
State
funds
has
already
been
dedicated
to
performing
55
priority
demonstration/
implementation
projects
identified
by
the
PEP.
Early
nutrient
action
projects
include
sewage
treatment
facility
upgrades
in
Riverhead
and
Sag
Harbor
and
improved
waste
treatment
systems
at
the
Corwin
Duck
Farm.
Public
education
and
outreach
initiatives,
an
Agricultural
Environmental
Management
(
AEM)
Initiative,
and
Clean
Water
Act
Section
319
(
Nonpoint
Source
Management
Program)
projects
are
also
key
components
of
the
management
program.
Peconic
Estuary
Program
CCMP
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criterion,
subject
to
interpretation
of
ongoing
modeling
efforts
and
submerged
aquatic
vegetation
studies.

Based
on
nitrogen
loading
evaluations,
the
PEP
has
determined
that
management
of
existing
residential
and
agricultural
lands
is
a
priority.
Sanitary
system
and
fertilizer
actions
are
emphasized
accordingly.
For
proposed
new
development,
residential
development
is
the
major
concern
on
an
estuary­
wide
basis,
particularly
in
the
western
estuary
and
on
the
South
Fork.
New
industrial
and
commercial
development
is
an
issue
prominent
mainly
in
the
western
estuary,
particularly
in
Riverhead
Town.

Modeling
and
Nitrogen
Loading
Workgroups
Based
on
the
overall
TN
guideline,
the
TN
shallow
water
criterion,
and
water
quality
preservation
policy,
the
PEP
will
establish
a
total
nitrogen
loading
goal
for
the
entire
watershed,
based
in
large
part
on
the
results
of
state­
of­
the­
art
surface
water
modeling
of
various
management
alternatives.
This
model
will
allow
evaluation
of
future
water
quality
conditions,
as
compared
with
current
conditions
and
recommended
guidelines
and
criteria.

Economic
consultant
data
on
resource
benefits,
implementation
costs,
and
financing
will
be
important
components
of
the
process.
Subwatersheds
for
stressed/
threatened
waterbodies
will
also
be
the
focus
of
particular
planning
attention.

Because
of
the
need
to
accelerate
the
quantitative
nitrogen
management
process,
a
short­
term,
focused
set
of
work
groups
is
recommended,
as
shown
in
Figure
3­
22.
These
work
groups
are
addressing
priority
management
issues
by
applying
PEP
modeling
and
assessment
tools
in
relation
to
existing
and
emerging
programs.
The
goal
is
to
set
quantitative
loading
targets
and
detailed
plans
for
load
management
(
timing,
costs,
parties,
etc.).
Work
group
members
include
representatives
from
the
PEP
Management
Conference
as
well
as
Federal,
state,
and
local
agency
representatives.
The
work
groups
convened
in
September
1999.
Each
work
group
will
produce
a
strategy
that
will
lay
out
the
steps
and
timeframe
for
setting
nitrogen
load
controls
Lead
parties
for
the
work
groups
will
be
integrally
involved
in
PEP
activities.
Therefore,
there
will
be
close
coordination
with
other
efforts,
such
as
critical
natural
resource
area
management
and
monitoring.
The
work
group
leaders
will
be
in
close
contact
with
each
other,
so
that
all
initiatives
are
coordinated.

The
Agricultural
Work
Group
is
charged
with
refining
existing
agricultural
nitrogen
loading
estimates
and
developing
an
implementation
plan
for
regional
nitrogen
load
reductions.
This
effort
includes
expanding
the
Agricultural
Environmental
Management
(
AEM)
Initiative
and
considering
"
Purchase
of
Development
Rights"
links
to
farm
management
plans.

To
date,
the
Agricultural
Work
Group
has
made
significant
progress
towards
their
goals,
including
producing
agricultural
use
GIS
maps,
and
determining
the
nitrogen
loading
rates
and
estimates
of
potential
reductions
for
specific
crops.
The
Work
Group
has
produced
an
Agricultural
Environmental
Management
Strategy,
located
in
Appendix
H.

An
ambitious
Agricultural
Environmental
Management
(
AEM)
Initiative
program
has
been
piloted
in
the
Peconic
Estuary.
Using
the
AEM
approach,
a
comprehensive
inventory
and
analysis
was
conducted
for
all
farms
within
one
sub­
watershed
to
assess
the
potential
impact
the
farms
may
have
on
that
part
of
the
Peconic
Estuary
and
shallow
aquifer.
Plans
were
developed
for
a
total
of
13
farms
Peconic
Estuary
Program
CCMP
C
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within
the
sub­
watershed
and
high
priority
BMPs
were
implemented.
This
program
will
be
a
model
for
agricultural
environmental
management
at
farms
throughout
the
study
area.

The
focus
of
the
Non­
Agricultural
Work
Group
includes
both
existing
and
prospective
nitrogen
loading.
For
existing
loads,
the
emphasis
is
on
residential
uses
and
BMPs
as
well
as
other
programs
(
primarily
dealing
with
fertilizer
and
sanitary
waste).
For
prospective
loads,
the
Non­
Agricultural
Work
Group
will
focus
on
residential
uses.
Efforts
will
be
directed
at
land
management
strategies,
including
zoning,
clustering,
clearing
restrictions,
and
model
ordinances.
This
group
will
address
nutrient
loadings
on
publicly
held
land
as
well
as
on
private/
commercial
properties,
such
as
golf
courses.

The
West
Estuary
TMDL
Work
Group
is
addressing
the
TMDL
process.
This
process
includes
refining
the
loading
analysis
for
the
western
Peconic
River
and
will
consider
the
costs
and
benefits
of
developing
a
separate
model
for
the
freshwater
portion
of
the
river.
Finally,
industrial
and
commercial
planning
analysis
for
the
Peconic
River
watershed
will
be
a
crucial
component
of
the
work
group's
efforts.

Each
of
the
work
groups
will
be
developing
and
evaluating
a
range
of
options
and
considering
costs
and
benefits.
The
surface
water
model
will
be
used
to
help
assess
benefits
of
the
management
actions.

MANAGEMENT
ACTIONS
A
number
of
important
completed
actions
and
accepted
policies,
as
well
as
new
proposed
solutions
to
nutrient­
related
issues,
are
included
in
the
nutrients
action
plan.
These
include
adoption
of
the
water
quality
hierarchy,
endorsement
of
the
nitrogen
management
work
group
process,
and
early
commitments
to
freeze
point
source
nitrogen
loading
to
the
western
estuary.
The
actions
also
reflect
major
commitments
to
sewage
treatment
plant
upgrades
at
Riverhead
Town
(
approximately
85
percent
of
a
$
7
million
project
to
be
funded
through
NYS
Clean
Water/
Clean
Air
Bond)
and
Sag
Harbor
(
at
least
$
500,000
in
NYS
Clean
Water/
Clean
Air
Bond
Act
funds
for
a
$
2
million
project),
as
well
as
wastewater
treatment
enhancements
at
the
Corwin
Duck
Farm
(
more
than
$
270,000
in
EPA
and
NYSDEC
funding).
The
following
actions
include
only
the
key
PEP
management
recommendations
and
actions
which
require
additional
follow­
up
attention,
commitments,
actions,
or
time
to
complete.

Within
the
CCMP,
some
steps
within
the
actions
have
been
identified
as
priorities,
as
indicated
under
the
step
number.
The
PEP
will
seek
to
implement
priority
actions
in
the
near
term.
Priorities
may
be
either
new
or
ongoing,
commitments
or
recommendations.
Completing
some
priority
actions
does
not
require
any
new
or
additional
resources,
because
they
are
being
undertaken
through
"
base
programs"
or
with
funding
that
has
been
committed.
In
other
cases,
in
order
to
complete
the
priority
actions,
new
or
additional
resources
need
to
be
secured
by
some
or
all
of
the
responsible
entities.
In
the
Agricultural
Environmental
Management
Strategy,
the
Agricultural
Work
Group
strongly
recommends
that
the
following
tasks
be
pursued:

Task
I
Develop
a
Long
Island
component
to
the
New
York
State
Agricultural
Environmental
Management
(
AEM)
program;

Task
II
Identify
potential
pilot
projects
to
demonstrate
Best
Management
Practices
and
test
them,
where
appropriate;

Task
III
Investigate
the
creation
of
a
farm
insurance
plan;

Task
IV
Provide
funding
for
increased
local
AEM
development
and
implementation;

Task
V
Investigate
and
implement
innovative/
alternative
finance
mechanisms
for
education
and
outreach
and
other
tasks
noted
above;
and,

Task
VI
Gather
and
analyze
economic
data
on
a
regular
basis
and
continue
to
promote
and
integrate
economic
analyses
and
support
mechanisms
into
the
AEM
initiatives.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
20
To
minimize
actions
that
require
tracking,
the
PEP
has
not
placed
"
completed"
actions
accomplished
in
early
implementation
actions
in
the
following
discussion
and
table.

NUTRIENTS
MANAGEMENT
ACTIONS
N­
1.
Continue
to
Use
and
Refine
Water
Quality
Standards
and
Guidelines.

N­
2.
Preserve
Water
Quality
East
of
Flanders
Bay.

N­
3.
Implement
a
Quantitative
Nitrogen
Load
Allocation
Strategy
for
the
Entire
Estuary.

N­
4.
Control
Point
Source
Discharges
from
STPs
and
Other
Dischargers.

N­
5.
Implement
Nonpoint
Source
Control
Plans.

N­
6.
Use
Land
Use
Planning
to
Control
Nitrogen
Loading
Associated
with
New
Development.

N­
7.
Ensure
that
Funding
Is
Distributed
Evenly
Between
Preservation
and
Mitigation
Projects.

N­
8.
Integrate
PEP
Recommendations
into
Other
Programs.

N­
9.
Sponsor
and
Coordinate
Research
and
Information
Gathering.

N­
10.
Monitor
Conditions
within
the
Estuary
System
to
Determine
the
Effectiveness
of
Management
Strategies.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
21
Addresses
Nutrients
Management
Objectives
1,
2,
3
and
6.

New
York
State
has
not
adopted
a
general
water
quality
standard
for
nitrogen.
However,
the
NYSDEC
has
adopted
a
marine
surface
water
total
nitrogen
guideline
for
the
Peconic
River/
Flanders
Bay
of
0.5
mg/
l
based
on
1988­
90
conditions.
This
guideline
forms
the
basis
for
the
"
no
net
increase"
discharge
policy
for
point
sources
of
nitrogen
in
the
western
estuary.

One
basis
for
the
nitrogen
criteria
is
achieving
State
dissolved
oxygen
standards.
EPA
is
revising
its
criteria
recommendations
for
dissolved
oxygen
in
marine
waters.
The
State
and
PEP
will
be
evaluating
EPA's
criteria
once
proposed
and
issued.
Any
revision
to
the
State
standard
for
dissolved
oxygen
may
affect
future
PEP
recommendations
for
total
nitrogen
criteria.

For
dissolved
oxygen
management,
this
action
recommends
evaluation
of
a
modification
of
the
NYSDEC's
total
nitrogen
guideline
to
0.45
mg/
l,
based
on
1994­
96
data.
This
guideline
is
exceeded
in
tidal
portions
of
the
Peconic
River
and
western
and
central
Flanders
Bay
and
a
few
peripheral
embayments.
The
total
nitrogen
guideline
will
be
used
as
an
assessment
tool
to
screen
relative
water
quality
in
various
bays
in
relation
to
dissolved
oxygen
conditions
for
a
given
time
period,
a
benchmark
against
which
to
evaluate
model
management
alternative
runs,
and
to
evaluate
the
need
to
develop
a
TMDL
under
the
Clean
Water
Act.

To
optimize
eelgrass
habitat
and
preserve
water
quality
in
eelgrass
habitat
areas,
a
more
stringent
total
nitrogen
criterion
of
0.4
mg/
l
is
recommended
for
shallow
estuary
waters
(
three
meters
or
less).
The
LISS
eelgrass
habitat
criteria
values
were
provisionally
adopted
as
working
guidelines
for
developing
this
criterion.
A
preliminary
SCDHS
analysis
of
mean
seasonal
water
quality
parameters
and
light
extinction
(
Kd)
with
respect
to
existing
SAV
beds
further
refined
the
LISS
parameters
for
the
Peconic
Estuary.
Based
on
this
analysis,
the
following
criteria
are
proposed
as
working
criteria
for
optimizing
eelgrass
habitat:
Kd:
0.75
±
0.05
(
m­
1);
chlorophyll­
a:
5.5
±
0.5
(
µ
g/
l);
and
TN:
0.4
(
mg/
l)
(
for
"
shallow
waters,"
three
meters
deep
or
less).
These
proposed
criteria
are
based
on
the
fact
that
lower
nutrient
levels
clearly
relate
to
greater
water
column
light
penetration,
an
important
factor
for
eelgrass,
which
needs
adequate
light
to
survive.

The
shallow
water
criteria
are
particularly
important
for
the
eastern
estuary,
due
to
the
potential
for
optimizing
eelgrass
habitat,
as
well
as
the
opportunity
for
preservation
of
water
quality
in
those
areas.
The
costs
and
benefits
of
nitrogen
reductions
for
the
relatively
small
areas
that
exceed
the
more
stringent
0.4
mg/
l
TN
criterion
will
be
carefully
examined
based
on
the
results
of
ongoing
studies.

For
the
time
being,
the
shallow
water
criteria
are
being
proposed
as
"
interim"
criteria
because
the
scientific
community
has
not
come
to
consensus
regarding
the
causal
factors
related
to
eelgrass
decline.
Substantial
additional
data
from
the
SAV
Long­
Term
Monitoring
Program
(
Cornell
Cooperative
Extension)
and
the
Eelgrass
Habitat
Criteria
Study
(
EEA,
Inc.,
1999)
will
be
synthesized
shortly.
When
coupled
with
the
expanded
SCDHS
monitoring
program,
with
additional
sites
at
eelgrass
beds
and
additional
years
of
data,
a
more
exhaustive
analysis
will
be
performed
to
refine
the
"
interim"
criteria.
N­
1.
Continue
to
Use
and
Refine
Water
Quality
Standards
and
Guidelines.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
22
Steps
N­
1.1
Integrate
monitoring
and
modeling
data,
studies,
and
reports
to
evaluate
the
application
Priority
of
the
0.45
mg/
l
total
nitrogen
guideline
to
the
Peconic
Estuary
as
a
means
of
attaining
and
maintaining
dissolved
oxygen
standards
and
for
use
in
developing
regional
load
allocation
strategies,
a
CWA
Section
303(
d)
listing,
and
TMDL
establishment,
to
attain
and
maintain
the
dissolved
oxygen
standard.

N­
1.2
Integrate
monitoring
and
modeling
data,
studies,
and
reports
to
evaluate
the
use
of
the
Priority
recommended
0.4
mg/
l
total
nitrogen
guideline
for
the
shallow
waters
of
the
estuary
to
optimize
eelgrass
habitats
and
for
use
in
developing
regional
load
allocation
strategies,
a
CWA
Section
303(
d)
listing,
and
TMDL
establishment.

N­
1.3
Review
and
revise
as
appropriate
the
marine
dissolved
oxygen
standards
based
on
LISS
efforts
to
develop
area­
specific
dissolved
oxygen
targets
and
EPA
efforts
to
develop
dissolved
oxygen
criteria
for
marine
waters.

Responsible
Entities
N­
1.1
PEP
Management
Conference
(
lead),
NYSDEC,
SCDHS,
and
Contractor
Tetra­
Tech,
Inc.

N­
1.2
PEP
Management
Conference
(
lead),
NYSDEC,
SCDHS,
and
Contractor
Tetra­
Tech,
Inc.

N­
1.3
NYSDEC
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
23
Addresses
Nutrients
Management
Objectives
4
and
6.

Eastern
estuary
waters
(
east
of
Flanders
Bay)
are
of
high
quality.
Preservation
plans
are
needed
to
prevent
degradation
so
these
waters
are
maintained
at
their
current
high
level
of
water
quality.
Therefore,
in
areas
east
of
Flanders
Bay,
including
embayments,
water
quality
that
meets
or
exceeds
water
quality
standards,
criteria,
or
guidelines
should
be
maintained.

Preservation
plans
will
be
developed
based
on
the
nitrogen
criteria
guidelines
discussed
above
and
the
recommendations
of
the
nitrogen
loading
work
groups.

Steps
N­
2.1
Develop
and
implement
water
quality
preservation
plans
to
protect
existing
water
quality
Priority
for
waters
east
of
Flanders
Bay
where
water
quality
meets
or
exceeds
established
standards,
criteria,
or
guidelines.
Plans
should
address
potential
point
and
nonpoint
pollutant
sources
as
well
as
strategies
for
preventing
and/
or
mitigating
impacts.

Responsible
Entities
N­
2.1
NYSDEC,
SCDHS
(
co­
leads),
EPA,
SCPD,
PEP
Management
Conference,
and
Towns
N­
2
Preserve
Water
Quality
East
of
Flanders
Bay.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
24
Addresses
Nutrients
Management
Objectives
1,
2,
4,
5
and
6.

Under
the
Federal
Clean
Water
Act
Section
303(
d),
States
must
estimate
load
allocations
for
point
and
nonpoint
source
pollutants
for
waterbodies
that
do
not
meet
their
designated
uses.
TMDLs
are
detailed
technical
water
quality
assessments,
which
determine
the
maximum
amount
of
a
given
pollutant
a
waterbody
can
assimilate
while
still
meeting
water
quality
standards
for
designated
uses.

The
State
will
be
evaluating
data
to
determine
waters
of
the
Peconic
system
that
should
be
included
on
the
State's
2002
303(
d)
list
submittal
for
violations/
exceedances
of
the
New
York
State
dissolved
oxygen
criterion.
The
State
will
establish
a
schedule
for
the
development
of
TMDLs
for
waterbody
segments,
if
any,
included
on
that
list.
This
schedule
will
take
into
account
the
status
of
the
PEP
water
quality
computer
model
and
any
revisions
to
the
State's
water
quality
standard
for
dissolved
oxygen
(
see
Action
N­
1.1).
The
computer
model,
once
calibrated
and
verified,
will
be
used
to
evaluate
management
alternatives
for
point
source
and
nonpoint
source
controls.
The
State
will
then
develop
a
TMDL
for
any
waterbodies
listed
on
the
303(
d)
list
and
associated
wasteload
allocations
for
point
sources
and
loading
allocations
for
nonpoint
sources.

A
formal
regulatory
TMDL
is
not
recommended
for
waters
not
included
on
the
303(
d)
list
at
this
time.
However,
in
the
future,
the
PEP
will
establish
a
total
nitrogen
loading
goal
for
the
entire
watershed,
based
on
modeling
results
and
nitrogen
guidelines.

A
variety
of
computer
modeling
exercises
can
be
used
to
determine
appropriate
management
actions
for
the
estuary.
For
example,
the
PEP
Hydrodynamic
and
Eutrophication
Model
will
be
a
key
tool
in
developing
a
nitrogen
load
control
target
for
the
overall
estuary.

The
surface
water
computer
model
can
be
used
to
evaluate
management
alternatives
for
land
use
and
pollution
control.
The
approach
is
to
initially
run
"
coarse"
(
best
and
worst­
case
runs)
management
alternatives.
The
results
will
be
evaluated
against
the
water
quality
guidelines
currently
in
use.
More
detailed
management
alternatives
will
be
developed
to
provide
more
specific
guidance
for
regional
load
targets.
These
will
include
land
use
and
pollution
control
alternatives
and
other
management
measures,
such
as
reversing
the
Shinnecock
Canal
flow
regimen.
Once
completed,
options
for
load
reductions,
such
as
advanced
treatment
and
outfall
relocation
in
the
case
of
a
STP,
can
be
evaluated,
as
well
as
the
significance
of
atmospheric
deposition
as
a
source
of
nitrogen
to
the
estuary.

United
States
Geological
Survey
(
USGS)
embayment
modeling
for
West
Neck
Bay,
Sag
Harbor,
and
Meetinghouse
Creek
is
complete,
and
the
USGS
is
performing
a
North
Fork
modeling
study.
USGS
seismic
reflection
work
for
Flanders
Bay
was
completed
this
past
summer
and
they
are
currently
analyzing
the
data.
A
Camp,
Dresser
and
McKee
regional
groundwater
model,
which
will
include
the
North
and
South
Forks
and
Shelter
Island,
is
ongoing.
Results
from
these
modeling
efforts
will
need
to
be
incorporated
in
PEP
characterization,
modeling,
and
management
activities.
N­
3
Implement
a
Quantitative
Nitrogen
Load
Allocation
Strategy
for
the
Entire
Estuary.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
25
Steps
N­
3.1
Initiate
the
development
of
load
allocation
targets
and
implementation
strategies
for
Priority
nitrogen
loading
to
the
entire
estuary,
with
particular
emphasis
on
subwatersheds
for
peripheral
creeks
and
embayments
(
e.
g.,
Meetinghouse
Creek,
West
Neck
Bay,
and
Sag
Harbor).
Any
subsequent
Clean
Water
Act
Section
303(
d)
listing
and
Total
Maximum
Daily
Load
(
TMDL)
established
for
the
"
western
estuary,"
the
Peconic
River/
Flanders
Bay
area
(
see
following
actions)
can
incorporate
these
interim
steps.
These
load
allocation
targets
will
be
based
on
surface
water
nitrogen
guideline
attainment.
In
addition,
the
appropriate
Nitrogen
Management
Work
Groups
and
the
Management
Committee,
will
evaluate
nonpoint
source
pollution
effects
on
groundwater
quality,
coupled
with
groundwater
impacts
on
the
surface
water
nitrogen
guideline,
and
will
thereby
consider
the
viability
of
subregional
groundwater
quality
targets
as
a
means
to
protect
surface
water
quality.

N­
3.2
Review
all
PEP
data
to
identify
water
segments
to
be
included
in
New
York
State's
Priority
2002
303(
d)
list.

N­
3.3
Establish
schedule
for
development
of
TMDL
for
Peconic
River/
Flanders
Bay
segments
Priority
included
on
303(
d)
list
based
on
completion
of
water
quality
model
and
adoption
of
revised
dissolved
oxygen
standard.

N­
3.4
Complete
calibration
and
verification
of
hydrodynamic
and
eutrophication
models
to
evaluate
management
alternatives
for
TMDL
land
use
and
pollution
control.

N­
3.5
Use
PEP
hydrodynamic
and
eutrophication
models
to
evaluate
management
alternatives.

N­
3.6
Develop,
as
appropriate,
TMDL/
wasteload
allocation
and
load
allocation
for
Peconic
River
and
Flanders
Bay
watershed.

N­
3.7
Evaluate
the
need
for
additional
assessment
and
modeling
to
evaluate
issues
such
as
sedimentary
denitrification.

Responsible
Entities
N­
3.1
Suffolk
County
with
NYSDEC,
Towns,
and
Nitrogen
Management
Work
Groups
N­
3.2
NYSDEC
N­
3.3
NYSDEC
N­
3.4
PEP
N­
3.5
PEP
N­
3.6
NYSDEC
N­
3.7
PEP
Peconic
Estuary
Program
CCMP
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Addresses
Nutrients
Management
Objectives
1,
2,
and
6.

Any
new
or
incremental
increases
in
point
source
nitrogen
loading
to
surface
waters
should
be
prohibited
if
the
discharge
is
to
surface
waters
in
the
environmentally
stressed
region
of
the
tidal
Peconic
River
and
western
Flanders
Bay.
The
surface
water
point
source
nitrogen
freeze
applies
to
all
facilities,
including
the
sewage
treatment
plants
at
Brookhaven
National
Laboratory
and
the
former
Grumman
plant.
Throughout
the
entire
Peconic
River
groundwater­
contributing
area,
any
substantial
new
or
incremental
point
source
nitrogen
loading
should
be
limited
if
it
discharges
to
surface
waters.
Substantial
groundwater
degradation,
which
adversely
affects
surface
waters,
should
also
be
limited.
This
means
that
new
groundwater­
discharging
sewage
treatment
plants
in
the
Peconic
River
groundwater­
contributing
area
generally
should
be
carefully
scrutinized.

As
a
long­
range
management
goal,
upgrades
to
the
Riverhead
STP
(
above
and
beyond
those
funded
by
the
NYS
Clean
Water/
Clean
Air
Bond
Act)
should
be
evaluated
with
respect
to
attainment
of
the
surface
water
quality
total
nitrogen
guideline
of
0.45
mg/
l.
Such
evaluations
can
be
performed
through
modeling
and
nitrogen
management
work
group
assessments.

Long­
range
Riverhead
STP
upgrades
could
be
in
the
form
of
a
groundwater
discharge
(
10
mg/
l
total
nitrogen,
using
conventional
denitrification),
a
relocated
surface
water
discharge
at
central
or
eastern
Flanders
Bay
(
approximately
25
mg/
l
total
nitrogen,
the
current
discharge
concentration),
or
a
surface
water
discharge
at
the
existing
location
(
approximately
four
mg/
l
total
nitrogen,
using
advanced
denitrification);
environmental
impacts
of
these
and
other
alternatives
would
require
assessment
before
selection.
Beneficial
reuse
of
treated
wastewater
(
i.
e.,
application
on
agricultural
land,
golf
courses,
or
soccer
fields,
including
seasonal
application)
should
also
be
evaluated.

Recommendations
and
actions
regarding
groundwater
discharges
and
the
Riverhead
STP
will
be
consistent
with
any
TMDL
work
and
Clean
Water
Act
section
303(
d)
listing
(
see
Action
N­
3).

Steps
N­
4.1
Evaluate
the
appropriateness
of
applying
for
a
"
Discharge
Restriction
Category"
to
prevent
new
nitrogen
discharges
from
point
sources
in
the
Peconic
River
and
the
western
portion
of
the
Peconic
Estuary.

N­
4.2
Ensure
continued
implementation
of
the
"
no­
net
increase"
policy
for
nitrogen
loading
from
point
sources
to
surface
waters
of
the
western
estuary.

N­
4.3
Determine
the
necessity
of
decreasing
nitrogen
loads
from
the
Riverhead
STP
and
other
permitted
discharges
and
develop
nitrogen
loading
limits
as
needed
to
meet
the
sitespecific
nitrogen
guideline
and
to
protect
against
DO
standard
violations,
based
on
TMDL
work.
(
See
Action
N­
3.5.)
N­
4
Control
Point
Source
Discharges
from
STPs
and
Other
Dischargers.
Peconic
Estuary
Program
CCMP
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N­
4.4
Consider
a
groundwater
application
of
the
point
source
nitrogen
freeze
in
the
Peconic
River/
Flanders
Bay
watershed,
(
currently
applied
only
to
surface
water
discharges),
based
upon
Nitrogen
Management
Work
Group
recommendations
and
TMDL
work.
(
See
Actions
N­
3.1
and
N­
3.5.)

N­
4.5
Upgrade
the
Sag
Harbor
Sewage
Treatment
Plant
and
continue
to
monitor
and
model
Sag
Harbor
Cove
to
assess
impacts
and
track
effectiveness
of
implementation.

N­
4.6
Evaluate
and
consider
implementing
a
beneficial
reuse
program
where
reclaimed
STP
water
and/
or
sludge
could
be
used
on
selected
golf
courses,
playing
fields,
and
farms.

Responsible
Entities
N­
4.1
SCDHS
(
lead
for
nomination)
and
PEP
N­
4.2
NYSDEC
(
lead)
and
PEP
N­
4.3
NYSDEC
(
lead)
and
PEP
Management
Conference
N­
4.4
PEP
(
lead)

N­
4.5
Sag
Harbor
Village,
NYSDEC
(
co­
leads),
SCDHS
(
lead
for
monitoring),
and
PEP
N­
4.6
SCDHS
and
NYSDEC
(
co­
leads)
Peconic
Estuary
Program
CCMP
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28
Addresses
Nutrients
Management
Objectives
2,
4,
and
6.

Many
nonpoint
sources
contribute
nutrients
to
the
estuary
system,
including
on­
site
disposal
systems
(
cesspools
or
septic
systems),
domestic
fertilizer
use,
agricultural
fertilizer
applications,
and
stormwater
runoff.
Section
6217(
g)
of
the
Coastal
Zone
Act
Reauthorization
Amendments
(
CZARA)
requires
States
to
develop
management
measures
to
address
nonpoint
sources
of
pollutants
in
coastal
areas.
In
accordance
with
Section
6217(
g),
the
PEP
should
ensure
that
appropriate
nonpoint
source
control
plans
are
developed
for
each
nonpoint
source
category
that
the
PEP
identifies
as
contributing
significantly
to
adverse
ecosystem
impacts
(
marinas/
boating
are
addressed
in
the
pathogens
module).
The
control
plan
will
include,
but
will
not
be
limited
to,
identification
and
assessment
of
management
practices
and
ways
to
implement
the
appropriate
practices.
In
addition,
the
plan
will
determine
whether
the
control
measures
are
adequate
to
solve
water
quality
problems
and
will
identify
additional
control
measures
that
may
be
necessary.
The
PEP
will
utilize
the
Base
Program
Analysis,
Nonpoint
Source
Management
Plan
Inventory
(
PEP,
1995),
in
conjunction
with
the
nitrogen
management
work
group
process
to
complete
this
action.

Substantial
degradation
of
existing
groundwater
quality
should
be
prevented,
especially
in
the
Peconic
River
area.
On­
site
disposal
systems
or
sanitary
systems/
cesspools,
along
with
fertilizer
applications,
contribute
most
of
the
locally
derived
anthropogenic
nitrogen
load
to
the
Peconic
estuary.

A
number
of
BMPs,
restrictions,
and
incentives
can
be
used
to
target
nitrogen
reduction
from
these
nonpoint
sources.

Mechanisms
for
sanitary
system
management
may
include:

 
Tax
credits
(
such
as
for
upgrades)
and
other
incentive
programs;

 
Mandatory
system
upgrades
within
defined
districts
on
property
transfers
or
on
issuance
of
building
permits
for
expansion;

 
Use
of
innovative
and
alternative
systems;

 
General
sanitary
system
regulation
reviews
to
evaluate
possible
areas
for
improvement;

 
Best
management
practices
such
as
the
proper
and
periodic
maintenance
of
sanitary
systems;
and,

 
Use
of
wastewater
management
districts
or
utilities.

The
SCDHS
already
has
policies
that
establish
thresholds
as
to
when
existing
sanitary
systems
should
be
upgraded
or
completely
relocated
(
e.
g.,
when
additional
habitable
area
is
being
added
to
an
existing
dwelling
as
is
the
case
with
new
bedrooms).
In
addition,
the
NYSDEC
Region
1
Tidal
Wetlands
permitting
program
also
applies
similar
strategies
to
existing
sanitary
systems.
Consideration
should
be
given
to
formalizing
such
policies
at
all
levels
of
government
for
programs
relevant
to
the
Peconic
Estuary.
N­
5
Implement
Nonpoint
Source
Control
Plans.
Peconic
Estuary
Program
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Mechanisms
for
fertilizer
management
may
include:

 
Tax
credits
(
such
as
for
using
native
plants
in
landscaping)
and
other
incentives;

 
Restrictions
on
the
sale
and/
or
use
of
some
products
(
e.
g.,
liquid
fertilizers);

 
Land
use
management
measures;

 
Best
management
practices,
such
as
low
maintenance
lawns,
slow­
release
fertilizers,
modification
of
fertilizer
application
rates;
and,

 
Organic
and/
or
slow­
release
fertilizers
(
via
a
tax
on
inorganic
fertilizers,
public
relation
endorsements
of
"
good"
products,
educational
campaigns
for
retailers
and
consumers,
etc.).

Agriculture
also
is
a
major
nonpoint
source
of
nitrogen
to
the
estuary.
The
Agricultural
Work
Group
has
been
charged
with
refining
existing
agricultural
nitrogen
loading
estimates
and
developing
an
implementation
plan
for
regional
nitrogen
load
reductions.
This
effort
will
include:

 
Expanding
the
Agricultural
Environmental
Management
(
AEM)
Initiative;

 
Considering
"
Purchase
of
Development
Rights"
links
to
farm
management
plans;
and,

 
Promoting
organic
farming
methods.

Under
the
ambitious
AEM
Initiative
program
piloted
in
the
Peconic
Estuary,
a
comprehensive
inventory
and
analysis
was
conducted
for
all
the
farms
within
one
sub­
watershed
to
assess
the
potential
impact
the
farms
may
have
on
the
Peconic
Estuary
and
shallow
aquifer.
Plans
were
developed
for
the
13
farms
and
high
priority
BMPs
were
implemented.
This
program
will
be
a
model
for
agricultural
environmental
management
at
farms
throughout
the
study
area.

A
recent
SCDHS
study
investigating
groundwater
impacts
entitled
Water
Quality
Monitoring
Program
to
Detect
Pesticide
Contamination
in
Groundwaters
of
Nassau
and
Suffolk
Counties,
NY
(
1999)
has
found
that
the
golf
courses
examined
were
not
having
major,
adverse
environmental
impacts
with
respect
to
nutrient
loading,
particularly
as
compared
with
traditional
row
crop
farms.
The
1999
report
documented
the
testing
of
31
wells
at
18
Long
Island
golf
courses
and
found
that
the
average
nitrate
concentration
was
4.3
mg/
l
(
the
median
nitrate
concentration
was
2.6
mg/
l),
which
is
the
equivalent
of
a
housing
density
of
less
than
one
residence
per
acre.
At
agricultural
sites,
the
1999
study
found
an
average
nitrate
concentration
of
11.7
mg/
l
and
the
SCDHS
1996
study
entitled
Nitrate
and
Pesticide
Impacts
of
Agriculture
on
Groundwater
Quality
Suffolk
County,
NY
found
a
20
year
nitrate
average
of
11.3
mg/
l.
Turf
management
practices
at
golf
courses
do
effectively
limit
nitrogen
inputs,
however,
monitoring
should
continue,
as
should
aggressive
golf
course
BMP
implementation.

The
SCDHS
has
done
a
follow­
up
study
this
year
with
an
expanded
list
of
analytes
and
with
new
monitoring
wells
at
five
more
golf
courses
in
the
county,
including
Shinnecock,
National,
and
Maidstone.
Preliminary
data
suggest
that
nitrogen
is
generally
relatively
well
controlled.
The
NYSDEC
has
been
funding
the
monitoring
program
for
three
years
at
about
$
100,000
per
year.
The
NYSDEC
recently
agreed
to
a
three­
year
one
million­
dollar
commitment
with
the
SCDHS
to
expand
the
monitoring
program.

Stormwater,
although
not
one
of
the
most
significant
inputs
on
a
regular
basis,
may
be
locally
important.
Therefore,
subwatershed
management
practices
should
also
consider
the
management
of
stormwater
nitrogen
loads.
Peconic
Estuary
Program
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Steps
N­
5.1
Ensure
that
the
Section
6217(
g)
management
measures
of
CZARA
are
appropriately
implemented,
in
support
of
the
overall
nitrogen
management
plan.

N­
5.2
Investigate
feasible
implementation
mechanisms
and
develop
a
plan
to
prevent
Priority
increases
and
encourage
decreases
in
nitrogen
in
groundwater
underflow
due
to
domestic
fertilizer
use.

N­
5.3
Investigate
feasible
implementation
mechanisms
and
develop
a
plan
to
prevent
Priority
increases
and
encourage
decreases
in
nitrogen
in
groundwater
underflow
due
to
on­
site
disposal
systems
(
sanitary
systems).

N­
5.4
Develop
a
regional
implementation
plan
for
agricultural
nitrogen
load
reductions
Priority
which
would
include
promoting
agricultural
best
management
practices,
expanding
agricultural
environmental
management
(
AEM)
strategies,
and
promoting
organic
farming
among
other
initiatives.

N­
5.5
Manage
stormwater
runoff
on
a
subwatershed
basis
to
control
nitrogen
inputs.

Responsible
Entities
N­
5.1
NYDOS
(
lead),
PEP,
EPA,
NOAA,
and
Nitrogen
Management
Work
Groups
N­
5.2
PEP
Management
Conference
and
Nitrogen
Management
Work
Groups
N­
5.3
PEP
Management
Conference
and
Nitrogen
Management
Work
Groups
N­
5.4
Nitrogen
Management
Work
Groups,
SCSWCD
(
co­
leads),
Cornell
Cooperative
Extension,
and
NYSDEC
N­
5.5
PEP
Management
Conference
(
lead),
Consultant
Horsley
and
Witten,
Inc.,
SCDHS,
SCPD,
and
SCSWCD
Peconic
Estuary
Program
CCMP
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31
Addresses
Nutrients
Management
Objectives
2,
3,
and
4.

Fully
40
percent
of
the
Peconic
Estuary
is
still
subject
to
development,
posing
a
substantial
potential
threat
to
water
quality
in
the
main
bays
as
well
as
in
the
embayments.
For
proposed
new
development,
residential
development
is
the
major
concern
on
an
estuary­
wide
basis,
particularly
in
the
western
estuary
and
on
the
South
Fork.
Under
a
scenario
in
which
100
percent
of
farmland
is
also
preserved,
nitrogen
loading
could
increase
substantially
in
every
major
region
of
the
estuary
(
see
Figures
3­
12
and
3­
13).
Overall,
a
total
nitrogen
increase
for
the
estuary
study
area
would
be
near
40
percent
(
about
41
percent
in
eastern
estuary,
and
34
percent
in
western
estuary).
In
the
eastern
estuary,
the
increase
on
the
South
Fork
would
be
most
profound
(
over
60
percent).

A
number
of
land
use
planning
measures
can
be
used
to
minimize
surface
water
quality
degradation
related
to
nitrogen
loading,
including
zoning
restrictions,
development
plan
review,
open
space
preservation,
and
use
of
model
ordinances.

The
Brown
Tide
Comprehensive
Assessment
Management
Plan
and
the
Peconic
Estuary
Program
Action
Plan
recommended
that
undeveloped
land
in
unsewered
areas
of
the
Peconic
River
groundwater­
contributing
area
should
be
upzoned
to
a
minimum
of
two
acres
per
unit
(
or
its
commercial,
industrial,
or
institutional
equivalent)
where
feasible,
subject
to
exceptions
where
necessary,
to
attain
even
more
substantial
regional
nitrogen
controls
(
e.
g.,
"
receiving
area"
and
"
Compatible
Growth
Area"
parcels
necessary
to
implement
the
Pine
Barrens
Land
Use
Plan).
Additional
natural
resources
benefits
can
be
attained
by
even
more
stringent
land
use
controls.
The
Nitrogen
Management
Work
Groups
will
review
coordination
between
the
PEP
and
the
Pine
Barrens
Plan
and
will
evaluate
the
degree
to
which
PEP
Action
Plan
recommendations
have
been
implemented.

Funding
available
for
open
space
acquisition
and
farmland
preservation
along
the
East
End
has
risen
dramatically
in
recent
years.
A
substantial
part
of
a
pool
of
funding
totaling
$
361
million
could
be
available,
largely
for
the
Suffolk
County
East
End.
These
funding
sources
will
be
invaluable
in
open
space
acquisition,
which
will
have
important
pollution
prevention
implications.

The
public
is
extremely
supportive
of
farmland
preservation,
as
evidenced
by
the
recent
voterapproved
farmland
preservation
programs.
Also,
the
PEP
Economic
Value
Assessment
study
found
that
the
public
was
willing
to
pay
more
for
farmland
preservation
than
several
other
environmental
programs.
Thus,
the
PEP
operates
under
the
presumption
that
farmland
preservation
goals
will
be
met,
and
deals
with
nitrogen
loading
issues
associated
with
farmland
through
the
Agricultural
Nitrogen
Management
Work
Group.

Several
model
ordinances,
such
as
the
Harbor
Protection
Overlay
District
and
model
stormwater
runoff
ordinances,
exist
and
can
be
applied
to
the
watershed.
Such
ordinances
need
to
be
coordinated
on
an
interjurisdictional
basis
to
maximize
benefits
to
the
estuary.
N­
6
Use
Land
Use
Planning
to
Control
Nitrogen
Loading
Associated
with
New
Development.
Peconic
Estuary
Program
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Steps
N­
6.1
Continue
and
expand
aggressive
open
space
preservation
programs
that
protect
habitat
and
living
resources,
as
well
as
groundwater
and
surface
water
quality
(
see
Chapter
7
for
a
description
of
how
nitrogen
stressed
subwatersheds
are
factored
into
recommendations).

N­
6.2
Evaluate
the
degree
to
which
the
Brown
Tide
Comprehensive
Assessment
Management
Plan
and
Peconic
Estuary
Program
Action
Plan
land
use
and
zoning
recommendations
have
been
implemented.

N­
6.3
Encourage
evaluation
of
design
alternatives
for
Pine
Barrens
credit
"
receiving
area"
parcels,
(
e.
g.,
clustering
away
from
the
river,
clearing
limits,
turf
area
restrictions,
xeriscaping,
etc.),
where
feasible
to
minimize
nitrogen
loading.
(
Subject
to
and
recognizing
the
overarching
provisions
of
the
Pine
Barrens
Land
Use
Plan
and
New
York
State
Environmental
Conservation
Law
[
ECL]
Article
57.)

N­
6.4
Review
the
Pine
Barrens
Land
Use
Plan
"
guidelines"
(
non­
binding)
for
development
in
the
Compatible
Growth
Area
and
develop
proposals
for
additional
"
standards"
(
binding)
for
development
based
on
Peconic
River
water
quality
protection
goals.

N­
6.5
Evaluate
nitrogen
loading
impacts
when
reviewing
Core
Preservation
Area
hardship
applications.

N­
6.6
Ensure
that
the
public
acquisition
of
private,
vacant
lands
in
Core
Preservation
Areas
within
the
Peconic
River
ground
watershed
is
given
high
priority.

N­
6.7
Utilize
the
strictest
practicable
standards
when
reviewing
Peconic
River
Development
Plans
(
e.
g.,
require
open
space
dedications,
maximum
practicable
setbacks
from
the
river,
and
natural
landscaping
to
eliminate
or
minimize
fertilizer
use).

N­
6.8
Evaluate
the
application
of
model
ordinances
such
as
the
Harbor
Protection
Overlay
District
and
model
stormwater
runoff
ordinances.

Responsible
Entities
N­
6.1
Local
governments,
Suffolk
County,
and
New
York
State
N­
6.2
SCDHS
(
lead),
NYSDEC,
SCPD,
PEP
Management
Conference,
and
local
governments
(
to
be
coordinated
with
Nitrogen
Management
Work
Group)

N­
6.3
SCDHS,
NYSDEC,
SCPD,
PEP
Management
Conference,
and
local
governments
(
to
be
coordinated
with
Nitrogen
Management
Work
Group)

N­
6.4
SCDHS,
NYSDEC,
SCPD,
PEP
Management
Conference,
and
local
governments
(
to
be
coordinated
with
Nitrogen
Management
Work
Group)

N­
6.5
SCDHS,
NYSDEC,
SCPD,
PEP
Management
Conference,
and
local
governments
(
to
be
coordinated
with
Nitrogen
Management
Work
Group)
Peconic
Estuary
Program
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N­
6.6
SCDHS,
NYSDEC,
SCPD,
local
governments
(
co­
leads),
and
PEP
Management
Conference
(
to
be
coordinated
with
Nitrogen
Management
Work
Group)

N­
6.7
SCDHS,
NYSDEC,
SCPD,
local
governments
(
co­
leads),
and
PEP
Management
Conference
(
to
be
coordinated
with
Nitrogen
Management
Work
Group)

N­
6.8
PEP
Management
Conference
and
Local
Government
Committee
Peconic
Estuary
Program
CCMP
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Addresses
Nutrients
Management
Objectives
2,
3,
and
4.

The
PEP
is
recommending
a
presumptively
even
split
for
funding
of
preservation
and
mitigation
efforts
(
50
percent
for
preservation,
50
percent
for
mitigation).
This
is
subject
to
feasibility
within
given
programs,
and
would
apply
in
the
absence
of
detailed
cost­
benefit
analyses,
which
would
indicate
other
appropriate
allocations.

Steps
N­
7.1
Evaluate
programs
in
which
a
50/
50
split
for
funding
of
preservation
and
mitigation
Priority
efforts
can
be
applied
(
e.
g.,
Section
319
Nonpoint
Source
Implementation;
NYS
Clean
Water/
Clean
Air
Bond
Act)
and
determine
mechanisms
for
its
implementation.

Responsible
Entity
N­
7.1
PEP
Management
Conference
N­
7
Ensure
that
Funding
is
Distributed
Evenly
Between
Preservation
and
Mitigation
Projects.
Peconic
Estuary
Program
CCMP
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Addresses
Nutrients
Management
Objectives
1,
2,
3,
4,
and
5.

Many
regulatory
and
nonregulatory
programs,
such
as
the
Pine
Barrens
Program,
the
East
Hampton
Harbor
Protection
Overlay
District,
the
State
Environmental
Quality
Review
Act
(
SEQRA),
and
the
Suffolk
County
Planning
Commission
review
process
may
be
important
mechanisms
for
implementation
of
PEP
recommendations.
Some
of
these
programs
may
need
to
be
reviewed
to
ensure
smooth
coordination
and
determine
whether
any
programmatic
changes
are
needed
to
improve
management
of
the
Peconic
Estuary.

Steps
N­
8.1
Integrate
PEP
recommendations
into
existing
land
use
and
regulatory
programs,
Priority
including
the
SEQRA
regulations
(
6NYCRR
Part
617),
Article
8
of
the
Environmental
Conservation
Law,
Suffolk
County
Water
Quality
Coordinating
Committee,
Suffolk
County
Planning
Commission
and
Suffolk
County
Council
on
Environmental
Quality
reviews,
the
Southold
Ground
Watershed
Protection
and
Water
Supply
Management
Strategy,
the
Wild,
Scenic
and
Recreational
Rivers
statute
and
regulations
(
6NYCRR
Part
666),
the
Freshwater
Wetlands
regulations
(
6
NYCRR
Part
663),
the
Tidal
Wetlands
Land
Use
regulations
(
6
NYCRR
Part
661),
and
the
Protection
of
Waters
regulations
(
6
NYCRR
Part
608).

Responsible
Entities
N­
8.1
PEP
Management
Conference
(
lead),
Nitrogen
Management
Work
Groups,
Suffolk
County
Planning
Commission,
and
NYSDEC
N­
8
Integrate
PEP
Recommendations
into
Other
Programs.
Peconic
Estuary
Program
CCMP
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Addresses
Nutrients
Management
Objectives
2,
3,
4,
and
5.

The
National
Estuary
Program
is
designed
to
develop
effective
management
plans
based
on
available
or
readily
obtainable
data,
using
measurable
performance
indicators
such
as
ambient
nitrogen
levels,
dissolved
oxygen
and
light
extinction.
However,
continued
research
and
information
gathering
will
be
needed
to
evaluate
the
status
of
the
estuary's
water
and
sediment
quality
and
ecology/
living
resources,
to
track
the
effectiveness
of
proposed
actions,
and
to
run
computer
modeling
programs.
Therefore,
the
PEP
long­
term
monitoring
and
assessment
effort
will
continue
in
a
coordinated
fashion
with
several
other
programs.
The
Brown
Tide
Research
Initiative
(
see
Chapter
2)
is
one
key
program
that
will
be
extremely
useful
with
respect
to
ecosystem
dynamics
and
nutrient
budgets
(
e.
g.,
sediment
nutrient
flux).
Another
program
sponsored
or
supported
by
the
PEP
includes
the
Living
Resources
Research
and
Monitoring
Plan.
Efforts
such
as
this
one
will
help
to
develop
a
strategy
for
assessing
linkages
between
submerged
aquatic
vegetation
habitat
criteria
and
other
water
quality
issues.
They
will
also
provide
the
long­
term
data
necessary
to
assess
subtle
individual
and
synergistic
ecosystem
impacts,
at
various
trophic
levels.
The
PEP
also
supports
efforts
by
the
Suffolk
County
Planning
Department
and
others
to
maintain
up
to
date
land
use
and
land
cover
databases
for
use
in
continuing
water
quality
and
habitat/
living
resources
assessments.
These
databases
can
be
used
to
document
trends
in
land
use
and
land
cover
and
characterize
habitat
types
and
pollution
loading
potential.

Also,
PEP
modeling
has
been
focused
on
the
estuary.
However,
the
Peconic
River
itself
is
a
significant
freshwater
resource
well
worth
investigating
and
managing.
Biological
resources
and
processes,
physical
modifications
(
dams),
and
sedimentation
(
and
possibility
for
dredging/
removal)
are
all
important
and
related
topics.
Integrated
investigations
of
the
river
(
nutrients,
toxics,
radionuclides,
etc.)
and
modeling
should
be
pursued.
The
PEP
will
continue
to
leverage
its
resources
with
respect
to
the
River,
where
possible
(
e.
g.,
toxic
monitoring),
and
other
programs
and
sources
of
funding
should
be
sought
to
expand
freshwater
investigations
and
management.

Steps
N­
9.1
Continue
to
sponsor
and
coordinate
research
efforts
addressing
nutrient­
related
issues.

N­
9.2
Establish
a
PEP
land
cover
initiative
to
assist
in
nutrient
loading
analyses.

N­
9.3
Update
the
land
use
database
on
a
regular
basis
and
prepare
a
proposal
outlining
the
Priority
objectives
and
needs
for
a
long­
term
monitoring
program.

N­
9.4
Continue
to
integrate
atmospheric
deposition
data
into
PEP
modeling
and
management
activities.
Assess
how
reductions
in
atmospheric
sources
through
the
Clean
Air
Act
will
affect
nitrogen
loadings
in
the
Peconic
System.

N­
9.5
Continue
to
incorporate
groundwater
information
in
PEP
characterization,
modeling,
and
management
activities.
This
includes
ongoing
groundwater
monitoring
programs,
as
well
as
improvements
to
modeling.
N­
9
Sponsor
and
Coordinate
Research
and
Information
Gathering.
Peconic
Estuary
Program
CCMP
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N­
9.6
Continue
to
incorporate
PEP
TAC
and
external
peer
review
in
the
modeling
development
and
application
process,
which
includes
dependent
analyses
of
water
quality
and
pollution
input
studies.
As
the
model
process
is
completed,
continue
to
solicit
and
use
TAC
and
external
peer
review
in
developing
programs
and
interpreting
and
applying
data.

Responsible
Entities
N­
9.1
PEP
Technical
Advisory
Committee
(
TAC)
(
lead)

N­
9.2
PEP
Management
Conference
through
contractor
(
lead)
and
NYSDOS
N­
9.3
SCPD
(
lead)
and
PEP
Management
Conference
N­
9.4
PEP
(
lead)
and
EPA
N­
9.5
PEP
Management
Conference
(
lead)

N­
9.6
Model
Evaluation
Group
and
PEP
TAC
(
co­
lead)
Peconic
Estuary
Program
CCMP
C
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38
Addresses
Nutrients
Management
Objectives
2,
3,
4,
and
5.

Monitoring
is
critical
for
measuring
water
quality
and
determining
the
need
for
continued
or
expanded
management
efforts.
A
number
of
water
monitoring
efforts
already
exist
within
the
Peconic
Estuary.
One
such
program
monitors
environmental
conditions
at
Meetinghouse
Creek.
Continued
monitoring
at
this
site
is
needed
to
determine
if
and
when
remediation
is
technologically,
economically,
and
environmentally
feasible.
The
need
for
additional
actions
at
the
Corwin
Duck
Farm
will
be
evaluated
using
modeling
and
nitrogen
management
work
group
assessments.
Other
efforts
that
are
needed
include
a
long­
term
surface
water
monitoring
program,
a
biennial
surface
water
quality
report
from
the
SCDHS,
and
the
continuation
of
marine
surface
water
quality
monitoring.
This
last
effort
should
be
linked
to
other
efforts,
such
as
eelgrass
monitoring.

Steps
N­
10.1
Continue
monitoring
the
effectiveness
of
remedial
actions
at
the
Corwin
Duck
Farm.

N­
10.2
Develop
and
conduct
a
long­
term
surface
water
monitoring
program,
with
input
from
the
PEP
TAC.

N­
10.3
Issue
a
biennial
update
to
the
SCDHS
surface
water
quality
report.

N­
10.4
Continue
monitoring
groundwater
impacts
of
various
land
uses,
such
as
residences,
farms,
and
golf
courses.

Responsible
Entities
N­
10.1
USDA­
NRCS,
SCSWCD
(
co­
leads)
and
Nitrogen
Management
Work
Groups
N­
10.2
SCDHS
(
lead)
and
PEP
N­
10.3
SCDHS
(
lead)

N­
10.4
SCDHS
(
lead)
N­
10
Monitor
Conditions
Within
the
Estuary
System
to
Determine
the
Effectiveness
of
Management
Strategies.
Peconic
Estuary
Program
CCMP
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BENEFITS
OF
MANAGEMENT
ACTIONS
Because
the
Peconic
Estuary
is
generally
of
high
quality
with
respect
to
dissolved
oxygen,
the
chief
benefit
will
be
to
prevent
substantial
degradation
to
surface
water
quality,
thereby
enhancing
a
healthy
(
oxygen­
rich)
marine
habitat
and
promoting
species
abundance
and
diversity.
Conditions
in
the
stressed
western
estuary
should
be
improved.
Submerged
aquatic
vegetation
habitat
may
be
enhanced,
and
there
could
even
be
beneficial
implications
with
respect
to
severity
and
frequency
of
future
Brown
Tide
blooms.

Surface
water
model
results
will
be
evaluated
against
the
nitrogen
guideline
as
one
measure
of
"
benefits,"
and
economic
consultant
input
will
be
used
to
determine
costs
and
financing
methods.
Programs
for
measuring
ecosystem
health
and
potential
degradation
with
respect
to
submerged
aquatic
vegetation,
benthic
community
structure,
and
other
issues
are
being
developed
by
the
Habitat
and
Living
Resources
Plan.
These
are
long­
term
programs,
and
may
be
helpful
in
better
quantifying
benefits
of
nutrient
controls.
However,
useful
results
are
not
likely
in
the
immediately
foreseeable
future.
Moreover,
documentation
of
severe
and
widespread
adverse
impacts
due
solely
to
nutrients
is
not
likely.
Therefore,
immediate
implementation
of
rational
and
cost­
effective
preservation
policies
and
actions
is
critical,
to
avoid
the
need
to
document
severe
adverse
impacts
and
implement
more
costly
mitigation
strategies.
This
is
particularly
critical,
given
the
fact
that
about
40
percent
of
the
watershed
is
subject
to
development,
and
development
pressures
are
rapidly
accelerating.

COSTS
OF
MANAGEMENT
ACTIONS
Because
the
Peconic
Estuary
is
generally
of
high
quality
with
respect
to
nutrients,
many
management
actions
are
currently
targeted
at
preservation.
Many
of
these
actions
rely
on
optimizing
the
preexisting
and
emerging
regulatory
and
non­
regulatory
programs
discussed
above
with
no
immediate
additional
costs
projected.

Costs
of
key
individual
management
actions,
such
as
sewage
treatment
plant
upgrades
and
duck
farm
waste
treatment
systems,
are
included
with
individual
management
actions
discussed
in
this
chapter.
Key
implementation
funding
sources
are
also
noted
and
are
discussed
in
greater
detail
in
the
Financing
Chapter.

The
most
important
element
in
developing
and
implementing
regional
nitrogen
load
controls
is
the
nitrogen
work
group
process,
which
will
be
integrally
coupled
with
the
completion
of
the
surface
water
modeling
and
economic
value
assessment/
finance
plan
efforts.
The
work
group
process
will
be
conducted
using
existing
PEP
resources.

Several
detailed
cost
estimates
could
not
be
completed
in
time
for
inclusion.
With
respect
to
the
Non­
Agricultural
Work
Group,
the
costs
and
benefits
of
a
wide
variety
of
regulatory
and
incentive
programs
related
to
fertilizers
and
sanitary
systems
will
be
evaluated.
Public
input
will
be
crucial
in
guiding
these
recommendations
and
actions.
Open
space
targets
and
structural
mitigation
efforts
also
will
be
considered.
The
costs
and
benefits
of
additional
modeling
for
the
freshwater
Peconic
River
will
be
evaluated.

The
total
cost
of
all
actions
proposed
for
nutrient
management
is
$
767,500
in
new
one­
time
costs
and
$
1,372,500
in
new
annual
costs.
This
estimate
does
not
include
the
full
estimated
costs
of
Peconic
Estuary
Program
CCMP
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40
implementing
agricultural
best
management
practices.
(
See
"
Action
Costs"
in
Chapter
1
for
an
explanation
of
how
these
costs
were
determined.)

NUTRIENTS
ACTIONS
SUMMARY
TABLE
Table
3­
3
provides
the
following
summary
information
about
each
of
the
actions
presented
in
this
chapter.

Status
An
action's
status
is
designated
in
the
table
by
either
an
"
R"
for
"
Recommendation"
or
a
"
C"
for
"
Commitment."
Actions
that
are
commitments
are
being
implemented
because
resources
or
funding
and
organizational
support
is
available
to
carry
them
out.
Actions
that
are
"
recommendations"
require
new
or
additional
resources
by
some
or
all
of
the
responsible
entities.
"
O"
refers
to
ongoing
activities;
"
N"
indicates
new
actions.

Timeframe
This
category
refers
to
the
general
timeframe
for
action
implementation.
Some
actions
are
ongoing
or
nearing
completion;
implementation
of
other
actions
is
not
anticipated
until
some
time
in
the
future.

Cost
Information
in
the
cost
column
represents
the
PEP's
best
estimate
of
the
costs
associated
with
action
implementation.
"
Base
Program"
means
that
no
new
or
additional
funds
will
be
needed
outside
of
the
responsible
entity's
operating
budget
to
implement
the
action.
Where
additional
funding
is
needed,
resources
to
implement
an
action
may
be
expressed
as
dollar
amounts
or
work
years
or
both.
One
full
time
equivalent
employee
or
"
FTE"
is
estimated
as
costing
$
75,000
per
year,
which
includes
salary,
fringe
benefits,
and
indirect
costs.
The
"
Action
Costs"
description
in
both
Chapter
1
and
Chapter
9
provides
an
expanded
explanation
of
base
programs
and
action
costs.
C
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Peconic
Estuary
Program
CCMP
Table
3­
3.
Nutrients
Management
Plan
Actions.

Action
Responsible
Entity
Timeframe
Cost
Status
N­
1
Continue
to
Use
and
Refine
Water
Quality
Standards
and
Guidelines.
(
Objectives
1,
2,
3,
and
6)

N­
1.1
Priority
Integrate
monitoring
and
modeling
data,
studies,
and
reports
to
evaluate
the
application
of
the
0.45
mg/
l
total
nitrogen
guideline
to
the
Peconic
Estuary
as
a
means
of
attaining
and
maintaining
DO
standards
and
for
use
in
developing
regional
load
allocation
strategies,
a
CWA
Section
303(
d)
listing,
and
TMDL
establishment,
to
attain
and
maintain
the
dissolved
oxygen
standard.
PEP
Management
Conference
(
lead),

NYSDEC,
SCDHS,

Contractor
Tetra­
Tech,

Inc.
2001
EPA
 
0.1
FTE
NYSDEC
 
0.1
FTE
SCDHS
 
0.1
FTE
C/
N
N­
1.2
Priority
Integrate
monitoring
and
modeling
data,
studies,
and
reports
to
evaluate
the
use
of
the
recommended
0.4
mg/
l
total
nitrogen
guideline
for
the
shallow
waters
of
the
estuary
to
optimize
eelgrass
habitats
and
for
use
in
developing
regional
load
allocation
strategies,
a
CWA
Section
303(
d)
listing,
and
TMDL
establishment.
PEP
Management
Conference
(
lead),

NYSDEC,
SCDHS,

Contractor
Tetra­
Tech,

Inc.
2001
Included
in
Step
N­
1.1
C/
N
N­
1.3
Review
and
revise
as
appropriate
the
marine
DO
standards
based
on
LISS
efforts
to
develop
area­
specific
DO
targets
and
EPA
efforts
to
develop
DO
criteria
for
marine
waters.
NYSDEC
Initiate
after
release
of
EPA
criteria
NYSDEC
 
0.1
FTE
C/
N
N­
2
Preserve
Water
Quality
East
of
Flanders
Bay.
(
Objectives
4
and
6)

N­
2.1
Priority
Develop
and
implement
water
quality
preservation
plans
to
protect
existing
water
quality
for
waters
east
of
Flanders
Bay
where
water
quality
meets
or
exceeds
established
standards,
criteria,
or
guidelines.
Plans
should
address
potential
point
and
nonpoint
pollutant
sources
as
well
as
strategies
for
preventing
and/
or
mitigating
impacts.
NYSDEC,
SCDHS
(

coleads
EPA,
SCPD,

PEP
Management
Conference,
Towns
December
2001
EPA
 
0.2
FTE
NYSDEC
 
0.2
FTE
SCDHS
 
0.2
FTE
SCPD
 
0.2
FTE
Towns
 
0.2
FTE
each
of
five
towns
C/
N
Table
continued
on
next
page
Peconic
Estuary
Program
CCMP
C
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Table
3­
3.
Nutrients
Management
Plan
Actions.
(
continued)
Table
continued
on
next
page
Action
Responsible
Entity
Timeframe
Cost
Status
N­
3
Implement
a
Quantitative
Nitrogen
Load
Allocation
Strategy
for
the
Entire
Estuary.
(
Objectives
1,
2,
4,
5,
and
6)

N­
3.1
Priority
Initiate
the
development
of
load
allocation
targets
and
implementation
strategies
for
nitrogen
loading
to
the
entire
estuary,
with
particular
emphasis
on
subwatersheds
for
peripheral
creeks
and
embayment
(
e.
g.,
Meetinghouse
Creek,
West
Neck
Bay,
and
Sag
Harbor).
Any
subsequent
Clean
Water
Act
Section
303(
d)
listing
and
Total
Maximum
Daily
Load
(
TMDL)
established
for
the
"
western
estuary,"
the
Peconic
River/
Flanders
Bay
area
(
see
following
actions)
can
incorporate
these
interim
steps.
These
load
allocation
targets
will
be
based
on
surface
water
nitrogen
guideline
attainment.
In
addition,
the
appropriate
Nitrogen
Management
Work
Groups
and
the
Management
Committee,
will
evaluate
nonpoint
source
pollution
effects
on
groundwater
quality,

coupled
with
groundwater
impacts
on
the
surface
water
nitrogen
guideline,
and
will
thereby
consider
the
viability
of
subregional
groundwater
quality
targets
as
a
means
to
protect
surface
water
quality.
Suffolk
County
with
NYSDEC,
Towns,

Nitrogen
Management
Workgroups
2000
­
2001
(
Nitrogen
Management
Workgroups
convene;
2001
(
strategy
produced)
Included
in
Actions
N­
1
and
N­
2.
C/
N
N­
3.2
Priority
Review
all
PEP
data
to
identify
water
segments
to
be
included
in
New
York
State's
2002
303(
d)
list.
NYSDEC
2001
NYSDEC
 
0.05
FTE
C/
N
N­
3.3
Priority
Establish
schedule
for
development
of
TMDL
for
Peconic
River/
Flanders
Bay
segments
included
on
303(
d)
list
based
on
completion
of
water
quality
model
and
adoption
of
revised
dissolved
oxygen
standard.
NYSDEC
Develop
schedule:

2001
Complete
TMDL:

December,
2002
Implementation
schedule:
To
be
determined
Included
in
Step
N­
3.2
C/
N
C
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Peconic
Estuary
Program
CCMP
Table
3­
3.
Nutrients
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
N­
3.4
Complete
calibration
and
verification
of
hydrodynamic
and
eutrophication
models
to
evaluate
management
alternatives
for
TMDL
land
use
and
pollution
control.
PEP
2001
(
Contractor
 
part
of
$
225,000
contract)
C/
O
N­
3.5
Use
PEP
hydrodynamic
and
eutrophication
models
to
evaluate
management
alternatives.
PEP
2001
Included
in
Actions
N­
1
and
N­
2
C/
O
N­
3.6
Develop,
as
appropriate,
TMDL/
wasteload
allocation
and
load
allocation
for
Peconic
River
and
Flanders
Bay
watershed.
NYSDEC
Contingent
upon
actions
N­
1.1,
N­
3.3,
and
N­
3.4
Included
in
Action
N­
1
and
Step
N­

3.2
C/
N
N­
3.7
Evaluate
the
need
for
additional
assessment
and
modeling
to
evaluate
issues
such
as
sedimentary
denitrification.
PEP
2001
Included
in
Actions
N­
1
and
N­
2
C/
O
N­
4
Control
Point
Source
Discharges
from
STPs
and
Other
Dischargers.
(
Objectives
1,
2,
and
6)

N­
4.1
Evaluate
the
appropriateness
of
applying
for
a
"
Discharge
Restriction
Category"
to
prevent
new
nitrogen
discharges
from
point
sources
in
the
Peconic
River
and
the
western
portion
of
the
Peconic
Estuary.
SCDHS
(
lead
for
nomination),
PEP
2001
Included
in
Actions
N­
1
and
N­
3
R
N­
4.2
Ensure
continued
implementation
of
the
"
no­
net
increase"
policy
for
nitrogen
loading
from
point
sources
to
surface
waters
of
the
western
estuary.
NYSDEC
(
lead),
PEP
Ongoing
Included
in
Actions
N­
1
and
N­
2
C/
O
N­
4.3
Determine
the
necessity
of
decreasing
nitrogen
loads
from
the
Riverhead
STP
and
other
permitted
discharges
and
develop
nitrogen
loading
limits
as
needed
to
meet
the
site­
specific
nitrogen
guideline
and
to
protect
against
DO
standard
violations,
based
on
TMDL
work.
(
See
Action
N­
3.5.)
NYSDEC
(
lead),
PEP
Management
Conference
Contingent
upon
actions
N­
1.1,
N­

3.3,
and
N­
3.4
Included
in
Actions
N­
1
and
N­
3
C/
N
N­
4.4
Consider
a
groundwater
application
of
the
point
source
nitrogen
freeze
in
the
Peconic
River/
Flanders
Bay
watershed,
(
currently
applied
only
to
surface
water
discharges),
based
upon
Nitrogen
Management
Work
Group
recommendations
and
TMDL
work.

(
See
Actions
N­
3.1
and
N­
3.5)
PEP
(
lead)
Contingent
upon
actions
N­
1.1,
N­

3.3,
and
N­
3.4
Included
in
Actions
N­
1
and
N­
3
R
Table
continued
on
next
page
Peconic
Estuary
Program
CCMP
C
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44
Table
3­
3.
Nutrients
Management
Plan
Actions.
(
continued)
Table
continued
on
next
page
Action
Responsible
Entity
Timeframe
Cost
Status
N­
4.5
Upgrade
the
Sag
Harbor
Sewage
Treatment
Plant
and
continue
to
monitor
and
model
Sag
Harbor
Cove
to
assess
impacts
and
track
effectiveness
of
implementation.
Sag
Harbor
Village,

NYSDEC
(
co­
leads),

SCDHS
(
lead
for
monitoring),
PEP
2001
(
Implementation:
$
2
million
upgrade,
using
at
least
$
500,000
in
NYS
Clean
Water/
Clean
Air
Bond
Act
funds)
Monitoring:
Base
Program
C/
O
N­
4.6
Evaluate
and
consider
implementing
a
beneficial
reuse
program
where
reclaimed
STP
water
and/
or
sludge
could
be
used
on
selected
golf
courses,
playing
fields,

and
farms.
SCDHS,
NYSDEC
(
co­
leads)
2001
NYSDEC
 
0.1
FTE
SCDHS
 
0.1
FTE
$
50,000
R
N­
5
Implement
Nonpoint
Source
Control
Plans.
(
Objectives
2,
4,
and
6)

N­
5.1
Ensure
that
the
Section
6217(
g)
management
measures
of
CZARA
are
appropriately
implemented,
in
support
of
the
overall
nitrogen
management
plan.
NYDOS
(
lead),
PEP,

EPA,
NOAA,
Nitrogen
Management
Work
Groups
Ongoing
EPA
 
0.1
FTE
NYSDEC
 
0.1
FTE
SCDHS
 
0.1
FTE
NYSDOS
 
0.1
FTE
NOAA
 
0.1
FTE
C/
O
N­
5.2
Priority
Investigate
feasible
implementation
mechanisms
and
develop
a
plan
to
prevent
increases
and
encourage
decreases
in
nitrogen
in
groundwater
underflow
due
to
domestic
fertilizer
use.
PEP
Management
Conference,
Nitrogen
Management
Work
Groups
Strategy:
2001
Implementation:

Post­
CCMP
Plan
Development:

EPA
 
0.2
FTE
NYSDEC
 
0.2
FTE
SCDHS
 
0.2
FTE
Implementation:
To
be
determined
C/
N
N­
5.3
Priority
Investigate
feasible
implementation
mechanisms
and
develop
a
plan
to
prevent
increases
and
encourage
decreases
in
nitrogen
in
groundwater
underflow
due
to
on­
site
disposal
systems
(
sanitary
systems).
PEP
Management
Conference,
Nitrogen
Management
Work
Groups
Strategy:
2001
Implementation:

Post­
CCMP
Included
in
Step
N­
5.2
C/
N
C
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Peconic
Estuary
Program
CCMP
Table
3­
3.
Nutrients
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
N­
5.4
Priority
Develop
a
regional
implementation
plan
for
agricultural
nitrogen
load
reductions
which
would
include
promoting
agricultural
best
management
practices,
expanding
agricultural
environmental
management
(
AEM)
strategies,
and
promoting
organic
farming
among
other
initiatives.
Nitrogen
Management
Work
Groups,
SCSWCD
(
co­
leads),
Cornell
Cooperative
Extension,

NYSDEC
Strategy:
December
2000
Implementation:

Post­
CCMP
EPA
 
0.1
FTE
NYSDEC
 
0.1
FTE
SCDHS
 
0.1
FTE
SCSWCD
­
$
175,000/
yr
for
staff
CCE
­
$
175,000/
yr
for
staff
$
250,000
­
$
500,000
for
program
development
$
1
million
annually
for
implementation,
start
up
C/
N
(
Strategy)

R
(
Implementation

N­
5.5
Manage
stormwater
runoff
on
a
subwatershed
basis
to
control
nitrogen
inputs.
PEP
Management
Conference
(
lead),

Consultant
Horsley
and
Witten,
Inc.,
SCDHS,

SCPD,
SCSWCD
Post­
CCMP
SCDHS
 
0.2
FTE
SCPD
 
0.2
FTE
SCSWCD
 
0.2
FTE
(
Contractor
 
Part
of
$
191,600
contract
(
Regional
Stormwater
Runoff
Management
Plan
and
Subwatershed
Plan))
R
N­
6
Use
Land
Use
Planning
to
Control
Nitrogen
Loading
Associated
with
New
Development.
(
Objectives
2,
3,
and
4)

N­
6.1
Continue
and
expand
aggressive
open
space
preservation
programs
that
protect
habitat
and
living
resources,
as
well
as
groundwater
and
surface
water
quality
(
see
Chapter
7
for
a
description
of
how
nitrogen
stressed
subwatersheds
are
factored
into
recommendations).
Local
governments,

Suffolk
County,
New
York
State
Ongoing
(
Part
of
$
361
million
(
sum
of
1/
4
%
sales
tax,
East
End
Land
Bank,
Greenway
Fund,
and
Community
Preservation
Fund
monies))
C/
O
N­
6.2
Evaluate
the
degree
to
which
the
Brown
Tide
Comprehensive
Assessment
Management
Plan
and
Peconic
Estuary
Program
Action
Plan
land
use
and
zoning
recommendations
have
been
implemented.
SCDHS
(
lead),

NYSDEC,
SCPD,
PEP
Management
Conference,
local
governments
(
to
be
coordinated
with
Nitrogen
Management
Work
Group)
2001
Included
in
Actions
N­
1,
N­
2,

N­
3,
and
N­
5
R
Table
continued
on
next
page
Peconic
Estuary
Program
CCMP
C
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Table
3­
3.
Nutrients
Management
Plan
Actions
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
N­
6.3
Encourage
evaluation
of
design
alternatives
for
Pine
Barrens
credit
"
receiving
area"
parcels,
(
e.
g.,
clustering
away
from
the
river,
clearing
limits,
turf
area
restrictions,
xeriscaping,
etc.),
where
feasible
to
minimize
nitrogen
loading
(
Subject
to
and
recognizing
the
overarching
provisions
of
the
Pine
Barrens
Land
Use
Plan
and
New
York
State
Environmental
Conservation
Law
[
ECL]
Article
57).
SCDHS,
NYSDEC,

SCPD,
PEP
Management
Conference,
local
governments
(
to
be
coordinated
with
Nitrogen
Management
Work
Group)
Ongoing
Included
in
Actions
N­
1,
N­
2,
N­
3,

and
N­
5
C/
O
N­
6.4
Review
the
Pine
Barrens
Land
Use
Plan
"
guidelines"

(
non­
binding)
for
development
in
the
Compatible
Growth
Area
and
develop
proposals
for
additional
"
standards"
(
binding)
for
development
based
on
Peconic
River
water
quality
protection
goals.
SCDHS,
NYSDEC,

SCPD,
PEP
Management
Conference,
local
governments
(
to
be
coordinated
with
Nitrogen
Management
Work
Group)
Post­
CCMP
EPA
 
0.1
FTE
NYSDEC
 
0.1
FTE
SCDHS
 
0.1
FTE
SCPD
 
0.1
FTE
R
N­
6.5
Evaluate
nitrogen
loading
impacts
when
reviewing
Core
Preservation
Area
hardship
applications.
SCDHS,
NYSDEC,

SCPD,
PEP
Management
Conference,
local
governments
(
to
be
coordinated
with
Nitrogen
Management
Work
Group)
Ongoing
Included
in
Actions
N­
1
and
N­
2
C/
O
Table
continued
on
next
page
C
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Peconic
Estuary
Program
CCMP
Table
3­
3.
Nutrients
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
N­
6.6
Ensure
that
the
public
acquisition
of
private,
vacant
lands
in
Core
Preservation
Areas
within
the
Peconic
River
ground
watershed
are
given
high
priority.
SCDHS,
NYSDEC,

SCPD,
local
governments
(
co­
leads),

PEP
Management
Conference
(
to
be
coordinated
with
Nitrogen
Management
Work
Group)
Ongoing
Included
in
Actions
N­
1
and
N­

2,
and
Step
N­
6.1
R
N­
6.7
Utilize
the
strictest
practicable
standards
when
reviewing
Peconic
River
Development
Plans
(
e.
g.,

require
open
space
dedications,
maximum
practicable
setbacks
from
the
river,
and
natural
landscaping
to
eliminate
or
minimize
fertilizer
use).
SCDHS,
NYSDEC,

SCPD,
local
governments
(
co­
leads),

PEP
Management
Conference
(
to
be
coordinated
with
Nitrogen
Management
Work
Group)
Ongoing
Included
in
Actions
N­
1,
N­
2,

and
N­
3
R
N­
6.8
Evaluate
the
application
of
model
ordinances
such
as
the
Harbor
Protection
Overlay
District
and
model
stormwater
runoff
ordinances.
PEP
Management
Conference,
Local
Government
Committee
Post­
CCMP
LGC
 
0.1
FTE
for
each
town
R
N­
7
Ensure
that
Funding
is
Distributed
Evenly
Between
Preservation
and
Mitigation
Projects.
(
Objectives
2,
3,
and
4)

N­
7.1
Priority
Evaluate
programs
in
which
a
50/
50
split
for
funding
of
preservation
and
mitigation
efforts
can
be
applied
(
e.
g.,

Section
319
Nonpoint
Source
Implementation;
NYS
Clean
Water/
Clean
Air
Bond
Act)
and
determine
mechanisms
for
its
implementation.
PEP
Management
Conference
Post­
CCMP
Base
Program
C/
N
Table
continued
on
next
page
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
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3­
48
Table
3­
3.
Nutrients
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
N­
8
Integrate
PEP
Recommendations
into
Other
Programs.
(
Objectives
1,
2,
3,
4,
and
5)

N­
8.1
Priority
Integrate
PEP
recommendations
into
existing
land
use
and
regulatory
programs,
including
the
SEQRA
regulations
(
6NYCRR
Part
617),
Article
8
of
the
Environmental
Conservation
Law,
Suffolk
County
Water
Quality
Coordinating
Committee,
Suffolk
County
Planning
Commission
reviews,
the
Southold
Ground
Watershed
Protection
and
Water
Supply
Management
Strategy,
the
Wild,
Scenic
and
Recreational
Rivers
statute
and
regulations
(
6NYCRR
Part
666),
the
Freshwater
Wetlands
regulations
(
6
NYCRR
Part
663),
the
Tidal
Wetlands
Land
Use
regulations
(
6
NYCRR
Part
661),
and
the
Protection
of
Waters
regulations
(
6
NYCRR
Part
608).
PEP
Management
Conference
(
lead),

Nitrogen
Management
Work
Groups,
Suffolk
County
Planning
Commission,
NYSDEC
Post­
CCMP
No
new
FTEs
R
N­
9
Sponsor
and
Coordinate
Research
and
Information
Gathering.
(
Objectives
2,
3,
4,
and
5)

N­
9.1
Continue
to
sponsor
and
coordinate
research
efforts
addressing
nutrient­
related
issues.
PEP
Technical
Advisory
Committee
(
TAC)
(
lead)
Ongoing
EPA
 
0.1
FTE
NYSDEC
 
0.1
FTE
SCDHS
 
0.1
FTE
C/
N
N­
9.2
Establish
a
PEP
land
cover
initiative
to
assist
in
nutrient
loading
analyses.
PEP
Management
Conference
through
contractor
(
lead),

NYSDOS
Begun
Fall
1999
($
75,000
initial
effort)
C/
O
N­
9.3
Priority
Update
the
land
use
database
on
a
regular
basis
and
prepare
a
proposal
outlining
the
objectives
and
needs
for
a
long­
term
monitoring
program.
SCPD
(
lead),
PEP
Management
Conference
2002
SCPD
 
0.2
FTE/
yr
R
N­
9.4
Continue
to
integrate
atmospheric
deposition
data
into
PEP
modeling
and
management
activities.
Assess
how
reductions
in
atmospheric
sources
through
the
Clean
Air
Act
will
affect
nitrogen
loadings
in
the
Peconic
System.
PEP
(
lead),
EPA
Ongoing
EPA
 
0.1
FTE
C/
O
Table
continued
on
next
page
C
H
A
P
T
E
R
T
H
R
E
E
3­
49
Peconic
Estuary
Program
CCMP
Table
3­
3.
Nutrients
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
N­
9.5
Continue
to
incorporate
groundwater
information
in
PEP
characterization,
modeling,
and
management
activities.
This
includes
ongoing
groundwater
monitoring
programs,
as
well
as
improvements
to
modeling.
PEP
Management
Conference
(
lead)
Ongoing
SCDHS
 
0.1
FTE
C/
O
N­
9.6
Continue
to
incorporate
PEP
TAC
and
external
peer
review
in
the
modeling
development
and
application
process,
which
includes
dependent
analyses
of
water
quality
and
pollution
input
studies.
As
the
model
process
is
completed,
continue
to
solicit
and
use
TAC
and
external
peer
review
in
developing
programs
and
interpreting
and
applying
data.
Model
Evaluation
Group,
PEP
TAC
(

coleads
Ongoing
Included
in
Actions
N­
1
and
N­
3
C/
O
N­
10
Monitor
Conditions
Within
the
Estuary
System
to
Determine
the
Effectiveness
of
Management
Strategies.
(
Objectives
2,
3,
4,
and
5)

N­
10.1
Continue
monitoring
the
effectiveness
of
remedial
actions
at
the
Corwin
Duck
Farm.
USDA­
NRCS,

SCSWCD
(
co­
leads),

Nitrogen
Management
Work
Groups
Ongoing
USDA­
NRCS
 
0.05
FTE
SCSWCD
 
0.05
FTE
C/
O
N­
10.2
Develop
and
conduct
a
long­
term
surface
water
monitoring
program,
with
input
from
the
PEP
TAC.
SCDHS
(
lead),
PEP
Post­
CCMP
See
Environmental
Monitoring
Plan
C/
O
N­
10.3
Issue
a
biennial
update
to
the
SCDHS
surface
water
quality
report.
SCDHS
(
lead)
Post­
CCMP
SCDHS
 
0.2
FTE/
every
two
years
R
N­
10.4
Continue
monitoring
groundwater
impacts
of
various
land
uses,
such
as
residences,
farms,
and
golf
courses.
SCDHS
(
lead)
Ongoing
SCDHS
 
0.2
FTE
C/
O
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
50
Figure
3­
1.
Location
of
Eelgrass
Beds
&
Routine
Marine
Surface
Water
Monitoring
Stations.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
51
Figure
3­
2.
Regional
Planning
Area
Boundaries.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
52
Figure
3­
3.
Water
and
Sediment
Quality
Technical
Characterization
Framework.
Water
&
Sediment
Quality
Technical
Characterization
Framework
Land
Use
Land
Cover
Pollutant
Loads
Groundwater
Model
Surface
Water
Monitoring
&
Modelling
Groundwater
Measurement
Toxics
Sediment
Accretion
Sediment
Flux
Brown
Tide
Research
Atmospheric
Loadings
Direct
Loadings
Water
Column
Sediment
Land
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
53
Figure
3­
4.
Routine
Marine
Surface
Water
Monitoring
Program.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
54
Figure
3­
5.
Mean
Summer
Total
Nitrogen
Concentrations.
0.10
0.20
0.30
0.40
0.50
0.60
0.70
0.0
5.0
10.0
15.0
20.0
25.0
Main
Stem
TN
(
mg/
l)

Transect
Distance
from
Mouth
of
Peconic
River
(
miles)
Mean
Summer
Total
Nitrogen
(
TN)
Concentrations
(
July­
Sept.,
1994­
96)

Proposed
TN
Guideline
(
for
DO)
(
0.45
mg/
l)

Proposed
Shallow
Water
TN
Criterion
(
0.4
mg/
l)
*
240
*
170
130
113
114
116
Note
*
=
Frequent
or
Occasional
D.
O.
Std.
Violations
Flanders
Bay
Great
Peconic
Bay
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
55
Figure
3­
6.
Average
Summer
Light
Extinction
Coefficients.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
56
Figure
3­
7.
Creek
Embayment
Mean
Summer
Total
Nitrogen
Concentrations.
0.10
0.20
0.30
0.40
0.50
0.60
0.70
0.0
10.0
20.0
30.0
40.0
Main
Stem
North
Fork
South
Fork
Shelter
Is.
Creek/
Embayment
Mean
Summer
TN
Concentrations
TN
(
mg/
l)

Transect
Distance
from
Mouth
of
Peconic
River
(
miles)
Proposed
TN
Guideline
(
for
DO)
(
0.45
mg/
l)

Notes
*
=
Frequent
or
Occasional
D.
O.
Std.
Violations;
^
=
not
above
guideline
for
Mar­
Nov;
station
220*
omitted
(
far
above
guideline);
data
from
Jul.­
Sep.,
1988­
96
baseline
for
main
stem
stations,
1994­
96
for
other
stations.
*

*
*
101
*
103
107
109
111
112^
106
*
119
124
122
104
127^
126^

131^

132
133
134
135
Proposed
Shallow
Water
TN
Criterion
(
0.4
mg/
l)

Flanders
Bay
Great
Peconic
Bay
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
57
Figure
3­
8.
Routine
Marine
Surface
Water
Monitoring
Program
Summer
Dissolved
Oxygen
(
DO)
Conditions
 
Surface
Samples.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
58
Figure
3­
9.
Nitrogen
Loading
Trends.
0
1000
2000
3000
4000
5000
1900
1920
1940
1960
1980
2000
Duck
Farms
­
Western
Estuary
Nonpoint
Source
­
Western
Estuary
Nonpoint
Source
­
Eastern
Estuary
Mean
Total
Nitrogen
Load
(
Lb/
Day)
Peconic
Estuary
­
Nitrogen
Loading
Trends*

*
Estimates
are
for
major
regional
sources
only.
"
Western
Estuary"
is
Peconic
River
&
Flanders
Bay.
Assumes
10
year
lag
for
groundwater
transport
of
nonpoint
sources.
All
estimates
are
preliminary,
and
loading
estimates
prior
to
1960
are
gross.
+
3,100
lb/
day
­
1,300
lb/
day
+
1,400
lb/
day
26
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
59
Figure
3­
10.
Land
Uses
in
Peconic
Estuary
Study
Area
(
1995).
Land
Uses
in
Peconic
Estuary
Study
Area
(
1995)

Western
Area
Eastern
Area
41,200
Acres
87,100
Acres
40%
Of
Study
Area
Acreage
is
Subject
to
Development
Residential,
Commercial,
&
Industrial
43%
Open
Space
29%

Vacant
15%
Agriculture
14%
Residential,
Commercial,
&
Industrial
39%
Open
Space
24%

Vacant
27%
Agric.
10%
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
60
Figure
3­
11.
Total
Nitrogen
Load
by
Land
Use.
0
1000
2000
3000
4000
5000
6000
Acres/
10
Fertilizer
(
lb/
day)

Sanitary
(
lb/
day)

Other/
aggregated
(
lb/
day)
Total
Nitrogen
(
TN)
Load
by
Land
Use
TN
Load
(
Lb/
Day)
and
Land
Use
(
Acres/
10)

TN
Loads
and
Land
Use
Type
Residential
Agriculture
Vacant/
Open
Space
Other
TN
ACRES
TN
ACRES
TN
ACRES
TN
ACRES
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
61
Figure
3­
12.
Estimated
Groundwater
Total
Nitrogen
Concentrations
Worst­
Case
Conditions.
0
2
4
6
8
10
12
North
Fork
South
Fork
Shelter
Island
Existing
Potential
Estimated
Groundwater
Total
Nitrogen
(
TN)
Concentrations
Worst­
Case
Conditions
*

*
Full
build­
out,
except
no
agricultural
conversion.
Regions
shown
in
graph
are
all
east
of
Flanders
Bay
TN
(
mg/
l)
9
mg/
l
3
mg/
l
3
mg/
l
10.7
mg/
l;
+
19%
(+
400
lb/
d)

4.4
mg/
l;
+
47%
(+
150
lb/
d)
4.8
mg/
l;
+
64%
(+
1,200
lb/
d)
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
62
Figure
3­
13.
Western
Estuary
­
Potential
Worst­
Case
Groundwater
Degradation.
0
2
4
6
8
10
12
Peconic
River
W/
O
Gauge
Peconic
River
East
North
Flanders
Bay
South
Flanders
Bay
Addition
Existing
Western
Estuary
­
Potential
Worst­
Case
Groundwater
Degradation
(
Full
build­
Out,
No
Agricultural
Conversion)

TN
(
mg/
l)

+
2.1
mg/
l
(+
420
lb/
day)
lb/
day
0.7
mg/
l
6
mg/
l
+
0.9
mg/
l
(+
100
lb/
day)
9
mg/
l
+
1.3
mg/
l
(+
60
lb/
day)

3
mg/
l
+
1.6
mg/
l
(+
120
lb/
day)
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
63
Figure
3­
14.
Estimated
Groundwater
Total
Nitrogen
Concentrations
No
Open
Space
and
Worst­
Case
Conditions.
0
2
4
6
8
10
12
14
North
Fork
South
Fork
Shelter
Island
Full
Build­
Out
No
Open
Space
Existing
Estimated
Groundwater
Total
Nitrogen
(
TN)
Concentrations
(
No
Open
Space
and
Worst­
Case
Conditions)*

9
mg/
l
1.7
mg/
l(+
19%)
1.7
mg/
l(+
19%)

*
Full
build­
out,
except
no
agricultural
conversion.
Regions
shown
in
graph
are
all
east
of
Flanders
Bay
All
percentages
are
calculated
in
relation
to
existing
groundwater
concentrations.
1.4
mg/
l
(+
47%)
1.8
mg/
l(+
64%)

3.5
mg/
l
(+
117%)
3.1
mg/
l(+
103%)

3
mg/
l
3
mg/
l
Western
estuary
TN
loading
would
increase
by
82%
with
no
open
space.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
64
Figure
3­
15.
Regional
Groundwater
Quality.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
65
cfs
=
cubic
feet
per
second
Figure
3­
16.
Groundwater
Inflow
Budget.
Groundwater
Inflow
Budget
*
Peconic
River
long­
term
mean
flow
as
measured
at
USGS
gauge.
**
West
Estuary
is
downstream
of
USGS
gauge,
and
includes
Flanders
Bay
&
western
Great
Peconic
Bay.
13%

19%

16%
45%
7%
Peconic
River*
(
37
cfs)

West
Estuary*
(
54
cfs)

South
Fork
(
127
cfs)

North
Fork
(
44
cfs)
Shelter
I.
(
20
cfs)
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
66
Figure
3­
17.
Total
Nitrogen
Loading
to
Peconic
River
and
Flanders
Bay.
Total
Nitrogen
Loading
to
Peconic
River
&
Flanders
Bay
0
200
400
600
800
1000
1200
1400
1600
1800
2000
Point
Nonpoint
Lb/
Day
Total
N
Peconic
River
(
140)
Riverhead
STP
(
170)
Meetinghouse
Creek
(
110)

Sediment
Flux
(
250)
Groundwater
(
1,320)

(
East
of
Peconic
River
USGS
Gauge
Station)
Atmosphere
(
160)
Stormwater
Runoff
(
30)
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
67
Figure
3­
18.
Total
Nitrogen
Loading
East
of
Flanders
Bay.
Peconic
Estuary
­
Total
Nitrogen
Loading
East
of
Flanders
Bay
0
5000
10000
15000
20000
25000
30000
Point
Nonpoint
Lb/
Day
Total
N
STPs
(
20)
Sediment
Flux
(
13,600)
Groundwater
(
4,500)
Atmosphere
(
6,900)
Stormwater
Runoff
(
100)
Peconic
Estuary
Program
CCMP
C
H
A
P
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E
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68
Figure
3­
19.
Surface
Water
Monitoring
Program
Percentage
of
Stations
with
Dissolved
Oxygen
(
DO)
Standard
Violations
vs.
Total
Nitrogen
(
TN)
Ranges.
0
10
20
30
40
50
60
70
80
90
100
Low
TN
Stations
Transition
TN
Stations
High
TN
Stations
Very
High
TN
Stations
Infrequent
(
1
violation
only)

Occasional
(
2­
5%
of
samples)

Frequent
(>
10%
of
samples)
Peconic
Estuary
Surface
Water
Monitoring
Program
Percentage
of
Stations
with
Dissolved
Oxygen
(
D.
O.)
Standard
Violations
vs
TN
Ranges
%
Stations
With
Violations
Station
Groups
by
Average
Total
Nitrogen
(
TN)
Ranges
(#=
number
of
stations
in
each
TN
range;
TN
data
averaged
for
1994­
96)
(<
0.39
mg/
l
TN)
(
0.39­
0.47
mg/
l
TN)
(
0.47­
0.5
mg/
l
TN)
(>
0.65
mg/
l
TN)
#
=
18
#
=
11
#
=
3
#
=
3
(
Surface
Samples)

Frequency
of
D.
O.
Standard
(
5
mg/
l)
Violation
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
T
H
R
E
E
3­
69
Figure
3­
20.
Total
Nitrogen
(
TN)
and
Dissolved
Oxygen
(
DO)
Standard
Violations
Summer
Conditions.
0.1
0.2
0.3
0.4
0.5
0.6
0.7
Total
Nitrogen
(
TN)
and
Dissolved
Oxygen
(
DO)
Standard
Violations
Summer
Conditions
*
(
Sorted
by
Descending
TN,
and
Divided
by
D.
O.
Standard
Violation
Categories)

mg/
l
Monitoring
Station
Data
Sorted
by
Descending
Mean
TN
(
excl.
Sta.
220)
Frequent
or
Occasional
DO
Std.
Viol.
Infrequent
or
No
DO
Standard
Violations
0.45
mg/
l
*
Stations
107
(
Town
Creek)
,
126/
127
(
Sag
Harbor),
&
131
(
Northwest
Creek)
are
also
recommended
as
mitigation
priorities
due
to
elevated
TN
&
depressed
mean
D.
O.

*
107
*
127
*
126
*
131
220
(
Meetnghs
Crk)

TN
*
July
through
September
data
through
1996.
TN
=
5.0
mg/
l
Peconic
Estuary
Program
CCMP
C
H
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70
Figure
3­
21.
Location
of
Macroalgae
(
1994).
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
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E
3­
71
Figure
3­
22.
Proposed
Nitrogen
Management
Work
Groups.
Peconic
Estuary
Program
NITROGEN
MANAGEMENT
WORK
GROUPS
General
Process
and
Charges
 
Timing
2000­
2001
(
initial
meetings):
2001
(
strategy)
 
Leads:
Office
of
the
Suffolk
County
Executive
(
Agricultural
Work
Group);
EPA
(
Non­
Agricultural
Work
Group);
SCDHS
(
West
Estuary
TMDL
Work
Group)
 
Start­
up:
Review
PEP
background
&
nitrogen
management
process
Establish
committee
membership
list,
charges,
and
goals/
timelines
 
Process/
Charges:
 
Use
existing
PEP
guidance/
data
(
land
use,
water
quality,
pollution
loading,
model
results,
etc.)
 
Evaluate
existing
programs,
as
needed
(
land
use
and
pollution
control)
 
Develop
strategy
(
including
timeline,
responsibilities,
and
cost
evaluation)
for
setting
and
attaining
loading
targets
and
implementing
load
controls
(
considering
alternatives,
cost
&
benefits)
 
Coordinate
management
and
monitoring
with
other
efforts
(
e.
g.,
critical
natural
resource
areas)

(
1)
Agricultural
Work
Group
(
Leads:
Office
of
Suffolk
County
Executive
and
PEP
Citizens'
Advisory
Committee
representative)
Core
Membership:
 
Cornell
Coop.
Ext.,
SCSWCD/
NRCS,
CCE,
L.
I.
Farm
Bureau,
NYS
Dept.
of
Ag.
&
Markets
 
NYSSWCC
 
NYSDEC,
EPA,
SC,
Town
Reps
 
Also:
Other
interested
MC,
TAC,
&
CAC
reps
Specific
Goals:
 
Refine
agricultural
total
nitrogen
(
TN)
loading
estimates
 
Develop
implementation
plan
for
regional
TN
load
reductions,
and
possibly
other
pollutants
­
Expand
Agricultural
Environmental
Management
Initiative
­
Consider
"
Purchase
of
Development
Rights"
link
to
farm
management
plans
(
2)
Non­
Agricultural
(
mainly
residential)
Work
Group
(
Leads:
EPA
and
Local
Government
Committee
designee)
Core
Membership:
 
EPA,
NYSDEC,
SC,
Town
Reps
 
Also:
Other
interested
MC,
TAC,
&
CAC
reps
Specific
Goals:
 
Develop
implementation
plan
strategy
for:
­
existing
TN
loading
(
primarily
residential
BMP­
type
abatement)
­
potential
new
development
TN
loading
(
primarily
residential
land
use
planning)
­
possibly
other
pollutants
(
toxics,
coliforms,
etc.)
 
May
include
recommendations
on
land
use
and
pollution
control,
including
model
programs,
zoning,
clearing
restrictions,
clustering,
fertilizer
controls,
etc.

(
3)
West
Estuary
Total
Maximum
Daily
Load
(
TMDL)
Work
Group
(
SCDHS
lead)
Core
Membership:
 
SC,
NYSDEC,
EPA,
Brookhaven,
Riverhead,
and
Southampton
Towns
 
Other
interested
MC,
TAC,
&
CAC
reps
Specific
Goals:
 
Refine
TN
loading
estimates
in
westernmost
Peconic
Estuary
 
Develop
strategy
for
setting
and
implementing
regional
TN
load
reductions
­
Provide
support
for
including
dissolved
oxygen­
impaired
waters
on
the
New
York
State
2002
Clean
Water
Act
Section
303(
d)
list
and
the
establishment
of
a
TMDL
as
a
management
tool;
consider
Peconic
River
(
freshwater)
model
­
Additional
industrial/
commercial
land
use/
pollution
control
planning
is
required
Peconic
Estuary
Program
CCMP
C
H
A
P
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E
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T
H
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