Document ID: EPA-HQ-OW-2002-0049-0104
Agency: epa
Document Type: Supporting & Related Material
Title: 
Posted Date: 2003-03-19T05:00Z

Peconic
Estuary
Program
C
H
A
P
T
E
R
F
O
U
R
4­
1
C
H
A
P
T
E
R
FOUR
HABITAT
AND
LIVING
RESOURCES
MANAGEMENT
PLAN
OBJECTIVES
1)
Preserve
and
enhance
the
integrity
of
the
ecosystems
and
natural
resources
present
in
the
study
area
so
that
optimal
quantity
and
quality
of
fish
and
wildlife
habitat
and
diversity
of
species
can
be
assured
and
conservation
and
wise
management
of
the
consumable,
renewable
natural
resources
of
the
estuary
are
promoted
and
enhanced.

2)
Protect
and
enhance
biogeographical
areas
within
the
Peconic
watershed
with
concentrations
of
high
quality
spawning,
breeding,
feeding,
and
wintering
or
seasonal
habitat
for
shellfish,
finfish,
waterfowl,
shorebirds,
anadromous
fish,
and
rare
plant,
animal,
and
natural
communities.

3)
Protect
and
enhance
the
ecosystems
and
the
diversity
of
ecological
communities
and
habitat
complexes
throughout
the
system,
particularly
tidal
wetlands,
eelgrass
meadows,
and
beaches
and
dunes
by
preventing
or
minimizing
loss,
degradation,
and
fragmentation
and
by
maintaining
and
restoring
natural
processes
essential
to
the
health
of
the
estuary
and
its
watershed.

4)
Restore
degraded
habitats
to
maintain
or
increase
native
species
and
community
diversity,
provide
connectivity
of
natural
areas,
and
expand
existing
natural
areas.

5)
Foster
recreational
and
commercial
uses
of
the
Peconic
Estuary
that
are
sustainable
and
compatible
with
protection
of
biodiversity.

6)
Protect
and
enhance
species
which
are
endangered,
threatened,
or
of
special
concern
throughout
the
system
by
mitigating
stresses
to
these
species
and
ensuring
essential
habitats
crucial
for
their
survival.

7)
Promote
coordination
and
cooperation
among
Federal,
state,
and
local
governments
and
stakeholders
to
maximize
protection,
stewardship,
and
restoration
of
the
Peconic
Estuary.

8)
Develop
and
carry
out
an
estuary­
wide
research,
monitoring,
and
assessment
program
to
guide
and
evaluate
management
decisions
concerning
the
estuary
and
to
ensure
management
and
policy
decisions
are
based
on
the
best
available
information.
Peconic
Estuary
Program
CCMP
C
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MEASURABLE
GOALS
Priority
living
resource
issues
for
the
Peconic
Estuary
include
submerged
aquatic
vegetation,
shellfish,
finfish
habitat,
and
"
critical
areas"
(
areas
of
particular
ecological
significance).
The
PEP
has
designated
Critical
Natural
Resource
Areas
(
CNRAs:
geographically
specific
locations
that
have
significant
biodiversity)
and
has
convened
a
Habitat
Restoration
Work
Group
to
address
the
enhancement
of
existing
resources
and
the
restoration
of
habitats.
While
the
list
of
threatened
and
impaired
natural
resources
is
extensive,
the
PEP
has
established
management
priorities
focused
on
protecting
existing
resources,
restoring
damaged
habitats,
and
enhancing
the
integrity
of
the
ecosystem
so
that
the
quantity
and
quality
of
fish
and
wildlife
can
be
assured.

The
PEP's
measurable
goals
with
respect
to
habitat
and
living
resources
include:

 
Protect
the
high
quality
habitats
and
concentrations
of
species
in
the
Critical
Natural
Resource
Areas
(
measured
by
acres
of
open
space
protected
and
development
of
model
ordinances).
[
See
Actions
HLR­
1,
HLR­
6,
HLR­
10,
HLR­
11,
HLR­
13,
HLR­
14,
HLR­
15,
HLR­
16]

 
Maintain
current
linear
feet
of
natural
shoreline
and
over
the
next
15
years
reduce
shoreline
hardening
structures
by
five
percent
(
measured
by
the
percent
change
of
natural
vs.
hardened
shorelines
through
GIS
mapping).
[
See
Actions
HLR­
1,
HLR­
2,
HLR­
5,
HLR­
8,
HLR­
13,
HLR­
15]

 
Maintain
current
eelgrass
acreage
(
2,100
acres
in
main
stem
of
the
estuary)
and
increase
acreage
by
ten
percent
over
10
years
(
measured
by
inter­
annual
aerial
surveys
with
GIS
and
SCUBA
assessments).
[
See
Actions
HLR­
1,
HLR­
3,
HLR­
4,
HLR­
6,
HLR­
9,
HLR­
10,
HLR­
15,
HLR­
16]

 
Maintain
and
increase
current
tidal
and
freshwater
marsh
acreage,
and
restore
areas
that
have
been
degraded
(
e.
g.,
restricted
flow,
Phragmites
australis
dominated,
hardened
shoreline)
(
measured
as
number
of
acres
of
marsh
with
GIS).
[
See
Actions
HLR­
1,
HLR­
2,
HLR­
4,
HLR­
5,
HLR­
7,
HLR­
8]

 
Maintain
a
policy
of
no
new
mosquito
ditches
and
not
re­
opening
ditches
that
have
filledin
by
natural
processes;
and
restore
10­
15
percent
of
mosquito
ditched
marshes
through
Open
Marsh
Water
Management
(
measured
by
the
number
of
acres
of
restored
tide
marsh
using
Open
Marsh
Water
Management).
[
See
Actions
HLR­
1,
HLR­
2,
HLR­
5,
HLR­
7,
HLR­
8]

 
Increase
the
number
of
piping
plover
pairs
to
115
with
productivity
at
1.5
(
over
a
threeyear
average),
distributed
across
the
nesting
sites
in
the
Peconic
Estuary
(
measured
by
annual
piping
plover
surveys).
[
See
Actions
HLR­
1,
HLR­
8,
HLR­
13,
HLR­
15,
HLR­
16]

 
Develop
recommendations
and
guidelines
to
reduce
impacts
to
marine
life
from
dredging­
related
activities
(
measured
by
amount
of
reduced
dredging
volumes
and
protected
benthic
habitat
acreage).
[
See
Actions
HLR­
1,
HLR­
3,
HLR­
5,
HLR­
6,
HLR­
15]

 
Foster
sustainable
recreational
and
commercial
finfish
and
shellfish
uses
of
the
Peconic
Estuary
that
are
compatible
with
biodiversity
protection
(
measured
by
juvenile
finfish
trawl
surveys,
bay
scallop
landings,
and
identifying,
protecting,
and
restoring
key
shellfish
and
finfish
habitat).
[
See
Action
HLR­
1,
HLR­
11,
HLR­
12]
Peconic
Estuary
Program
CCMP
C
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3
 
Enhance
the
shellfish
resources
available
to
harvesting
through
reseeding,
creation
of
spawning
sanctuaries
and
habitat
enhancement
(
measured
by
scallop
and
clam
abundance/
landings).
[
See
Actions
HLR­
4,
HLR­
7,
HLR­
8,
HLR­
9,
HLR­
10,
HLR­
12,
HLR­
16,
HLR­
17]

 
Link
land
usage
with
habitat
quality
in
tidal
creeks
(
measured
by
continued
funding
of
benthic
and
water
quality
surveys
to
measure
the
quality/
impacts
to
the
habitats
within
selected
tidal
creeks).

 
Ensure
that
the
existing
and
future
aquaculture
(
shellfish
and
finfish)
and
transplanting
activities
are
situated
in
ecologically
low­
productive
areas
of
the
estuary
and
that
they
are
mutually
beneficial
to
the
aquaculture
industry,
natural
resources,
and
water
quality
(
measured
by
the
extent
and
location
of
aquaculture/
transplant
facilities,
water
quality
measures,
and
natural
resource
data).
[
See
Actions
HLR­
1,
HLR­
3,
HLR­
4,
HLR­
6,
HLR­
10,
HLR­
15,
HLR­
17]

 
Annually
initiate
five
percent
of
the
projects
identified
in
the
Habitat
Restoration
Workgroup
Plan
for
the
Peconic
Estuary
(
measured
by
the
number
of
projects
funded
and
implemented
annually).
[
See
Actions
HLR­
7,
HLR­
8]
Peconic
Estuary
Program
CCMP
C
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INTRODUCTION
The
eastern
end
of
Long
Island,
New
York
and
the
Peconic
Estuary
contain
a
large
variety
of
natural
communities,
from
dwarf
pitch
pine
forests
to
soft­
bottom
benthos
in
the
main
bays;
all
of
which
are
important
to
the
ecology
and
productivity
of
this
ecosystem.
There
is
a
larger
percentage
of
undisturbed
habitats
and
a
greater
diversity
of
natural
communities
within
this
watershed,
on
a
per
unit
area
basis,
than
anywhere
else
in
the
coastal
zone
of
New
York
State.
These
communities
are
home
to
a
number
of
species
that
are
endangered
or
threatened
globally,
nationally,
and
locally.
According
to
the
New
York
State
Natural
Heritage
Program,
there
are
111
endangered,
threatened,
rare,
or
special
concern
terrestrial
and
freshwater
species
documented
in
the
Peconic
Estuary
and
its
watershed
 
13
insects,
one
freshwater
fish,
two
amphibians,
one
reptile,
12
birds,
and
82
vascular
plants.
There
are
a
total
of
553
separate,
confirmed
occurrences
of
these
111
species
in
the
watershed.
Another
45
rare
species
 
one
amphibian
and
the
rest
plants
 
have
been
historically
reported
in
the
Peconics
but
have
not
been
documented
recently.
In
addition
to
these,
there
are
four
species
of
endangered
or
threatened
sea
turtles
and
eight
species
of
marine
mammals
(
seals,
porpoises,
and
whales)
which
are
found
in
or
migrate
through
the
Peconic
Estuary.

Many
economically
important
species
spend
all
or
part
of
their
lives
in
the
estuary.
These
species
enhance
the
productivity
of
the
estuary
and
its
contiguous
waters.
The
Peconic
Estuary
provides
important
habitat,
as
well
as
spawning
and
nursery
grounds,
to
a
wide
variety
of
marine
organisms
 
most
notably
shellfish,
such
as
bay
scallops,
hard
clams,
and
fish,
such
as
bay
anchovy,
Atlantic
silverside,
scup
(
also
called
porgy),
summer
flounder
(
also
called
fluke),
winter
flounder,
windowpane
flounder,
weakfish
(
also
called
grey
sea
trout),
and
tautog
(
also
called
blackfish).
One
of
the
most
important
underwater
habitats
of
the
estuary
is
the
meadows
of
eelgrass
found
along
the
edges
of
the
eastern
end
of
the
Peconic
Estuary.
These
eelgrass
beds
provide
food,
shelter,
and
nursery
grounds
to
many
marine
animals
including
worms,
shrimp,
scallops
and
other
bivalves,
crabs,
and
fish.
Eelgrass
beds
stabilize
the
bay
bottom
and
are
also
an
important
component
of
the
nutrient
cycle
in
the
estuary.

In
addition
to
individual
species,
there
are
entire
habitats
or
natural
communities
rarely
found
on
the
east
coast
of
the
United
States
and
only
found
in
this
region
of
the
State,
such
as
the
Pine
Barrens.
Some
of
these
habitats
are
currently
in
danger
of
being
reduced
to
remnants
or
of
being
lost
completely.
It
is
for
these
reasons
that
The
Nature
Conservancy
designated
the
Peconic
Bioreserve
as
one
of
the
Last
Great
Places
in
the
Western
Hemisphere.

HABITATS
AND
LIVING
RESOURCES
OF
THE
PECONIC
ESTUARY
SYSTEM
The
Peconic
Estuary
Program
(
PEP)
identified
species
of
"
special
emphasis"
which
are
plants
and
animals
that
have
been
identified
as
Federal
trust,
endangered
or
threatened,
State
protected,
natural
heritage
listed,
and
of
commercial
and
recreational
importance.

For
convenience
in
discussing
the
variety
of
habitats
and
species
found
in
the
Peconic
Estuary
System,
this
chapter
has
divided
the
estuary
system
into
several
zones.
Each
of
these
zones
are
discussed
individually
 
first
in
terms
of
the
habitat
and
living
resources
associated
with
the
zone,
and
second
in
relation
to
observed
impacts
and
impairments.
These
zones
consist
of
the:
1)
deep
water;
2)
shallow
water
(
including
embayments);
3)
intertidal­
shoreline;
4)
Peconic
River,
freshwater
wetlands,
and
coastal
ponds;
and
5)
terrestrial
zones.
A
detailed
description
of
the
ecology
of
these
Peconic
Estuary
Program
CCMP
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areas
has
also
been
described
in
the
separate
Living
Resources
of
the
Peconic
Estuary
Characterization
Report.

Deep
Water
Zone
The
deep­
water
zone
is
defined
for
this
program
as
that
portion
of
the
main
stem
of
the
estuary
in
which
the
water
depth
is
greater
than
three
meters
(
approximately
10
feet).
These
open
waters
of
the
Peconic
Estuary
include
most
of
Flanders,
Great
Peconic,
Little
Peconic,
Noyack,
Southold,
and
Gardiners
Bays;
portions
of
Northwest
and
Orient
Harbors;
and
Shelter
Island
Sound.
This
zone
includes
everything
from
the
overlying
water
column
to
the
bottom
communities.

Finfish
The
deep,
open
waters
contain
a
large
portion
of
the
adult
finfish,
which
are
harvested
commercially
or
recreationally
in
the
Peconic
Estuary
System.
To
assess
the
use
of
deep
waters
of
the
Peconic
Estuary
by
juvenile
finfish,
the
NYSDEC
has
conducted
trawl
surveys
for
juveniles
in
the
open
waters
west
of
Shelter
Island
over
the
past
decade.
Results
from
these
trawl
surveys
indicate
that
these
waters
contain
juveniles
of
many
species
of
finfishes
and
are
an
especially
important
nursery
area
for
tautog,
weakfish,
scup,
winter
flounder,
bay
anchovy,
Atlantic
silversides,
butterfish,
bluefish,
and
northern
puffer.
Many
of
these
species
are
found
at
locations
throughout
the
estuary
and
may
seasonally
or
diurnally
move
back
and
forth
between
the
deep
and
shallow
water
zones.

Shellfish
Natural
populations
of
commercially
and
recreationally
important
shellfish
species
have
never
been
abundant
in
the
deep­
water
zone
of
the
Peconic
Estuary
System
according
to
NYSDEC
shellfish
surveys.
Natural
populations
of
hard
clams
in
waters
greater
than
approximately
four
feet
(
1.2
m),
which
were
never
very
high,
have
declined
in
abundance
as
have
the
levels
of
other,
non­
commercial
shellfish
species.
Fishermen
have
reported,
though,
that
scallops
are
common
in
greater
than
ten
feet
of
water.
At
one
time,
oysters
were
the
most
valuable
commercial
species
in
the
Peconic
Estuary
System.
The
populations
were
not
natural,
but
came
from
the
seeding
of
bottom
waters
for
grow­
out
(
primarily
in
the
deep­
water
zone).
This
practice
has
been
discontinued,
and
oysters
are
rarely
found
in
this
zone.

Other
shellfish,
which
are
found
in
the
deep
waters
in
relatively
great
abundance
(
in
both
surveys),
include
channeled
and
knobbed
whelks
(
colloquially
called
conchs
or
winkles),
slipper
shells
(
locally
called
quarterdecks),
blood
arks,
oyster
drills,
and
jingle
shells.

Other
Invertebrates
The
results
of
the
NYSDEC
juvenile
finfish
trawl
survey
and
the
PEP
deep
water
shellfish
survey
have
provided
evidence
of
the
presence
of
a
large
variety
of
other
invertebrates
inhabiting
the
system.
Species
found
in
this
zone
include
green,
lady,
and
blue
crabs,
spider
crabs,
horseshoe
crabs,
mantis
shrimp,
and
long­
finned
squid.
There
are
also
areas
of
the
bottom
in
which
the
sediment
is
completely
bound
up
in
dense
mats
of
tubes
built
by
amphipods
and
populations
of
polychaete
and
oligochaete
worms,
which
are
common
members
of
benthic
communities
throughout
the
estuary.

Birds
The
deep­
water
zone
is
used
by
a
variety
of
birds
for
feeding,
notably
sea
ducks
such
as
red­
breasted
mergansers,
three
species
of
scoters
(
Melanitta
perspicillata,
fusca,
and
nigra),
and
common
eiders.
Peconic
Estuary
Program
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Sea
ducks
are
so­
called
because
they
feed
and
rest
in
deep,
open
coastal
waters
and
rarely,
if
ever,
come
to
shore
while
in
the
Peconics.
The
sea
ducks
do
not
breed
and
rear
their
young
in
the
Peconic
system
but
use
it
exclusively
as
an
over­
wintering
site.
These
waterfowl
are
found
in
high
concentrations
during
the
early
months
of
the
year
at
a
number
of
sites
(
see
Figure
4­
1).
They
feed
primarily
on
shellfish
such
as
blue
mussels
and
benthic
invertebrates.
For
example,
diving
ducks
such
as
scaup
and
canvasbacks
are
found
in
2­
18
meters
of
water
and
feed
on
submerged
aquatic
vegetation,
bivalves
and
hard
clams.

Sea
Turtles
and
Marine
Mammals
Deep
waters
are
the
preferred
habitat
of
the
four
species
of
sea
turtles,
two
species
of
cetaceans,
(
whales,
dolphins,
and
porpoises),
and
five
species
of
pinnipeds
(
seals)
that
are
found
regularly
in
the
estuary.
All
of
these
animals
feed
on
a
variety
of
marine
organisms
in
the
open
waters.
The
most
common
species
of
pinnipeds
are
harbor
seals
and
less
common
are
the
harp
seals
and
grey
seals.
These
seals
are
found
in
association
with
a
number
of
haul­
out
areas
around
the
eastern
Peconics
and
Block
Island
Sound.
The
number
of
seals
in
the
New
York
region
has
increased
dramatically
in
the
past
decade,
and
these
animals
are
now
found
year
round
in
the
Peconics
instead
of
only
in
winter.

Only
two
species
of
cetacean
 
the
bottle­
nosed
dolphin
and
the
harbor
porpoise
 
have
been
sighted
in
the
Peconics
in
recent
history.
Occurrences
of
these
animals
in
New
York
waters
also
have
increased
greatly
in
the
past
decade.
Occasionally,
a
right
whale
has
been
sighted
in
Block
Island
Sound
and
at
the
eastern
end
of
Gardiners
Bay.

Three
of
the
four
sea
turtle
species
found
in
the
Peconics
use
the
system
extensively
at
the
end
of
April
through
October
and
a
number
are
found
in
waters
greater
than
10
feet
(
three
meters).
Kemp's
ridleys,
the
smallest
and
most
endangered
of
all
sea
turtles,
use
the
Peconics
as
juveniles
for
feeding
on
spider
crabs.
Loggerhead
turtles
and
green
sea
turtles
also
feed
in
the
system
as
juveniles
and
are
found
throughout
the
Peconics.
Studies
have
found
that
the
Peconic
bays
are
important
developmental
habitat
during
the
early
life
stages
of
Kemp's
ridley
and
green
turtles.
Leatherback
turtles
are
only
occasionally
found
in
the
estuary.

Shallow
Water
Zone
This
zone
is
defined
as
those
waters
in
the
main
bays
with
a
depth
of
less
than
three
meters
(
approximately
10
feet)
that
remain
submerged
through
the
tidal
cycle.
This
zone
also
includes
subtidal
portions
of
all
tidal
creeks,
ponds,
and
large
embayments
in
the
Peconic
Estuary.

Finfish
Many
juvenile
forms
of
finfish
are
found
to
feed
in
the
shallow
water
zone.
Some
species
of
adult
finfish
move
in
close
to
shore
to
spawn
and
reproduce
(
e.
g.,
weakfish,
winter
flounder,
and
Atlantic
silversides).
Others
spawn
in
the
ocean
and
the
larvae
move
inshore,
metamorphose,
and
the
juveniles
feed
in
the
shallow
areas
(
i.
e.,
nursery
areas)
until
they
are
large
enough
to
migrate
back
offshore
(
e.
g.,
bluefish,
summer
flounder).
Because
of
these
differential
uses
by
a
number
of
species,
the
entire
shallow
water
zone
appears
to
be
crucial
to
local
populations
of
breeding
finfish.
Past
surveys
have
indicated
that,
for
some
species
(
e.
g.,
weakfish,
winter
flounder,
and
scup),
the
area
from
Great
Peconic
Bay
to
Montauk
Point,
both
deep
and
shallow
waters,
appears
to
be
much
more
productive
than
other
estuaries
and
embayments
around
Long
Island.
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Shellfish
A
survey
of
shellfish
in
shallow,
subtidal
waters
was
performed
by
the
PEP
in
summer
1997.
Results
of
this
study
determined
that
although
shallow
water
regions
make
up
only
6.6
percent
of
the
estuary,
they
contribute
the
majority
of
the
commercial
shellfish
harvest.
Both
scallops
and
hard
clams
are
harvested
from
the
shallow
water
zone,
although
bay
scallop
populations
are
extremely
susceptible
to
the
recurring
Brown
Tide
algae
bloom.
With
the
crash
of
the
scallops
in
the
1980s
due
to
the
Brown
Tide,
East
End
fishermen
began
to
harvest
hard
clams
in
greater
numbers.
There
is
also
a
thriving
transplant
industry
in
the
Peconic
Estuary
System
with
private
harvesters
transferring
thousands
of
hard
clams
from
uncertified
waters
of
Raritan
Bay
in
New
York
Harbor
to
the
Peconic
Estuary
for
biological
cleansing
before
later
reharvest
and
sale.
Despite
greater
numbers
in
shallow
waters,
PEP
research
has
found
an
overall
low
abundance
of
clams,
indicating
the
possibility
of
low
recruitment,
high
mortality,
and/
or
preferential
harvesting
of
small
size
classes.

Birds
There
are
more
birds
feeding
in
the
shallow
water
zone
than
in
the
deep­
water
zone.
These
birds
consist
of
waders,
such
as
herons
and
egrets,
and
waterfowl
such
as
puddle
and
bay
ducks.
Puddle
ducks
(
also
called
dabbling
ducks)
are
usually
found
in
shallow
embayments
and
frequently
feed
on
land
as
well
as
in
the
water.
Black
ducks
and
mallards
are
examples
of
puddle
ducks.
Bay
ducks
are
similar
to
sea
ducks
in
that
they
spend
most
of
their
time
offshore
in
deep
waters,
although
they
remain
in
fairly
sheltered
embayments
rather
than
the
open
ocean.
Examples
of
bay
ducks
include
greater
and
lesser
scaup,
canvasbacks,
and
redheads.
Raptors
such
as
osprey
and
shorebirds
such
as
the
terns
(
e.
g.,
least
tern
and
roseate
tern)
also
depend
on
fish
in
these
areas
for
food.
Critical
areas
for
puddle
and
bay
ducks
are
shown
in
Figure
4­
1.
Wading
birds
are
found
throughout
the
estuary.

Submerged
Aquatic
Vegetation
Most
of
the
beds
of
estuarine
submerged
aquatic
vegetation
are
found
in
the
shallow
water
zone
according
to
a
PEP
study
performed
by
Cashin
Associates.
Submerged
aquatic
vegetation
is
defined
as
beds
of
rooted
vascular
plants
or
macroalgae,
both
of
which
require
complete
immersion
for
all
or
most
of
the
day
to
survive.
Submerged
aquatic
vegetation,
particularly
eelgrass,
is
of
great
ecological
importance
in
shallow
environments.
Eelgrass
beds
provide
shelter
and
food
for
a
variety
of
juvenile
finfish
and
shellfish
as
well
as
many
other
invertebrates.
Shelter
is
provided
not
only
by
the
actual
structure
of
the
eelgrass
blades
but
also
by
the
fact
that
eelgrass
beds
dampen
currents,
resulting
in
a
low
velocity
zone
among
the
blades.
Food
for
the
resident
species
is
provided
by
epiphytes
and
their
associated
grazers
on
grass
blades
as
well
as
increased
suspended
material
which
falls
to
the
bottom
as
a
result
of
the
slow
currents
within
the
beds.
These
rooted
plants
also
stabilize
the
underlying
substrate
and
prevent
scouring
and
erosion.
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Figure
4­
1.
Waterfowl
Breeding,
Migration,
&
Wintering
Areas.
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Macroalgae
beds
are
generally
considered
poorer
habitat
compared
to
eelgrass.
Since
macroalgae
are
not
rooted,
they
do
not
stabilize
soft
bottoms.
Rather,
they
are
easily
uprooted
and
can
be
carried
some
distance
where
they
foul
eelgrass
beds,
beaches,
and
bare
bottoms.

The
most
abundant
species
of
rooted
vascular
plant
in
the
shallow
water
zone
is
eelgrass,
although
some
small
areas
of
widgeon
grass
are
also
found
in
brackish
waters.
Eelgrass
beds
are
found
around
Shelter
Island
and
to
the
east
along
the
fringes
of
Gardiners
Bay
and
within
a
few
small
embayments
and
creeks
(
see
Figure
4­
2).
Critical
areas
for
eelgrass
are
currently
considered
to
be
all
those
areas
where
this
species
currently
exists.
More
areas
may
be
identified
for
restoration
purposes
after
eelgrass
habitat
criteria
studies
have
been
completed.
The
macroalgae
species
that
occur
in
greatest
abundance
throughout
the
system
are
green
fleece,
an
invasive
species,
and
sea
lettuce.
Fishermen
have
reported
sets
of
scallops
in
areas
of
green
fleece
in
the
western
portion
of
Peconic
Bay.

Intertidal/
Shoreline
Zone
As
suggested
by
the
name,
this
zone
includes
all
areas
around
the
edge
of
the
estuary
that
are
periodically
inundated
by
tides
or
are
found
upland
of
the
mean
high
tide
line.
This
includes
all
tidal
wetlands,
mud
and
sand
flats,
beaches,
and
dunes.
The
location
of
tidal
wetlands
in
the
Peconics
is
shown
in
Figure
4­
3.

Data
from
the
NYSDEC
aerial
photographs
taken
in
1974
indicate
there
were
roughly
12,466
acres
(
5,049
hectares)
of
vegetated
and
unvegetated
tidal
wetlands
in
the
Peconic
Estuary.
Approximately
3,898
acres
of
this
is
vegetated
salt
marsh
of
different
types.
According
to
the
NYSDEC's
tidal
wetlands
trends
analysis
program,
approximately
33
acres
of
high
marsh
have
been
created
in
Great
Peconic
Bay
when
comparing
the
original
1974
inventory
to
present
conditions.
According
to
the
USFWS,
approximately
256
acres
of
all
types
of
wetlands
were
lost
between
1972
and
1994.
The
definitions
for
wetlands
were
different
for
both
of
these
analyses.
A
comparison
of
these
analyses
is
being
conducted
by
NYSDEC.

Because
of
tidal
fluctuations,
this
zone
is
home
to
a
wide
variety
of
organisms,
which
are
adapted
to
the
twice­
daily
inundations
of
seawater.
There
is
an
entire
invertebrate
community,
which
is
associated
almost
exclusively
with
the
intertidal
area.
Organisms
found
only
in
these
areas
include
several
species
of
snails
and
bivalves,
fiddler
and
other
crabs,
various
species
of
polychaete
and
oligochaete
worms,
and
a
huge
variety
of
microorganisms.

Marshes
Marshes
play
an
important
role
in
estuarine
ecology.
The
vegetated
areas
stabilize
the
shoreline
and
protect
small
tidal
ponds
and
creeks,
which
are
ideal
areas
for
juvenile
fish
and
invertebrates
to
grow
and
reproduce.
The
vegetated
areas
are
also
prime
nesting
areas
for
some
species
of
waterfowl
and
waterbirds,
such
as
puddle
ducks,
which
rely
on
the
physical
protection
and
abundant
food
sources
provided
by
these
areas.
Marshes
also
provide
food
for
large
herbivores,
such
as
deer,
and
omnivores,
such
as
raccoons.
Salt
marshes
are
home
to
the
diamondback
terrapin,
an
exclusively
estuarine
reptile.
These
animals
live
in
the
marsh,
but
lay
their
eggs
in
soft
sand,
usually
at
the
upper
margins
of
the
marsh
and
beaches.
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Figure
4­
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Eelgrass.
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Figure
4­
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Tidal
Wetlands.
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The
marshes
also
play
a
role
beyond
that
of
habitat
for
birds
and
fishes
and
invertebrates.
They
provide
a
hydrologic
buffer
zone
that
acts
in
two
ways.
These
habitats
are
capable
of
filtering
a
large
amount
of
surface
runoff
from
land,
buffering
the
estuarine
waters
from
excess
nutrients
and
contaminants
that
might
be
contained
in
stormwater
runoff.
Conversely,
they
can
absorb
a
large
amount
of
floodwater
from
the
estuary
during
storm
surges.
In
this
way,
they
are
vital
as
a
transition
zone
between
the
estuary
and
the
terrestrial
environment.

Mud
and
Sand
Flats
and
Sandy
Beaches
Several
species
of
commercially
important
bivalves
are
found
on
intertidal
mudflats,
including
hard
clams
and
soft
clams.
These
areas
are
also
used
by
finfish
for
spawning
and
nursery
grounds
with
the
adults,
larvae,
and
juveniles
moving
on
and
off
these
unvegetated
areas
with
the
tides.

The
estuary
margins
are
extremely
important
to
birds.
Wading
birds
and
raptors
feed
over
the
mud
and
sand
flats
at
high
tide.
Sandy
beach
strands
are
used
for
nesting
by
shorebirds,
such
as
terns
and
plovers.
The
proximity
to
saltwater
and
a
reliable
food
source
are
key
for
these
species.

Sandy
beaches
are
found
throughout
the
system.
In
addition
to
the
endangered
beach
sand­
nesting
birds
previously
mentioned,
beaches
are
home
to
a
variety
of
rare
plants
that
are
exclusively
adapted
to
these
nutrient­
poor
environments.
These
are
all
found
upland
of
the
mean
high
tide
and
include
various
succulents
and
grasses,
such
as
seabeach
knotweed.
Horseshoe
crabs
also
actively
use
the
sandy
beaches.

Coastal
Bluffs
and
Islands
Another
habitat
found
along
open
shorelines
is
coastal
bluffs.
This
habitat
is
not
as
abundant
around
the
Peconic
Estuary
System
as
on
the
northern
shore
of
Long
Island,
but
a
few
areas
exist
in
the
Peconic
Estuary
System.
These
habitats
are
vulnerable
to
erosion
by
wind
and
waves.
Coastal
bluffs
can
support
some
vegetation,
which
stabilizes
them
to
some
extent
but
are
eventually
eroded
inland.
There
are
few
species
adapted
exclusively
to
these
areas;
erosion
is
of
concern
for
areas
immediately
landward
of
the
bluff.
Bluffs
are
an
important
part
of
the
beach
system
and
are
an
excellent
source
of
sand
for
the
beaches.
In
addition
to
the
edges
of
the
estuary
around
the
forks,
there
are
several
small
coastal
islands
(
exclusive
of
Gardiners
and
Robins
Islands)
which
could
be
considered
to
fall
within
the
intertidal/
shoreline
zone.
Although
not
strictly
within
the
PEP
study
area,
they
are
included
here
because
of
their
significance
to
the
region.
These
small,
rocky
islands
lie
east
of
Plum
Island.
They
serve
as
haul­
out
areas
for
marine
pinnipeds,
and
support
large
colonies
of
terns
(
Great
Gull
Island
in
particular).

Peconic
River,
Freshwater
Wetlands,
and
Ponds
This
zone
comprises
the
entire
freshwater
surface
drainage
of
the
Peconic
Estuary
including
freshwater
creeks
and
coastal
ponds.
The
Peconic
River
and
its
basin
make
up
the
largest
fraction
of
this
zone
in
the
study
area.

The
freshwater
environment
is
crucial
to
the
Peconic
system,
because
it
is
the
influx
of
fresh
water
that
makes
the
system
estuarine.
A
mix
of
fresh
and
salt
water
is
vital
for
the
growth
and
development
of
many
species,
some
of
which
cannot
survive
in
highly
saline
seawater.
As
with
salt
marshes,
freshwater
swamps,
bogs,
and
vernal
ponds
are
also
important
as
areas
that
absorb
and
filter
stormwater
runoff
and
support
a
variety
of
fish,
invertebrate,
and
bird
species.
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There
are
approximately
3,739
acres
of
freshwater
wetlands
in
the
Peconic
Estuary
System,
which
are
hydrologically
connected
via
permanent
surface
water
to
the
estuary
(
as
compared
to
those
that
are
connected
via
groundwater
or
are
ephemeral
wetlands).
Approximately
55
percent
of
these
are
associated
with
the
Peconic
River
and
its
tributaries,
comprising
a
total
of
2,079
acres.
There
are
also
a
number
of
small
pockets
of
freshwater
wetlands
that
do
not
connect
to
the
Peconic
River
but
are
within
the
boundaries
of
the
Peconic
Estuary
study
area.
These
pocket
wetlands
contain
many
rare
and
endangered
species
and
represent
important
habitats.

Fresh
water
ponds
connected
to
the
Peconic
River
and
the
upper
reaches
of
the
river
itself
are
home
to
a
New
York
State
listed
"
special
concern"
fish,
the
banded
sunfish,
found
only
in
pine
barren
ponds
in
the
eastern
United
States.
There
are
also
two
species
of
rare
amphibians
found
in
the
Peconic
River
basin,
the
tiger
salamander,
which
requires
quiet
ponds
with
good
water
quality
to
reproduce,
and
the
southern
leopard
frog.
The
river
and
a
few
other
streams
in
the
Peconic
region
continue
to
sustain
runs
of
alewife,
an
anadromous
fish.
Although
the
Peconic
River
has
been
dammed,
each
spring
these
fish
can
be
found
at
the
base
of
the
first
dam,
attempting
to
move
upstream.
A
temporary
fish
ladder
was
installed
in
the
spring
of
2000
to
provide
fish
passage
above
the
first
dam
in
downtown
Riverhead.
Puddle
ducks
are
also
found
in
abundance
at
several
freshwater
ponds
around
the
eastern
end
of
the
Island.

Terrestrial
Zone
Although
this
zone
makes
up
the
remainder
of
the
habitats
within
the
study
area,
a
major
focus
in
this
Management
Plan
will
be
on
natural
terrestrial
communities
that
are
directly
adjacent
to
or
heavily
influenced
by
the
presence
of
the
estuary.

The
terrestrial
zone
starts
landward
of
habitats
that
are
inundated
by
tides
but
not
including
the
Peconic
River,
freshwater
wetlands,
and
ponds.
There
are
a
number
of
characteristic
plant
communities,
which
occur
in
this
upland
coastal
zone
around
the
Peconic
Estuary.
Soil
type,
hydrology,
and
microclimates
determine
the
occurrence
of
these
communities.
Forest
types
include
maritime
red
cedar
(
found
on
the
long,
narrow
peninsula
of
Orient
State
Park),
maritime
oak
(
found
on
the
exposed
bluffs
of
Jessups
Neck
and
Mashomack
Preserve),
oak­
holly
(
on
the
Montauk
peninsula),
and
pitch­
pine
oak
(
the
dominant
community
in
the
central
Long
Island
Pine
Barrens).
The
Peconic
watershed
may
also
contain
significant
examples
of
other
communities
such
as
the
chestnut­
oak
forest.

Other
significant
coastal
upland
communities
include
remnant
maritime
grasslands
(
found
in
the
Peconics
at
Conscience
Point,
Montauk,
and
the
Shinnecock
Hills)
and
maritime
heathlands
(
found
at
Montauk
Mountain).
These
communities
consist
of
tall
grasses
and
shrubs
and
are
notable
for
their
lack
of
large
trees
and
diversity
of
specialized
plants
and
insects.

All
these
plant
communities
contain
insects,
birds,
and
other
organisms,
which
are
specifically
adapted
to
them.
In
recent
years,
nine
of
13
insect
species,
two
of
12
bird
species,
and
many
of
the
82
vascular
plants
identified
as
threatened,
endangered,
or
species
of
special
concern
have
been
documented
in
the
terrestrial
zone.
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OVERALL
QUALITY
AND
USE
IMPAIRMENTS
Impacts
to
most
of
the
habitats
and
species
in
the
estuary
system
are
the
result
of
either
physical
alteration
of
the
land
and
seascape
or
chemical
contamination
of
waterways
from
compounds
deriving
primarily
from
land­
based
sources.
Examples
of
the
former
include
channel
dredging,
filling
of
lowlying
areas,
hardening
of
the
shoreline
(
e.
g.,
bulkheads,
docks,
and
groins)
and
clearing
of
land
for
human
uses.
Chemical
contamination
occurs
when
excessive
amounts
of
natural
compounds,
elements,
or
toxic
anthropogenic
compounds
are
released
into
the
system.

Invasive
species
are
another
threat
to
habitat
and
living
resources
of
the
estuary
system.
Non­
indigenous
species
are
of
particular
concern
because
these
species
often
have
no
natural
predators
and,
thus,
either
parasitize
and
kill
or
out­
compete
the
native
species
for
food
and
space.

Physical
Alteration
Physical
alteration
has
occurred
throughout
the
Peconic
Estuary
and
its
watershed.
Low­
lying
marshes
and
swamps
historically
have
been
ditched
and
drained
for
mosquito
control
or
filled
for
construction
or
agriculture.
Dredging
has
been
carried
out
on
most
of
the
inlets
and
navigation
channels
in
the
embayments
and
surrounding
creeks.
Bulkheads,
rip­
rap
and
other
structures
have
been
widely
used
to
stabilize
waterfront
property
throughout
the
estuary.
These
structures
have
altered
shoreline
erosion
and
accretion
patterns
and
reduced
the
amount
of
natural
shoreline
available
to
living
organisms.
Roads
have
also
disconnected
and
degraded
many
tidal
wetland
systems
in
the
past.
Although
culverts
have
been
installed
to
reconnect
these
wetlands,
they
are
often
poorly
maintained
and
do
not
flush
properly.
Hence
they
often
block
migratory
fish
from
spawning
and
further
reduce
habitat
quality.
Much
of
the
uplands
have
been
cleared,
historically
for
agriculture
and
recently
for
residential
developments.
In
this
respect
the
Peconic
Estuary
is
no
different
from
other
parts
of
the
country,
although
such
clearing
has
not
occurred
to
the
degree
that
it
has
around
other
estuaries
in
the
region.
Natural
communities
most
affected
by
development
include
wetlands,
beaches,
grasslands,
forests,
and
coastal
ponds.

In
addition
to
direct
impacts,
development
and
land
use
have
also
led
indirectly
to
the
degradation
of
habitat
and
changes
in
natural
communities.
Filling
for
roads
and
railroads
has
cut
off
the
flow
of
water
to
a
number
of
tidal
wetlands.
Over
time,
the
vegetation
has
changed
(
including
invasion
of
nuisance
species),
and
the
marsh
has
either
become
a
freshwater
wetland
or
it
has
gradually
filled
in
and
become
upland.
Dams
have
been
built
on
a
number
of
the
streams
emptying
into
the
Peconics,
preventing
the
movement
of
anadromous
fish
into
fresh
water
for
spawning.
It
is
believed
that
dredging
has
changed
the
current
patterns
in
small
embayments
and
creeks,
which
has
led
to
changes
in
sediment
distribution,
suspended
solids
in
the
water
column,
and
community
composition.
The
use
of
hard
structures
along
the
shoreline
has
led
to
the
loss
of
wetlands
and
beaches
as
well
as
the
scouring
of
shallow
areas
with
impacts
to
the
shallow
water
benthic
communities.
In
many
cases,
the
changes
associated
with
bulkheads
may
have
been
quite
localized
and
subtle,
with
no
apparent
Environmental
Criteria
(
Laws
&
Regulations)

Since
habitat
and
living
organisms
are
resources
to
be
protected
rather
than
pollutants
to
be
controlled
and
discouraged,
it
is
difficult
to
describe
them
in
terms
of
standards
or
guidelines.
There
are
numerous
laws
that
regulate
the
human
use
of,
or
interaction
with,
these
resources.
They
have
been
promulgated
at
Federal,
State,
County,
and
town
levels.
Most
of
these
regulations
are
aimed
at
individual
species
or
a
particular
habitat
type
or
natural
community.
An
overview
of
these
laws
and
regulations
can
be
found
in
Appendix
K.
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impairment
to
human
uses
of
the
area.
However,
many
small
changes
can
lead
to
widespread
cumulative
damage
of
natural
communities
throughout
the
system.

Chemical
Contamination
Chemical
contamination
can
have
a
variety
of
effects.
The
addition
of
toxic
substances
can
have
an
acute
or
chronic
toxic
effect
on
many
species.
Extensive
contamination
of
the
surface
water
in
the
Peconics
with
toxic
substances,
however,
has
been
rare,
and
long­
term
impacts
on
populations
of
living
organisms
have
probably
been
minimal
(
see
Chapter
6).
One
of
the
most
significant
chemical
contaminants
in
the
Peconics
has
been
excess
nitrogen
(
see
Chapter
3).
Inputs
of
nitrogen
can
lead
to
phytoplankton
blooms,
the
loss
of
rooted
macrophytes,
such
as
eelgrass,
or
hypoxic
conditions
that
can
kill
sedentary
benthic
organisms
and
cause
mobile
species
to
relocate.
Sediment
loading
may
also
be
included
in
this
category
since
many
contaminants
attach
to
particles.
Such
loading
also
results
in
siltation,
which
is
a
physical
alteration.
Resources
most
affected
by
chemical
contamination
include
eelgrass
beds,
soft­
bottom
benthic
communities,
wetlands,
and
plankton
communities.

Invasive
Species
Invasive
species
can
impact
native
plant
and
animal
communities
around
the
estuary.
For
example,
Phragmites
australis
is
an
invasive
species
that
forms
monotypic
stands
in
disturbed
tidal
wetland
areas.
While
recent
evidence
suggest
that
Phragmites
australis
has
some
habitat
value
(
e.
g.,
fish
and
bird
habitat),
these
stands
have
generally
decreased
the
overall
habitat
value
for
native
species,
alter
nutrient
cycling
regimes,
and
are
a
fire
hazard.
Non­
indigenous
plant
and
animal
species,
which
have
been
either
accidentally
or
purposefully
introduced
to
Long
Island,
can
also
represent
a
threat.
These
species
can
out­
compete
indigenous
populations,
causing
irreparable
damage
to
the
local
ecosystem.
There
are
already
non­
indigenous
species
in
the
Peconics
(
e.
g.,
the
marine
macroalgae
Codium
fragile
or
Green
Fleece)
whose
impact
on
the
environment
is
unknown.
Green
Fleece
is
abundant
throughout
the
estuary.
Because
fishermen
have
reported
sets
of
scallops
in
areas
of
Codium
fragile
in
the
western
portion
of
Peconic
Bay,
its
significance
needs
further
evaluation.

Deep
Water
Zone
Water
quality
in
the
deep
water
zone
east
of
Flanders
Bay
is
generally
excellent
with
respect
to
dissolved
nutrients,
oxygen,
and
suspended
solids.
There
are
no
significant
concentrations
of
toxic
contaminants
or
pathogens
found
in
this
zone.
The
Brown
Tide
algae
bloom
was
found
in
these
areas
and
in
shallow
waters
and
enclosed
embayments.
The
effects
on
finfish
and
benthic
communities
is
unknown.

Finfish
Populations
of
many
species
of
finfish
that
inhabit
the
deep
water
zone
of
the
Peconics
have
been
greatly
reduced
in
the
past
few
decades.
The
major
cause
of
this
impairment
is
probably
overfishing
by
both
commercial
and
recreational
participants
on
the
entire
Atlantic
coast.
Other
causes
may
include
the
loss
of
feeding
and
reproductive
habitat.
Some
fishermen
believe
that
it
might
be
juvenile
mortality.
With
the
data
available,
it
is
impossible
to
determine
how
much
of
the
decline
in
finfish
populations
in
the
Peconic
Estuary
is
due
to
habitat
losses
as
compared
to
overfishing.
It
is
not
clear
at
all
how
previous
activities
such
as
commercial
trawling,
recreational
fishing,
oyster
culturing,
recreational
boating,
and
dredging
may
have
affected
local
populations
through
habitat
disturbance
and
modification
in
this
zone.
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Shellfish
A
shellfish
survey
conducted
in
the
deep
water
(
greater
than
three
meters)
of
the
Peconic
Estuary
showed
this
zone
to
have
a
low
abundance
of
commercially
important
species,
despite
supporting
a
rich
benthic
fauna
overall.
For
example,
a
comparison
between
a
1979­
80
open
water
shellfish
survey
conducted
by
the
NYSDEC
and
a
1995
survey
conducted
by
the
PEP
and
the
NYSDEC
at
the
same
sites
show
that
natural
populations
of
hard
clams
in
waters
greater
than
approximately
four
feet
(
1.2
m),
which
were
never
very
high,
have
declined
in
abundance
as
have
the
levels
of
other,
noncommercial
shellfish
species.
It
is
not
clear
if
these
communities
have
changed
or
became
impaired
in
recent
years.
A
number
of
historical
activities
may
have
seriously
affected
these
bottom
communities,
including
trawling
for
fish
and
dredging
of
oysters.
Boating
activities
and
the
use
of
lime
for
starfish
control
may
also
be
responsible
for
bay
bottom
impacts.

Commercial
trawling
for
finfish
existed
in
the
estuary
until
the
State
imposed
a
ban
on
this
activity
in
1994.
There
is
anecdotal
information
that,
in
addition
to
soft
bottoms,
trawling
may
have
damaged
or
destroyed
hard
bottom
substrates
such
as
shell
hash,
along
with
the
communities
that
depend
on
them.
Widespread
oyster
culturing
in
soft­
bottom
areas
also
may
have
affected
benthic
communities.
In
this
process,
juvenile
oysters
were
laid
out
in
deep
water
areas
and
then
dredged
up,
an
activity
that
repeatedly
rakes
up
the
bottom.
There
are
no
data,
however,
on
the
impacts
of
these
activities
on
benthic
communities
before,
during,
or
after
the
most
intensive
period
of
oyster
aquaculture,
trawling,
or
boating
activities
in
the
Peconic
Estuary.

Most
of
the
oyster
grow­
out
activities
and
clam
cleansing
that
currently
takes
place
in
the
estuary
is
done
on
trays
or
shellfish
cages.
The
State­
sponsored
transplant
program
transfers
hard
clams
from
Raritan
Bay
in
New
York
Harbor
to
deep
water
portions
of
the
Peconics
for
cleansing
before
they
are
marketed.
Most
of
the
transplanted
shellfish
are
not
placed
on
the
bottom
for
later
dredging,
but
on
racks
or
cages
which
are
pulled
up
after
a
21­
day
cleansing
period.
It
is
not
clear
how
these
ongoing
activities
are
affecting
benthic
communities.
Possible
benefits
could
include
spawning
of
naturally
occurring
populations
and
improved
local
water
quality
through
the
shellfish's
natural
seawater
filtration
process.

Birds
Sea
ducks
are
found
in
the
estuary
primarily
from
November
to
April.
They
use
the
deep
water
portions
of
the
estuary
for
feeding
and
resting.
There
are
no
obvious
impairments
to
these
populations
aside
from
local
impairments
by
either
hunting,
which
is
permitted
at
certain
times
of
the
year,
or
damage
to
their
food
supply
(
shellfish
and
other
benthic
invertebrates).

Sea
Turtles
and
Marine
Mammals
Marine
mammal
and
sea
turtle
populations
in
the
Peconics
are
increasing.
The
reasons
for
these
increases
are
likely
the
result
of
the
protection
of
these
animals
from
hunting
and,
in
the
case
of
turtles,
protection
of
their
breeding
grounds
outside
of
the
region.
The
main
potential
for
impairment
to
these
populations
in
the
Peconic
Estuary
is
damage
to
or
loss
of
feeding
grounds
(
in
the
case
of
all
species
of
marine
mammals
and
sea
turtles)
or
loss
of
or
damage
to
haul­
out
areas
(
in
the
case
of
Oysters
were
originally
the
most
valuable
commercial
species
in
the
Peconic
Estuary
system.
The
populations
were
not
natural,
however,
but
came
from
the
seeding
of
bottom
waters
for
grow­
out
(
primarily
in
the
deep
water
zone).
These
cultivated
populations
were
the
basis
for
the
reputation
of
Peconic
Bay
oysters
in
the
past.
The
oyster
industry
began
declining
in
the
1960s
due
to
the
loss
of
seed
in
Connecticut,
and
by
the
1980s,
landings
of
this
species
accounted
for
only
a
small
percentage
of
the
shellfish
harvested
from
the
Peconic
Estuary
system.
The
1979/
1980
NYSDEC
survey
yielded
no
oysters;
the
1995
PEP
survey
found
only
one.
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seals).
Since
the
sea
turtles
subsist
on
certain
macrocrustacean
species
or
macroalgae,
damage
or
modification
of
their
habitat
or
their
food
species
could
adversely
or
positively
affect
the
species.
Threats
to
individual
animals
include
collisions
with
motorboats
or
possibly
with
trawls,
entanglements,
and
attacks
on
hauled­
out
seals.

Shallow
Water
Zone
Shellfish
Shellfish
populations
in
the
Peconics
have
fluctuated
over
time.
Most
of
these
fluctuations
have
been
the
result
of
natural
variations
in
the
environment.
The
algae
bloom
known
as
Brown
Tide
wiped
out
the
scallop
populations
in
the
mid­
1980s
and
again
in
the
mid­
1990s,
but
it
is
not
known
if
anthropogenic
factors
played
a
role
in
the
appearance
of
these
recurring
blooms
(
see
Chapter
2).
The
scallop
populations
have
never
regained
levels
seen
during
pre­
Brown
Tide
years.
Aside
from
Brown
Tide,
the
greatest
limitation
to
shellfish
harvesting
in
the
shallow
water
zone
at
the
current
time
is
the
closure
of
shellfish
beds
due
to
pathogen
contamination.
These
closures
may
prevent
over­
harvesting
of
some
species
of
shellfish
and
provide
spawning
sanctuaries
for
future
stocks.
Despite
that,
pathogens
are
a
threat
to
human
health
and
closures
are
an
impairment
to
the
shellfish
industry.

Submerged
Aquatic
Vegetation
The
PEP
recognizes
that
some
of
the
most
important
underwater
habitats
of
the
estuary
are
the
meadows
of
eelgrass
found
along
the
eastern
end
of
the
Peconic
Estuary.
These
eelgrass
beds
provide
food,
shelter,
and
nursery
grounds
to
many
marine
animals
including
the
commercially
important
bay
scallop.
Eelgrass
beds
are
also
an
important
contributor
to
the
detrital
food
web
by
providing
carbon
and
nutrients
to
bacteria
and
fungi,
which
in
turn
are
prey
for
numerous
marine
invertebrates
and
fish.
Many
of
the
eelgrass
beds
along
the
East
Coast
were
wiped
out
by
a
mysterious
"
wasting
disease"
in
the
1930s.
It
is
believed
now
that
the
disease
was
caused
by
the
slime
mold
Labyrinthula
zosterae.
The
beds
were
extremely
slow
to
recover
and
many
areas
have
not
been
recolonized
to
this
day.

According
to
anecdotal
information,
eelgrass
was
once
found
throughout
the
estuary
and
may
have
been
lost,
in
part,
to
effects
from
Brown
Tide
that
first
occurred
in
Peconic
waters
in
1985.
The
PEP
study
performed
by
Cashin
Associates
in
1996
confirmed
a
decline
in
eelgrass
beds.
The
Cashin
survey
estimated
that
there
are
8.5
square
km
of
eelgrass
in
the
estuary,
while
Dennison
estimated
in
1989
13.5
square
km
of
eelgrass
in
Gardiners
Bay
alone.
Cashin
Associates
also
reported
a
decline
in
eelgrass
beds
from
March
to
October
1994
that
was
unrelated
to
a
Brown
Tide
bloom.
Poor
water
quality,
including
high
levels
of
nitrogen
and
suspended
sediments,
have
been
implicated
as
causes
leading
to
declines
in
eelgrass
beds
in
the
Peconics
as
well
as
other
estuaries
along
the
Atlantic
seaboard.
In
addition
to
these
factors,
which
operate
on
relatively
large
scales,
eelgrass
beds
can
also
be
damaged
by
scallop
dredging
and
motorboat
traffic,
both
of
which
snag
and
uproot
the
plants.
But
according
to
fishermen,
if
a
scallop
dredge
is
catching
eelgrass
roots,
it
means
it
is
not
catching
scallops
and
hence
not
worthwhile.

Intertidal/
Shoreline
Zone
The
impairments
to
tidal
wetlands,
mudflats,
and
shoals
are
among
the
best
documented
and
well
known
in
the
region.
In
an
effort
to
improve
and
increase
agricultural
land,
prevent
local
flooding,
improve
waterways
for
use
by
vessels,
and
control
mosquitoes,
these
intertidal
habitats
have
been
dredged,
filled,
ditched,
and
diked.
Considered
for
years
to
be
"
useless"
property,
it
has
only
been
in
Peconic
Estuary
Program
CCMP
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the
last
few
decades
that
governments
and
the
general
public
have
come
to
realize
the
important
role
that
these
habitats
play
in
nurturing
many
of
the
estuarine
species
valued
by
humans.

As
discussed
earlier
in
this
chapter,
actual
loss
of
tidal
wetlands
in
the
Peconics
has
been
close
to
zero
in
the
past
few
decades.
Unfortunately,
there
are
few
reliable
estimates
of
the
percentage
of
vegetated
salt
marsh
loss
prior
to
the
1970s,
let
alone
any
estimates
of
the
loss
of
unvegetated
intertidal
habitats.
Nevertheless,
it
is
probably
safe
to
say
that
there
was
a
significant
loss
of
these
habitats
in
certain
locations
around
the
estuary,
particularly
in
those
areas
that
have
been
occupied
by
humans
for
generations.

Although
wetland
loss
has
been
minimal
in
the
past
few
decades,
many
areas
of
salt
marsh
have
been
degraded
by
adjacent
land
use
practices.
The
State
Tidal
Wetlands
Law
and
Federal
Clean
Water
Act
prohibit
physical
alteration
of
wetlands
and
require
a
permit
for
all
activities
in
areas
adjacent
to
the
wetlands.
If
the
activity
will
cause
significant
harm
to
the
wetland,
a
permit
may
be
modified
or
denied.
Because
this
law
allows
development
and
dredging
in
areas
adjacent
to
wetlands,
there
is
the
risk
of
habitat
degradation
over
time.
Even
though
these
activities
may
not
cause
direct
loss
of
wetlands,
there
is
the
danger
that
they
will
impair
the
ability
of
these
habitats
to
function
as
they
should.
Therefore,
while
the
extent
of
wetlands
may
not
decrease
in
the
future,
the
quality
of
those
wetlands
may
become
very
poor.
Such
impaired
marshes
often
appear
to
be
functioning
wetlands,
but
are,
in
fact,
unable
to
support
the
extensive
wildlife
communities
they
once
did,
or
to
absorb
and
filter
the
same
amount
of
water
and
contaminants
in
surface
runoff.
Fragmentation
is
also
a
problem
where
marshes
are
parsed
into
small
pieces
interrupted
by
filled
areas,
docks,
roads,
culverts
or
bulkheads.
These
small
fragments
are
incapable
of
functioning
the
way
larger
tracts
of
marsh
do,
although
they
may
still
provide
habitat
for
a
limited
variety
of
organisms.
Additionally,
leaching
of
toxic
chemicals
from
wood
preservatives
in
bulkheads
(
e.
g.,
creosote,
copper­
chromium­
arsenic)
may
have
adverse
effects
on
the
biota
of
shallow­
water
habitats
that
are
adjacent
to
these
structures
(
see
Chapter
6).

Over
the
long
term,
it
is
estimated
that
the
current
laws
protecting
tidal
wetlands
will
effectively
protect
only
about
60
percent
of
the
existing,
privately­
owned
areas.
The
biggest
long­
term
threat
is
the
development
of
small
waterfront
lots
(
existing
before
the
tidal
wetlands
law
was
taken
into
account
when
subdivision
plans
were
approved).
Under
existing
State
law,
if
an
owner
is
not
able
to
build
a
structure
on
his/
her
property
that
is
compatible
with
existing
zoning
due
to
the
existence
of
wetlands,
the
State
will
either
have
to
permit
the
filling
of
the
marsh
to
accommodate
the
structure
or
compensate
the
owner
for
the
property.
The
economically
feasible
choice
in
most
cases
is
to
allow
filling
rather
than
purchasing
the
property.

The
placement
of
bulkheads
and
other
hard
structures
at
the
water
line
represents
another
long­
term
threat
to
the
tidal
wetlands
fragmentation.
If
sea­
level
continues
to
rise,
these
structures
will
prevent
the
natural
shoreward
migration
of
the
wetlands.
In
time,
the
wetlands
will
be
submerged
and
cease
to
exist.

Tidal
wetlands
around
the
Peconic
Estuary
System
have
also
been
adversely
affected
by
the
invasion
of
huge
colonies
of
the
common
reed
Phragmites
australis.
This
plant
can
successfully
colonize
tidal
marshes
that
have
been
disturbed,
as
well
as
areas
that
are
undisturbed,
replacing
Spartina
species.
The
addition
of
impervious
areas
such
as
roads,
parking
lots,
and
driveways
increases
stormwater
runoff
and
can
result
in
lowered
salinity
 
a
condition
favored
by
this
plant,
which
propagates
in
water
with
reduced
salinity.
Because
Phragmites
colonies
are
clonal
(
i.
e.,
they
propagate
as
individual
plants
from
a
single
rhizome
root
system),
as
long
as
part
of
a
rhizome
is
in
fresh
or
brackish
water,
a
colony
can
propagate
into
higher
salinity
waters.
This
accounts
for
the
presence
of
Peconic
Estuary
Program
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these
plants
in
the
salt
marsh
far
from
fresh
water.
Despite
its
invasive
nature,
researchers
have
found
that
tidal
marsh
invertebrates
(
e.
g.,
snails,
amphipods,
and
isopods),
which
are
prey
species
for
mummichogs,
were
common
to
abundant
in
reed
grass­
dominated
regions,
as
well
as
in
areas
covered
by
typical
tidal
marsh
vegetation
along
a
salinity
gradient
of
the
lower
Connecticut
River.
Therefore,
the
potential
value
of
Phragmites
also
needs
to
be
ascertained.

Many
species
of
birds
are
vulnerable
to
loss
of
intertidal
habitat
in
the
Peconic
Estuary
System.
Puddle
ducks,
Canada
geese,
and
black
ducks
use
these
areas
for
feeding,
breeding,
and
rearing
young,
particularly
since
wetlands
and
tidal
creeks
have
historically
been
reduced
in
size
and
physically
altered.
Loss
of
wetland
and
intertidal
habitat
has
had
the
effect
of
concentrating
overwintering
ducks
and
geese
into
the
remaining
unaltered
areas
around
the
estuary.
Increased
concentrations
of
these
birds
in
poorly
flushed
embayments
may
lead
to
increased
loading
of
pathogen
indicators
into
the
waters,
which
may
in
turn
result
in
closure
of
adjacent
shellfish
beds
to
harvesting
(
see
Chapter
5).

Beaches
and
dunes,
as
well
as
wetlands
have
been
adversely
impacted
by
human
activities,
primarily
through
direct
or
indirect
physical
alteration.
Dunes
act
as
barriers,
which
protect
areas
behind
them
from
overwash
and
erosion
by
wind
and
storms;
they
are
stabilized
by
vegetation
adapted
to
the
exposed
environment.
Dune
habitats
have
been
destroyed
throughout
the
region
as
vegetation
has
been
removed
or
when
they
have
been
irreparably
damaged
by
pedestrian
and
vehicular
traffic.
Dunes
also
have
been
excavated
to
make
way
for
parking
lots
and
summer
homes.
Conversely,
dunes
migrate
naturally,
and
over­
stabilization
of
these
land
forms
with
non­
indigenous
vegetation
or
hard
structures
such
as
fencing
or
groins,
has
also
led
to
a
loss
of
habitat.
Species
which
use
beaches
or
dunes
for
nesting,
such
as
diamondback
terrapins
and
shorebirds,
have
been
forced
to
abandon
many
sites
due
to
human
disturbance
(
from
foot
traffic,
off­
road
vehicles,
boats
and
jet­
skis
in
the
shallow
zones,
and
construction),
as
well
as
poaching
and
predation
by
gulls,
crows,
foxes,
raccoons,
and
feral
cats.
Dredging
and
construction
of
bulkheads
and
jetties
also
have
caused
loss
of
beaches.
These
activities
change
current
patterns,
altering
erosion
and
transport
processes.
In
some
cases,
beaches
have
been
nourished
and
maintained
by
dredging/
placement
operations.

The
protection
from
chemical
degradation
afforded
to
marshes
and
mudflats
under
the
Tidal
Wetlands
Law
is
limited.
Stormwater
runoff
from
roads,
private
property,
and
marinas
is
a
common
problem
around
the
Peconic
Estuary.
This
flow
can
carry
toxic
substances
such
as
motor
oil,
polynuclear
aromatic
hydrocarbons
(
PAHs)
from
engine
exhaust,
and
heavy
metals
from
tire
and
engine
wear
as
well
as
lawn
and
garden
herbicides,
pesticides,
and
fertilizers.
In
addition,
road
sand
and
sediment
from
improperly­
contained
construction
sites
are
washed
into
these
low­
lying
areas.
Regulations
generally
do
not
allow
the
direct
discharge
of
this
runoff
into
tidal
wetlands,
but
indirect
inputs
are
common.

Peconic
River,
Freshwater
Wetlands,
and
Ponds
Threats
to
freshwater
wetlands
are
potentially
greater
than
to
tidal
wetlands
because
the
laws
protecting
these
habitats
are
weaker.
Specifically,
wetlands
less
than
12.4
acres
in
size
are
not
protected
under
the
New
York
State
Environmental
Conservation
Law
(
ECL)
Article
24,
the
Freshwater
Wetlands
Protection
Program,
unless
they
are
shown
to
be
of
local
importance.
This
State
law
provides
for
the
preservation
and
protection
of
freshwater
marshes,
swamps,
sloughs,
bogs
and
flats
over
12.4
acres
(
five
hectares)
that
support
aquatic
or
semi­
aquatic
vegetation.
Smaller
wetlands
may
also
be
protected
if
deemed
to
be
of
local
importance.
Additionally
some
local
governments
also
have
regulations
that
protect
freshwater
wetlands.
Permits
are
required
for
almost
all
activities
within
Peconic
Estuary
Program
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or
adjacent
to
wetlands
[
within
100
ft
(
30.5
m)
of
a
wetland
boundary].
Activities
requiring
permits
include:
1)
construction
of
buildings,
roadways,
septic
systems,
bulkheads
or
dams;
2)
placement
of
fill,
excavation
or
grading;
3)
modification
or
restoration
of
existing
structures;
4)
drainage;
and
5)
application
of
pesticides.
All
agricultural
activities
are
exempted
from
this
law.
Most
of
the
freshwater
wetlands
in
the
Peconic
Estuary
drainage
basin
are
smaller
than
12.4
acres,
but
they
have
all
been
designated
as
being
of
local
importance
and
any
activities
in
these
areas
require
a
State
permit.

Freshwater
wetlands
and
ponds
are
threatened
by
the
same
activities
as
tidal
wetlands
and
creeks,
including
sedimentation,
hardening
of
the
shoreline,
and
stormwater
runoff,
as
well
as
groundwater
draw­
down
and
dams.
Even
wetlands
in
the
Peconic
River
drainage
basin,
which
are
protected
by
being
in
parkland
or
in
the
Pine
Barrens
Core
Preservation
Area,
are
impaired
due
to
erosion
caused
by
vehicular
and
foot
traffic,
runoff,
and
groundwater
draw­
down
by
drinking
water
wells
for
nearby
housing
developments.
The
loss
of
these
small
wetlands
would
result
in
the
extinction
of
local
populations
of
organisms
dependent
on
these
swamps
and
ponds.
These
species
include
the
banded
sunfish,
several
species
of
amphibians,
and
a
variety
of
aquatic
plants
and
insects.

Another
potential
threat
to
small
freshwater
ponds
and
wetlands
is
toxic
contamination.
These
areas
may
receive
this
contamination
from
a
variety
of
sources,
including
runoff
and
aerosol
deposition
from
agricultural
and
residential
application
of
pesticides
and
herbicides.
Unlike
the
Tidal
Wetlands
Law,
the
Freshwater
Wetlands
Law
does
have
a
provision,
which
prevents
the
use
of
herbicides
and
pesticides
in
the
vicinity
of
these
areas
as
a
protective
measure
for
finfish.
Unfortunately,
the
NYSDEC
Division
of
Fish
and
Wildlife
does
not
have
the
staff
to
enforce
this
provision
except
in
cases
of
gross
and
obvious
contamination.
For
this
reason,
low­
level,
chronic
impacts
from
these
toxic
sources
remain
a
threat
to
these
habitats.

Several
stretches
of
the
Peconic
River
have
been
designated
as
scenic
or
recreational
under
the
State
Wild,
Scenic,
and
Recreational
Rivers
Act,
which
means
that
permits
are
required
for
activities
that
take
place
along
the
banks
in
those
sections.
These
activities
may
be
limited
if
they
violate
the
scenic
or
recreational
nature
of
the
river.
The
Peconic
River,
however,
has
already
been
extensively
modified
in
the
past
through
damming,
bulkheading
and
toxic
contaminants
from
Brookhaven
National
Laboratory
(
see
Chapter
6).
Runoff
and
erosion
have
also
caused
some
degradation
in
the
water
quality.
Further
indirect
impacts
to
the
upstream
portion
of
the
river
from
changes
in
land
use
should
be
minimized
by
the
implementation
of
the
Pine
Barrens
Plan,
which
will
preserve
land
around
the
Peconic
River.

Terrestrial
Zone
The
most
significant
threats
to
terrestrial
communities
are:
1)
outright
loss
to
agriculture
or
residential
development;
2)
fragmentation
of
remaining
communities;
3)
fire
suppression;
and
4)
invasive
species.
Larger
continuous
areas
of
terrestrial
habitat
are
more
biologically
diverse
and
have
higher
densities
of
individuals.
Reducing
the
size
of
natural
areas
or
dividing
them
up
into
pieces
with
barriers
such
as
roads
or
developments
will
result
in
fewer
species
and
individuals
living
in
the
pieces,
even
if
the
total
area
is
not
reduced.
Overall
size
and
continuity
are
especially
critical
for
species
which
are
territorial,
including
many
birds
and
mammals.
Other
species,
such
as
neo­
tropical
warblers,
require
large
tracts
of
woodland
for
successful
reproduction.
In
the
case
of
these
birds,
their
small
open
nests
are
vulnerable
to
predation
by
foxes
and
domestic
cats
or
parasitism
by
cowbirds.
Because
predators
and
cowbirds
only
penetrate
woodlands
to
a
certain
distance,
survival
of
viable
Peconic
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populations
of
warblers
depends
on
the
existence
of
forests,
which
are
large
enough
to
exclude
predator
species
and
cowbirds
from
a
significant
portion
of
the
habitat.
The
dwarf
pitch
pine
forests
in
the
Pine
Barrens
depend
on
fire
for
survival.
Periodic
burnings
initiate
germination
in
the
pitch
pine
seeds
and
also
destroy
undergrowth
species.
Without
fire,
these
trees
and
their
associated
plant
and
animal
communities
will
not
reproduce
and
will
be
replaced
by
scrub
oaks.
Grassland
habitats
also
depend
on
fire
to
some
extent.
Successful
long­
term
maintenance
of
these
communities
depends
on
periodic
burnings
to
prevent
plant
succession
to
shrubs
and
trees.
The
native
grasses
are
drought
tolerant,
so
burning
which
destroys
young
trees
only
removes
aboveground
stems
and
shoots
of
these
species,
without
damaging
the
deep
root
systems,
and
allows
regeneration.

All
native
plant
communities
around
the
estuary
are
threatened
by
the
invasion
of
non­
indigenous
plant
and
animal
species,
which
have
been
either
accidentally
or
purposefully
introduced
to
Long
Island.
Often
these
species
have
no
natural
predators
and,
thus,
they
either
parasitize
and
kill
or
outcompete
the
native
species
for
food
and
space.
Although
nuisance
species
are
a
problem
in
all
environments,
their
impacts
in
terrestrial
environments
have
been
particularly
well­
documented.

MANAGEMENT
STRATEGY
AND
ACTIONS
The
Peconic
Estuary
and
its
watershed
are
sites
of
human
activity
of
all
kinds.
In
addition
to
residential,
commercial,
and
agricultural
land
uses,
the
area
supports
a
significant
tourism
industry.
Fishing,
shellfishing,
boating,
swimming,
hiking,
and
hunting
are
only
some
of
the
recreational
uses
actively
pursued
in
the
estuary
and
surrounding
watershed.
Many
of
these
activities
depend
on
the
existence
of
high
quality
water
and
healthy
living
resources.
Shellfish,
such
as
bay
scallops
and
hard
clams,
and
finfish,
such
as
winter
flounder
and
weakfish,
support
large
groups
of
commercial
and
recreational
enthusiasts.
Upland
habitats
sustain
many
species
that
are
recreationally
important,
such
as
deer
and
birds.
Undisturbed
habitat
also
provides
aesthetic
benefits,
which
add
to
the
enjoyment
of
other
activities.
All
these
resources
need
to
be
conserved
and
enhanced
as
much
as
possible
for
these
purposes
and
future,
currently
unforeseen
uses
of
the
system.
It
is
also
important
to
remember
that
living
communities
other
than
our
own
are
valuable
and
necessary
in
their
own
right
and
not
just
as
they
are
directly
useful
to
humans.
Humans
are
part
of
the
overall
ecology
of
the
planet
and
need
to
conserve
all
components
of
our
ecosystem.
The
PEP
has
tried
to
develop
recommendations
for
the
management
of
the
estuary
and
its
watershed
that
will
foster
recreational
and
commercial
uses
of
the
Peconic
Estuary
that
are
sustainable
and
compatible
with
protection
of
biodiversity.
It
is
possible
that
through
the
implementation
of
these
recommendations
there
will
be
an
enhancement
of
economically
and
ecologically
important
species.

Good
water
quality
is
extremely
important
for
the
protection
and
restoration
of
estuarine
and
maritime
communities.
However,
since
water
quality
is
addressed
through
other
chapters
of
this
draft
Management
Plan,
the
management
actions
in
this
chapter
will
not
focus
on
actions
linked
to
the
impacts
of
contaminants
on
habitat
and
living
resources.
The
actions
will
be
focused
primarily
on
the
impacts
of
habitat
fragmentation
and
habitat
degradation
on
living
organisms,
and
the
protection
and
restoration
of
natural
communities
in
and
around
the
estuary
from
causes
other
than
poor
water
quality.
Since
the
Peconic
Estuary
is
in
excellent
health
compared
to
neighboring
estuaries,
these
actions
are
aimed
at
prevention
of
incremental
and
cumulative
problems.
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Critical
Natural
Resource
Areas
Although
it
is
clear
that
the
entire
estuary
is
ecologically
important,
the
PEP
has
chosen
to
apply
the
concept
of
"
critical
natural
resource
areas"
to
focus
protection
efforts
on
the
variety
of
species
and
natural
communities
that
exist
within
the
PEP
study
area.
Critical
Natural
Resource
Areas
(
CNRAs)
are
geographically­
specific
locations
that
currently
have
significant
biodiversity
and
may
require
an
extra
level
of
protection
(
management
and/
or
regulation)
to
preserve
their
unique
characteristics.
Many
of
these
areas
are
presently
threatened
by
development
or
uses
that
could
degrade
their
quality.

In
March
1996,
the
U.
S.
Fish
and
Wildlife
Service
(
USFWS)
Coastal
Ecosystems
Program
generated
a
list
of
species
and
species
habitats
for
the
watershed
(
referred
to
as
species
of
special
emphasis).
This
list
was
reviewed
by
the
PEP
Natural
Resources
Committee
and
used
as
the
basis
for
examining
the
waters
and
watershed
of
the
Peconics.
The
list
included
USFWS
trust
species,
threatened
and
endangered
species,
anadromous
and
migratory
species,
New
York
State
Natural
Heritage
Program
species
and
communities
of
concern,
and
important
commercial
and
recreational
species.

The
PEP,
together
with
area
stakeholders,
followed
a
two­
step
process
to
identify
potential
CNRAs.
First,
the
PEP
and
stakeholders
identified
97
"
hot
spots"
in
the
system
that
represented
(
1)
feeding,
breeding,
and
over­
wintering
areas
for
species
of
special
emphasis;
(
2)
key
reproductive
areas
(
spawning,
breeding
colonies,
nest
sites)
for
species
of
special
emphasis;
(
3)
areas
with
significant
concentrations
and
co­
occurrence
of
species
of
special
emphasis;
and
(
4)
imperiled
natural
communities
or
exemplary
examples
of
common
natural
coastal
communities.
Once
these
hotspots
were
identified
and
mapped,
larger
CNRAs
were
delineated
to
encompass
multiple
proximate
and
overlapping
hot
spots.
Through
this
process,
17
CNRAs
have
been
defined
which
encompass
most
of
the
hot
spots.
These
17
CNRAs
are
roughly
outlined
in
Figure
4­
4.

Now
that
these
CNRAs
have
been
very
broadly
delineated
on
a
purely
technical
basis,
additional
personnel,
including
natural
resource
managers
and
planners
from
all
levels
of
government
will
be
consulted.
Based
on
these
discussions,
recommendations
and
commitments
for
management
and/
or
regulation
of
the
CNRAs
will
be
developed.

In
addition
to
management
actions
directed
at
CNRAs,
the
PEP
is
developing
management
actions,
which
are
focused
on
specific
habitats
or
species
that
exist
throughout
the
estuarine
system,
whether
they
are
contained
in
critical
areas
or
not
(
i.
e.,
deep
water
and
shallow
water
management
zones).
This
approach
recognizes
the
interconnected
and
interdependent
nature
of
the
estuary
system.

Therefore,
there
will
be
many
areas
in
and
around
the
estuary,
which
are
worthy
of
protection
and,
more
importantly,
of
restoration,
which
will
not
fall
within
one
of
the
critical
areas.
It
is
not
the
intent
of
the
PEP
to
protect
only
certain
high­
quality
areas
at
the
expense
of
areas
with
poorer
quality
habitat
which
have
the
potential
to
improve
or
which
may
yet
serve
important
ecosystem
functions.
The
management
of
habitats
and
living
resources
in
the
Peconics
will
require
a
blend
of
protecting
existing
natural
areas
and
restoring
or
enhancing
others
in
an
effort
to
achieve
the
best
natural,
sustainable
ecosystem
possible.
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Figure
4­
4.
PEP
Critical
Natural
Resource
Areas
(
CNRAS).
Peconic
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Program
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Habitat
Restoration
Work
Group
To
address
the
enhancement
of
existing
resources
or
restoration
of
habitats,
which
have
been
lost
or
degraded,
the
PEP
has
convened
a
Habitat
Restoration
Work
Group
(
HRWG).
The
purpose
of
this
group
is
to
identify
and
prioritize
the
significant
natural
habitats
of
the
system,
develop
overall
habitat
restoration
goals,
identify
locations
where
these
habitats
can
be
restored,
and
develop,
in
conjunction
with
public
and
private
landowners,
specific
restoration
projects.

The
short­
term
goal
of
the
HRWG
is
to
identify
specific
habitat
restoration
projects
within
the
Peconic
Estuary
and
Peconic
River
and
their
watersheds,
which
are
ready
for
immediate
funding.
The
voters
of
New
York,
in
November
1996,
passed
the
Clean
Water/
Clean
Air
Bond
Act,
which
has
the
restoration
of
aquatic
habitats
as
one
of
it
goals.
This
Act,
which
was
pioneered
by
Governor
George
E.
Pataki,
provides
$
30
million
jointly
for
the
Peconic
Estuary
and
South
Shore
Estuarine
Reserve.
It
is
the
expectation
of
the
PEP
that
a
portion
of
those
funds
will
be
used
for
aquatic
habitat
restoration
projects.
The
long­
term
(
2­
3
years)
goal
of
the
work
group,
to
be
carried
out
in
parallel
with
the
short­
term
goal,
is
to
identify
the
natural
habitats
throughout
these
areas,
which
are
most
in
need
of
restoration
as
well
as
to
develop
criteria
for
inclusion
of
projects
in
a
prioritized
restoration
list.
It
is
hoped
that,
eventually,
the
two
goals
will
merge
after
a
year
so
that
projects
which
are
submitted
for
Bond
Act
funding
incorporate
identified
habitats
and
restoration
criteria
developed
for
the
Peconic
Estuary
study
area
as
a
whole.
The
HRWG
also
will
develop
habitat­
specific
restoration
criteria
as
well
as
criteria
for
monitoring
restoration
projects.

MANAGEMENT
ACTIONS
The
designation
of
critical
areas
and
the
identification
and
prioritization
of
habitat
restoration
sites
will
be
two
of
the
most
significant
efforts
carried
out
by
the
PEP.
These
efforts,
although
done
separately
and
through
different
processes,
are
intended
to
compliment
each
other
and,
in
some
cases,
will
be
done
in
coordination.
The
implementation
of
measures
recommended
by
PEP
to
protect
and
restore
natural
habitats
will
be
crucial
in
the
management
of
the
entire
system.

The
actions
listed
below
have
been
developed
in
consensus
by
the
PEP
Management
Conference
to
meet
the
natural
resources
objectives
listed
at
the
beginning
of
this
chapter.
These
proposed
actions
reflect
the
best
measures
that
can
be
taken
to
preserve
the
habitats
and
living
resources
of
the
estuary.

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.
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HABITAT
AND
LIVING
RESOURCES
ACTIONS
HLR­
1
Use
Critical
Natural
Resource
Areas
(
CNRAs)
to
Develop
and
Implement
Management
Strategies
to
Protect
High
Quality
Habitats
and
Concentrations
of
Species
of
Special
Emphasis.

HLR­
2
Manage
Shoreline
Stabilization,
Docks,
Piers,
and
Flow
Restriction
Structures
to
Reduce
or
Prevent
Additional
Hardening
and
Encourage
Restoration
of
Hardened
Shorelines
to
a
Natural
State.

HLR­
3
Assess
the
Impacts
of
Dredging
Activities
on
Habitat
and
Natural
Resources
and
Develop
Recommendations
and
Guidelines
for
Reducing
those
Impacts.

HLR­
4
Examine
and
Promote
Methods
of
Shellfish
Harvesting
that
are
Most
Compatible
with
Establishment
and
Growth
of
Eelgrass
Beds
and
Vegetated
Salt
Marshes.

HLR­
5
Implement,
Enforce,
and
Encourage
the
Continuation
of
Current
Policies
and
Regulations
Protective
of
Wetlands.

HLR­
6
Evaluate
the
Effectiveness
of
Current
Policies
in
Preserving
Eelgrass
Habitat
and
Develop
Ways
to
Provide
Increased
Protection
for
all
Extant
Eelgrass.

HLR­
7
Develop
and
Implement
an
Estuary­
Wide
Habitat
Restoration
Plan
(
HRP).

HLR­
8
Develop
and
Implement
Specific
Restoration
Projects.

HLR­
9
Monitor
and
Evaluate
the
Success
of
Restoration
Efforts.

HLR­
10
Develop
an
Aquaculture
Plan
for
the
Peconic
Estuary.

HLR­
11
Determine
the
Suitability
of
Artificial
Reefs
in
the
Peconic
Estuary.

HLR­
12
Foster
Sustainable
Recreational
and
Commercial
Finfish
and
Shellfish
Uses
of
the
Peconic
Estuary
that
are
Compatible
with
Biodiversity
Protection.

HLR­
13
Protect
Nesting
and
Feeding
Habitat
of
Shorebirds.

HLR­
14
Protect
Sea
Turtles
and
Marine
Mammals.

HLR­
15
Utilize
Land
Use
Planning,
BMPs,
and
Other
Management
Measures
to
Reduce
the
Negative
Impacts
of
Human
Uses
and
Development
on
the
Estuary
System.

HLR­
16
Develop
and
Implement
a
Living
Resources
Research,
Monitoring,
and
Assessment
Program.

HLR­
17
Establish
a
Working
Group
to
Examine
the
Role
of
Grazers
and
Filter
Feeding
Organisms
in
Influencing
Water
Quality
and
Productivity
to
Better
Understand
Food
Web
Dynamics
and
to
Develop
Management
Applications.
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Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
2,
3,
6,
7,
and
8.

Delineate
CNRAs
There
are
many
natural
areas
within
the
Peconics
that
are
of
very
high
ecological
quality
and
provide
important
spawning,
breeding,
nursery,
and
feeding
habitats
for
a
diversity
of
rare,
keystone,
and
commercially
important
species
of
fish,
shellfish,
birds,
sea
turtles,
and
sea
mammals.
Many
of
these
areas
are
comprised
of
interconnected
marine,
estuarine,
and
upland
systems.
To
further
protect
these
existing
high
quality
natural
areas,
CNRAs
were
delineated
in
two
expert
workshops
and
refined
at
meetings
with
the
Towns.
Known
data
sets
were
acquired
and
digitized
using
a
geographic
information
system
(
GIS).
Using
these
maps
further,
non­
mapped
data
were
collected
by
convening
a
scientific
group
meeting
on
March
26,
1996.
Twenty­
eight
biologists
with
expertise
in
a
wide
variety
of
specialties
used
the
USFWS
species
and
species
habitat
list
and
the
USFWS
mapped
natural
resources
GIS
data
and
identified
97
"
hotspots"
within
the
Peconics.

Seventeen
CNRAs
were
identified
on
July
30,
1996
by
a
second
group
of
biologists
who
combined
the
already
mapped
data
and
the
"
hot
spots"
to
delineate
the
"
critical
areas."
These
areas
encompassed
terrestrial,
tidal,
and
subtidal
lands
and
waters,
and,
in
many
cases,
included
protected
areas
within
the
watershed
where
Federal,
State,
town,
and
other
organizations
have
acquired
property
for
conservation
purposes.
The
boundaries
of
the
CNRAs
also
closely
correlate
to
existing
Federal,
State,
and
town
designations.

Further
meetings
were
conducted
during
the
Spring
of
1998
with
town
planners,
conservation
boards,
and
other
interested
officials
from
the
Towns
of
East
Hampton,
Southampton,
Riverhead,
Southold,
and
Shelter
Island
to
finalize
the
CNRAs.
Adjustments
were
completed
during
the
summer
of
1998,
and
ArcInfo/
GIS
map
files
were
created.
Twenty­
nine
ArcInfo/
GIS
files
containing
CNRA
data
and
maps
are
available
on
CD­
ROM
at
the
PEP
Office.

Most
of
these
areas
are
undeveloped
and
primarily
in
public
ownership,
but
there
are
developed
areas
within
or
adjacent
to
the
CNRAs.
Although
the
entire
estuary
is
important
to
natural
resources
and
many
of
the
species
found
in
the
CNRAs
are
also
found
outside
of
the
CNRAs,
it
is
recognized
that
these
high
quality
areas
require
special
attention
to
prevent
incremental
and
cumulative
ecological
degradation.

The
draft
boundaries
with
assessment
of
each
area
need
to
be
finalized
(
e.
g.,
benthic/
underwater
mapping).
Analyses
of
existing
data
sets
should
be
performed
to
identify
any
information
gaps
that
need
to
be
filled
and
to
evaluate
individual
and
cumulative
threats
to
the
CNRAs.
Compilation
of
data
sets
is
necessary
to
obtain
a
comprehensive
inventory
of
information.
These
data
sets
include
the
USFWS
Federal
trust
listings,
Federally
listed
endangered
and
threatened
species,
State
protected
species,
biological
conservation
statistics
of
the
NY
Natural
Heritage
Program,
water
quality
data
collected
by
SCDHS,
NYSDOS
Significant
Coastal
Fish
and
Wildlife
Habitats
(
SCFWH),
land
use
data
collected
by
the
Suffolk
County
Planning
Department
(
land
use
and
change
inventory,
population
and
population
saturation
inventory,
water
dependent
uses,
land
available
for
development)
biological
data
collected
by
NYSDEC,
and
marine
data
collected
in
surveys
for
the
HLR­
1
Use
Critical
Natural
Resource
Areas
(
CNRAs)
to
Develop
and
Implement
Management
Strategies
to
Protect
High
Quality
Habitats
and
Concentrations
of
Species
of
Special
Emphasis.
Peconic
Estuary
Program
CCMP
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PEP.
GIS
analyses
will
be
used
to
integrate
these
data
sets
and
evaluate
impacts.
This
information
will
strengthen
our
understanding
of
the
CNRAs
and
lay
the
groundwork
for
developing
implementation
strategies
to
manage
and
protect
these
areas.

Protect
CNRAs
There
are
already
a
variety
of
programs
in
existence
that
seek
to
preserve,
protect,
restore,
or
call
attention
to
coastal
resources
in
conjunction
with
human
activities
around
the
Peconic
Estuary
System.
These
include
the
Significant
Coastal
Fish
and
Wildlife
Habitats,
Local
Waterfront
Revitalization
Plans,
the
New
York
Open
Space
Conservation
Plan,
the
Peconic
Bioreserve,
and
others.
Many
of
these
efforts,
however,
are
focused
on
specific
habitats
or
communities
or
are
very
small
in
scope
geographically.
The
CNRAs
encompass
whole
ecosystems
and
include
portions
of
the
estuary
as
well
as
freshwater
and
terrestrial
zones.
The
designated
CNRAs
will
merge
a
variety
of
existing
efforts
into
the
management
of
large
areas
containing
a
range
of
valuable
natural
resources.
Specific
protection
efforts
for
the
CNRAs
are
emphasized,
including
zoning,
land
use
planning,
environmental
review,
land
acquisition
and
other
protection
tools,
limitations
on
marina
construction
and
expansion,
and
installation
of
shoreline
hardening
structures.

As
part
of
the
designation
process
for
CNRAs,
the
PEP
has
identified
and
mapped
(
very
broadly)
the
resources
at
these
sites
that
require
protection.
Land
in
the
Peconic
watershed
available
for
development
has
been
mapped
by
the
Suffolk
County
Planning
Department
based
on
current
use
and
zoning.
Through
these
two
efforts,
specific
parcels
of
land
that
contain
significant
habitats
and
species
to
be
protected
can
be
identified
(
see
Chapter
7).

Protection
of
open
space
should
be
a
key
component,
although
other
zoning
and
land
use
controls
should
be
applied.
The
most
decisive
means
of
protecting
these
resources
is
for
a
government
or
private
conservation
organizations
to
acquire
the
property
and
manage
it
for
preservation
purposes.
Currently,
the
New
York
State
Open
Space
Preservation
Plan
identifies
priority
parcels
for
acquisition
by
the
State.
Open
space
acquisition
programs
funded
by
local
governments
or
other
groups
largely
use
this
document
to
guide
their
acquisition
decisions.
The
purchase
of
conservation
easements
is
a
less
expensive
alternative
and
may
be
equally
protective
of
the
resources.
If
direct
acquisition
or
conservation
easements
are
not
possible,
local
governments
should
work
with
landowners
and
developers
to
create
site
plans
that
maximize
protection
of
the
resources
while
allowing
suitable
use
of
properties
(
see
Chapter
7).

Many
current
and
potential
activities
within
the
CNRAs
may
affect
their
long­
term
viability.
The
following
activities
may
have
serious
individual
and
potential
cumulative
impacts:
docks,
shoreline
stabilization
structures,
dredging,
marinas,
artificial
reefs,
fish
farms,
fishing,
pesticides,
golf
courses,
jet
skis,
swimming
pools,
sewage
treatment
and
disposal,
building
and
adjacent
upland
development,
and
clearing
of
vegetation.
As
boundaries
are
finalized,
additional
threats
may
be
recognized
that
need
to
be
addressed.

Coordinate
CNRA
Activities
with
the
Significant
Coastal
Fish
and
Wildlife
Habitat
Program
As
part
of
the
Coastal
Zone
Management
Program,
which
is
managed
by
the
NYSDOS,
Significant
Coastal
Fish
and
Wildlife
Habitats
(
SCFWH)
were
designated
more
than
ten
years
ago.
Many
of
these
sites
overlap
with
or
are
contained
within
the
large
CNRAs
identified
by
PEP.
Narratives
for
Peconic
Estuary
Program
CCMP
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these
sites
are
in
the
process
of
being
updated
with
current
natural
resources
information,
and
the
designation
and
scoring
of
these
sites
are
being
revised
on
the
basis
of
this
new
information.
In
order
to
foster
consistency
and
coordination,
the
PEP,
NYSDOS,
and
NYSDEC
should
work
together
to
review
updated
Peconics
region
SCFWH
designations,
and
to
ensure
that
the
CNRA
initiative
complements
existing
protection
and
management
mechanisms,
including
the
SCFWH
and
Local
Waterfront
Revitalization
Plan
programs.
In
addition,
all
governmental
agencies
should
use
the
SCFWH
guidelines
to
evaluate
potential
impacts
that
may
occur
when
development
and
other
activities
are
considered
in
these
areas.

Steps
HLR­
1.1
Collect
and
interpret
natural
resource,
water
quality,
and
land
use
data
sets.
Use
GIS
Priority
technology
to
finalize
a
comprehensive
inventory
of
species,
natural
communities
and
water
quality,
refine
maps
(
including
development
of
maps
of
each
CNRA),
and
evaluate
individual
and
cumulative
threats
within
each
CNRA.

HLR­
1.2
Finalize
CNRA
boundaries
and
adopt
CNRAs
by
appropriate
levels
of
government.
Priority
HLR­
1.3
Develop
management
recommendations
and
plans
to
protect
CNRAs
in
each
town
in
Priority
coordination
with
existing
Federal,
State,
county,
and
municipal
programs
that
address
individual
and
potential
cumulative
impacts
including,
but
not
limited
to,
docks,
shoreline
stabilization
structures,
dredging,
marinas,
artificial
reefs,
fish
farms,
shellfish
culture,
fishing,
pesticides,
golf
courses,
motorized
personal
watercraft,
swimming
pools,
sewage
treatment
and
disposal,
building
and
adjacent
upland
development,
and
clearing
of
vegetation.

HLR­
1.4
Protect
the
CNRAs
through
land
acquisition
and
other
protection
tools
(
e.
g.,
clearing
Priority
restrictions,
setback
requirements,
zoning,
Transfer
of
Development
Rights)
principally
within
the
areas
themselves
and
including
essential
watershed
buffers
(
see
Chapter
7).

HLR­
1.5
Prohibit
the
installation
of
new
shoreline
hardening
structures
within
CNRAs.
Investigate
ecologically
enhancing,
innovative
designs
to
replace
or
use
as
an
alternative
to
hard
structures.

HLR­
1.6
Coordinate
PEP
recommendations
for
CNRAs
with
the
NYSDOS
Significant
Coastal
Fish
and
Wildlife
Habitat
Program
and
Local
Waterfront
Revitalization
Plan
Programs.

HLR­
1.7
Encourage
increased
use
of
the
NYSDOS
Significant
Coastal
Fish
and
Wildlife
Habitat
Program
guidelines
by
appropriate
Federal,
State,
county,
and
municipal
agencies.

HLR­
1.8
Examine
the
possibility
of
establishing
marine
reserves
(
e.
g.,
protect
eelgrass
beds)
within
the
CNRAs.

HLR­
1.9
Discourage
expansion
of
existing
marinas
and
the
creation
of
new
ones
within
the
PEP
CNRAs.
The
marina
expansion
and
creation
issue
will
be
further
evaluated
as
part
of
a
comprehensive
strategy
dealing
with
shoreline
hardening,
marinas,
docks,
and
public
access
(
see
HLR­
1.3).
Peconic
Estuary
Program
CCMP
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Responsible
Entities
HLR­
1.1
NYSDEC,
The
Nature
Conservatory
(
TNC)
(
co­
leads)
with
towns
and
USFWS
assistance
HLR­
1.2
NYSDEC,
The
Nature
Conservatory
(
co­
leads);
PEP
Natural
Resources
Subcommittee;
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
Riverhead,
and
Brookhaven;
NYSDEC;
OPRHP;
Suffolk
County
Parks
Department;
USFWS;
and
NYSDOS
HLR­
1.3
NYSDEC,
and
The
Nature
Conservatory
(
co­
leads)
to
assist
local
governments
in
coordination
with
PEP
Management
Conference,
EPA,
SCDHS
HLR­
1.4
NYSDEC;
NYS
Office
of
Parks;
Recreation
and
Historic
Preservation;
Suffolk
County
Planning
Department;
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
Riverhead,
and
Brookhaven
HLR­
1.5
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
Riverhead,
villages,
and
NYSDEC,
TNC,
SCDHS,
EPA,
Peconic
BayKeeper
HLR­
1.6
NYSDOS
(
lead),
NYSDEC,
and
PEP
Natural
Resources
Subcommittee
HLR­
1.7
NYSDOS
(
lead),
NYSDEC,
towns,
USACE,
USFWS,
and
NMFS
HLR­
1.8
PEP
Natural
Resources
Subcommittee,
EPA,
NYSDEC,
SCDHS
HLR­
1.9
Contingent
upon
adoption
of
CNRAs
(
see
HLR­
1.2)
Peconic
Estuary
Program
CCMP
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Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
3,
4,
6,
7,
and
8.

Hardened
Shorelines
and
Physical
Barriers
Bulkheads
can
result
in
erosion
or
deposition
of
sediments
up
or
downstream
of
the
structure,
which
may
result
in
the
destabilization
of
the
shoreline
and
encourage
adjacent
landowners
to
install
hardening
structures
along
the
shoreline.
The
scour
in
front
of
hardened
structures
could
also
eliminate
the
productive
and
protective
features
of
intertidal
and
shallow
water
areas.
Loss
of
shallow­
water
habitats
will
negatively
impact
shellfish,
forage
and
juvenile
fish
and
other
species
that
use
these
areas
for
spawning,
feeding,
or
mating
(
e.
g.,
horseshoe
crabs
and
birds).
This
"
domino
effect"
of
replacing
natural
shoreline
with
human­
made
structures
in
a
relatively
short
period
of
time
is
increasing
in
some
areas
and
resulting
in
considerable
risk
to
remaining
natural,
vegetated
shoreline.
Furthermore,
hardened
shorelines
prevent
the
natural
shoreward
migrations
of
salt
marshes,
which
is
particularly
important
to
consider
with
respect
to
rising
sea­
level.
In
addition
to
the
loss
of
beach
and
inter­
tidal
habitats,
bulkheads
can
adversely
impact
the
living
resources
from
the
leaching
of
toxins
such
as
copper,
chromium
and
arsenic
that
are
used
to
treat
lumber
(
see
Chapter
6).

Past
construction
of
physical
barriers
to
tidal
flow,
such
as
tide
gates,
culverts,
and
dams,
may
have
resulted
in
significant
changes
to
hydrography,
such
as
reduced
flushing
and
decreased
salinity
in
various
bodies
of
water.
Such
structures
also
have
blocked
the
passage
of
anadromous
fish
such
as
alewives,
into
creeks
and
the
Peconic
River.
Decreased
salinity
can
result
in
a
change
to
the
system
from
salt
marsh
to
fresh
or
brackish
wetlands
or
to
conditions
which
favor
the
invasion
of
the
nuisance
species,
Phragmites
australis.
Lower
flow
and
exchange
of
water
may
lead
to
increased
sedimentation
and
accumulation
of
toxic
compounds,
subsidence
of
the
marsh
surface,
drying
of
marsh
substrates,
and
increased
erosion.
Over
the
long
term,
these
conditions
may
result
in
the
conversion
of
the
marsh
to
terrestrial
habitat.

Many
of
these
restrictions
have
been
in
place
for
a
considerable
period
of
time
and
the
surrounding
habitats
have
adjusted
to
the
new
flow
regime.
In
some
cases,
these
equilibrations
may
have
resulted
in
conversion
of
one
type
of
habitat
to
another
of
equal
value
(
e.
g.,
estuarine
or
brackish
tidal
marshes
to
nontidal
freshwater
wetlands),
and
removing
the
structure
may
not
result
in
a
gain
in
habitat.
In
other
cases,
the
habitats
upstream
from
the
structure
may
have
become
severely
degraded
and
may
no
longer
support
a
biological
community
of
comparable
diversity
and
quality.

An
inventory
of
hardened
shorelines
and
physical
barriers
is
the
first
step
to
assess
the
impacts
that
these
structures
may
have
on
local
natural
resources.
An
inventory
of
hardened
shorelines
will
also
establish
a
baseline
from
which
estimates
can
be
made
regarding
the
rate
at
which
natural
shorelines
are
being
replaced
by
hard
structures.
Such
an
inventory
is
currently
underway
for
all
shoreline
hardening
structures
in
the
Peconic
Estuary.
Dams
have
already
been
mapped
in
the
PEP
Geographic
Information
System
by
the
USFWS,
but
the
status
of
other
structures
is
unknown.
All
watershed
creeks
should
be
inventoried
for
physical
barriers.
This
information
can
then
be
used
in
the
development
of
site­
specific
recommendations
for
these
practices.
HLR­
2
Manage
Shoreline
Stabilization,
Docks,
Piers,
and
Flow
Restriction
Structures
to
Reduce
or
Prevent
Additional
Hardening
and
Encourage
Restoration
of
Hardened
Shorelines
to
a
Natural
State.
Peconic
Estuary
Program
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The
PEP
CAC
has
recommended,
"
ideally,"
a
no
net
increase
in
hardened
shoreline
and
no
loss
in
habitat
policy.
State
policy,
while
permitting
hard
structures
under
some
circumstances,
gives
preference
to
non­
structural
measures
where
possible.
East
End
local
governments
can
further
this
policy
through
the
adoption
of
local
laws.
A
potential
alternative
is
for
the
East
End
Towns
to
create
and
adopt
local
regulations
that
further
control
the
installation
of
such
structures
in
the
Peconics.
A
recent
example
of
how
shoreline
hardening
structures
can
be
managed
by
local
governments
is
the
Town
of
East
Hampton's
proposed
Coastal
regulations.
The
Town
of
East
Hampton
has
developed
different
management
zones
for
its
coastlines
to
reduce
impacts
to
natural
resources
resulting
from
shoreline
hardening
structures.
If
adopted,
the
proposed
regulations
would
prohibit
new
shoreline
hardening
structures
from
being
installed
in
certain
zones,
while
other
zones
would
require
a
natural
resources
permit
from
the
town.
Similar
regulations
could
also
be
adopted
by
the
other
East
End
towns.

In
order
to
encourage
property
owners
to
remove
existing
structures,
incentive
programs
should
be
developed
under
which
owners
would
get
some
financial
benefit
for
removing
structures
and
replacing
them
with
a
natural
shoreline.
This
program,
coupled
with
a
public
education
program
on
the
benefits
of
natural
shorelines
and
a
program
that
disallows
additional
hardening
in
certain
areas,
could
lead,
in
time,
to
restoration
of
habitats.
Extensive
legal
research
would
be
required
to
implement
this
action
and
may
require
legislation.
Exploration
of
natural,
softer­
solution
alternatives
to
shoreline
protection
are
also
encouraged.
Possible
incentives
could
include
the
following:

 
"
Bulkhead
removal
districts"
where
groups
of
property­
owners
could
have
removal
costs
subsidized
by
local
governments
(
alternatively,
the
cost
to
the
municipality
of
removal
could
be
reimbursed
by
land
owners
over
a
period
of
time
through
property
taxes);

 
A
local
property
tax
reduction
for
a
period
of
time
to
encourage
property­
owners
to
remove
hard
structures
at
their
own
expense;
and,

 
A
program
for
purchasing
conservation
easements
on
shorefront
property
(
or
that
portion
of
properties
within
a
certain
distance
of
the
water).

Docks
and
Marinas
Marinas
provide
a
valuable
service
to
the
boating
public
and
allow
for
a
concentration
of
boats
such
that
individual
docks
and
mooring
areas
are
not
needed
throughout
the
estuary.
They
also
represent
a
significant
portion
of
the
economic
value
generated
by
the
estuary.
However,
the
structures
and
activities
associated
with
marinas
may
cause
damage
or
degradation
to
local
water
quality
and
living
organisms.
Improperly
sited
and
designed
marinas
may
also
cause
unnecessary
damage
to
adjacent
communities.

The
best
management
practices
(
BMPs)
documented
in
the
Coastal
Nonpoint
Source
Control
Program
(
CZARA,
Section
6217)
are
protective
of
natural
communities
and
habitats
while
allowing
the
continued
operation
of
marina
facilities.
The
PEP
has
funded
a
demonstration
project
of
a
model
marina,
which
implements
a
number
of
the
CZARA
BMPs.
These
BMPs
should
be
implemented
throughout
the
estuary
in
order
to
minimize
the
overall
impacts
of
marina
operations
on
the
system.

The
cumulative
impacts
of
docks
will
eventually
contribute
to
the
degradation
of
local
water
quality
and
natural
communities
through
fragmentation
of
habitats,
shading
of
submerged
aquatic
vegetation
and
other
potential
impacts.
It
is
not
clear
just
how
many
of
these
structures
exist
in
the
Peconics
and
exactly
where
they
are
located.
A
concentrated
effort
to
identify
all
of
them
and
to
assess
the
impacts
Peconic
Estuary
Program
CCMP
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that
they
have
had
and
are
having
on
adjacent
natural
communities
will
help
in
the
development
of
recommendations
on
how
to
manage
them
in
the
future.

Steps
HLR­
2.1
Quantify
and
map
all
hardened
shoreline,
docks
and
piers,
and
flow­
restriction
structures
Priority
in
the
Peconic
Estuary
and
assess
the
overall
impacts
of
stabilization
structures
on
natural
resources.
Develop
recommendations
to
promote
alternative
shoreline
management
and
incentives
for
maintaining
and
restoring
natural
shorelines.

HLR­
2.2
Review
existing
regulations
for
shoreline
hardening
structures
at
all
levels
of
government,
encourage
consistent
policies
and
strengthen
regulations
where
appropriate.

HLR­
2.3
Establish
and
enforce
a
policy
of
"
no
net
increase"
of
hardened
shoreline
in
the
Peconic
Priority
Estuary
and,
if
possible,
a
net
decrease
in
hardened
shoreline.
Use
HLR­
1
and
HLR­
2
as
a
mechanism
to
establish
this
strategy.

HLR­
2.4
Develop
a
variety
of
financial
incentives
and
programs
to
encourage
property
owners
to
Priority
remove
or
modify
hardened
shoreline
structures
and
replace
them
with
natural
vegetation
and
other
vegetated
(
bioengineered)
alternatives
to
restore
the
natural
shoreline
of
the
estuary.

Responsible
Entities
HLR­
2.1
Contract
with
Cornell
and
USFWS;
NYSDEC,
EPA,
SCDHS,
NYSDOS,
Towns
HLR­
2.2
PEP
Natural
Resources
subcommittee
through
contract
HLR­
2.3
PEP
Management
Conference
(
lead);
NYSDEC;
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
Riverhead;
villages;
NYSDOS;
USACE;
PEP;
SCDHS;
EPA
HLR­
2.4
Peconic
BayKeeper
(
lead);
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
and
Riverhead;
villages;
HRWG;
NYSDEC;
SCDHS;
PEP
Peconic
Estuary
Program
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Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
2,
3,
6,
and
7.

The
Suffolk
County
Department
of
Public
Works
(
SCDPW)
periodically
dredges
approximately
62
sites,
with
12
of
these
dredged
on
a
yearly
basis.
About
50,000
cubic
yards
of
sediment
are
dredged
by
SCDPW
in
the
Peconics
every
year
(
see:
Suffolk
County's
Generic
Environmental
Impact
Statement
for
dredging
in
the
Peconic
Estuary).
All
SCDPW
dredging
is
done
to
maintain
Federal,
State,
and
town
navigational
channels.
Permission
for
new
dredging
has
not
been
granted
for
years;
only
maintenance
dredging
has
been
permitted.
Dredging
is
usually
done
because
of
the
accumulation
of
sediment
that
fills
in
channels
and
basins,
effectively
reducing
the
depth
and
the
draft
of
vessels
that
can
use
these
areas.
Sediment
accumulation
at
these
sites
may
be
the
result
of
changes
in
the
shoreline
or
in
adjacent
land
uses,
such
as
increases
in
impervious
surfaces
(
and
a
corresponding
increase
in
stormwater
runoff);
the
loss
of
buffering
vegetation
along
the
shoreline;
hardening
of
the
shoreline
by
the
replacement
of
natural
vegetation
with
bulkheads
and
rip­
rap;
historical
hydrological
modifications
from
diking,
draining,
and
filling
of
shoreline
areas
or
creation
of
dredge
spoil
islands;
and
loss
of
submerged
aquatic
vegetation
which
would
normally
stabilize
bottom
sediments.
These
changes
can
alter
currents
and
the
effects
of
tides,
allowing
erosion
or
scouring
and
subsequent
resuspension
of
particles.
The
need
for
repeated
dredging
may
be
reduced
or
eliminated
in
the
long
term
if
some
of
these
problems
are
remediated.

A
variety
of
concerns
have
arisen
over
the
years
about
the
impacts
of
dredging
on
natural
communities.
One
concern
is
that
dredging
disturbs
habitat
used
by
different
species
during
various
life
stages,
such
as
reproduction.
For
example,
it
is
possible
that
the
current
window
of
time
during
which
dredging
is
allowed
may
not
be
sufficiently
protective
of
winter
flounder,
which
spawn
in
mid­
to
late
winter
in
shallow
embayments
and
creeks
and
have
demersal
eggs.
Endangered
shorebirds,
which
nest
on
beaches
from
April
through
August,
also
are
vulnerable
to
disturbance.
Other
possible
impacts
include
damage
to
existing
eelgrass
beds
or
the
creation
of
water
quality
conditions
that
are
not
favorable
to
eelgrass
(
high
turbidity).
The
re­
suspension
of
toxic
chemicals,
including
metals,
PAHs,
PCBs,
and
pesticides,
which
tend
to
be
found
in
association
with
particles
in
aquatic
systems,
is
another
concern.
In
the
past,
dredged
material
from
the
Peconic
Estuary
System
has
shown
very
little
contamination;
however,
examination
of
sediments
in
the
Peconic
Estuary
System
by
PEP
contractors
has
shown
that
some
chemicals
can
be
found
in
a
few
sites
at
concentrations
above
background.
For
that
reason,
it
may
be
useful
to
have
newly­
dredged
material
tested
occasionally.
The
NYSDEC
is
drafting
marine
dredging
and
disposal
protocols,
which
will
provide
guidance
on
testing
requirements.

In
order
to
foster
public
discussion
about
dredging
and
its
impacts,
the
PEP
will
sponsor
a
workshop
for
all
interested
parties
to
define
specific
concerns.
The
workshop
should
result
in
the
production
of
a
report
containing
consensus­
based
dredging
recommendations
and
guidelines.
The
guidelines
should
be
specific
for
each
site
dredged
in
the
Peconic
Estuary
System
and
should
include
descriptions
of
each
site
and
the
natural
resources
of
concern
at
each
site,
including
endangered
species.
The
guidelines
should
also
include
recommendations
on
timing,
frequency,
and
equipment,
as
well
as
dredged
material
placement.
HLR­
3
Assess
the
Impacts
of
Dredging
Activities
on
Habitat
and
Natural
Resources
and
Develop
Recommendations
and
Guidelines
for
Reducing
those
Impacts.
Peconic
Estuary
Program
CCMP
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Steps
HLR­
3.1
Hold
a
"
Dredging
Summit"
for
the
Peconic
Estuary
System
to
address
specific
concerns
Priority
(
i.
e.,
impacts
on
shorebird
nesting,
demersal
fish
eggs,
benthic
communities,
and
the
potential
release
of
contaminants)
and
develop
dredging
guidance
on
an
embaymentspecific
basis
and
for
identified
CNRAs.
Integrate
dredging
guidance
into
existing
regulatory
programs.

HLR­
3.2
Assess
navigational
dredging
in
tidal
creeks
and
embayments
(
utilizing
Suffolk
County's
Priority
Generic
Environmental
Impact
Statement)
for
damages
or
impacts
to
eelgrass
beds
and
other
habitats
and
develop
permit
conditions
to
minimize
impacts
that
potentially
could
result
in
habitat
loss
and
degradation.
Determine
if
navigational
dredging
locally
impairs
water
quality
to
the
point
of
precluding
restoration
of
eelgrass.

HLR­
3.3
Determine
the
need
for
frequency
of
maintenance
dredging
and
develop
recommendations
to
reduce
runoff
and
erosion
in
creeks
to
reduce
the
need
for
maintenance
dredging.

Responsible
Entities
HLR­
3.1
NYSDEC
(
lead)
through
contractor;
USACE;
NYSDOS;
SCDPW;
EPA;
SCDHS;
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
and
Riverhead;
and
other
interested
stakeholders
HLR­
3.2
PEP
through
contractor,
NYSDEC,
DOS,
SCDHS
HLR­
3.3
Frequency
of
dredging:
SCDPW
(
lead);
Runoff
recommendations:
NYSDEC,
NYSDOS
(
co­
leads),
PEP,
SCDHS
Peconic
Estuary
Program
CCMP
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Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
3,
5,
6,
and
8.

Eelgrass
beds
are
the
preferred
habitat
of
bay
scallops,
and
dredging
for
scallops
is
frequently
done
near
the
few
remaining
eelgrass
beds
in
the
estuary.
Certain
types
of
dredges
or
improper
operation
of
dredges
can
result
in
uprooting
or
damaging
the
plants,
which
may,
over
time,
lead
to
permanent
damage
to
the
beds.
In
other
areas
of
the
country,
beds
of
seagrasses
are
frequently
damaged
and
scarred
by
boat
propellers,
which
become
tangled
in
the
seagrass
when
the
boats
are
run
at
high
speed
through
the
beds.
It
is
not
clear
if
the
potential
damage
caused
by
either
scallop
dredges
or
boat
propellers
from
commercial
and
recreational
vessels
is
significant
in
Peconic
Estuary
eelgrass
beds.
This
issue
should
be
investigated
to
determine
if
further
recommendations
should
be
made
regarding
types
of
equipment
or
methods
of
dredging,
or
recommendations
regarding
the
speed
and
manner
at
which
boats
should
be
operated
when
over
eelgrass
beds.

The
Towns
of
Riverhead
and
Southampton
permit
the
use
of
a
method
of
shellfish
harvesting
known
as
propeller
dredging.
In
this
method,
the
propeller
of
a
boat
engine
(
either
attached
to
a
boat
or
not)
is
used
to
churn
away
soft
sediments
where
soft
clams
are
found.
The
New
York
State
Environmental
Conservation
Law
allows
for
"
churning"
for
soft
clams
only
below
the
low
tide
mark.
The
method
can
be
a
faster,
less
labor­
intensive
method
of
removing
sediment
and
finding
the
buried
shellfish.
Unfortunately,
this
method
also
disturbs
much
larger
areas
and
may
be
more
damaging
to
certain
communities
over
the
long
term.
Fishermen
contend
that
churning
is
not
done
near
eelgrass
beds,
only
in
mudflats
and
subtidal
areas,
where
it
is
believed
to
increase
productivity.
Communities
of
particular
concern
include
eelgrass
beds,
mudflats,
and
shallow
subtidal
areas
adjacent
to
vegetated
tidal
wetlands.
This
potential
for
permanent
damage
to
sensitive
communities
should
be
examined
in
comparison
to
disturbance
and
damage
caused
by
other
methods
of
harvesting
shellfish
before
recommendations
are
developed
regarding
this
method.
The
State
permits
the
use
of
rakes
and
tongs
on
public
bottom
for
hard
clams
while
dredges
are
allowed
on
private
lands.

Hard
clams,
soft
clams,
and
oysters
are
found
in
unvegetated
mudflats
(
usually
where
mud
and
sand
meet)
and
harvesters
typically
concentrate
in
these
areas.
In
many
cases,
however,
harvesters
may
work
their
way
in
the
mudflats
right
up
to
the
edge
of
the
vegetated
zone,
where
the
salt
marsh
peat
forms.
These
commercial
species
of
shellfish
are
not
found
in
the
vegetated
or
peat
areas.
Digging
for
shellfish
right
at
this
edge
destabilizes
the
vegetation
and
renders
these
areas
vulnerable
to
erosion
with
subsequent
loss
of
Spartina.
This
may
contribute
over
time
to
loss
of
the
vegetated
wetlands.
Therefore,
this
practice
should
be
discouraged
or
banned.

Steps
HLR­
4.1
Examine
methods
of
harvesting
clams,
scallops,
and
other
shellfish
and
determine
which
are
most
compatible
with
eelgrass
establishment
and
growth.
Develop
recommendations
for
harvesting
methods,
frequency,
and
timing,
which
will
allow
recovery
of
eelgrass
throughout
the
estuary
and
enhance
shellfish
productivity.
HLR­
4
Examine
and
Promote
Methods
of
Shellfish
Harvesting
that
are
Most
Compatible
with
Establishment
and
Growth
of
Eelgrass
Beds
and
Vegetated
Salt
Marshes.
Peconic
Estuary
Program
CCMP
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HLR­
4.2
Discourage
harvesting
of
shellfish
at
the
edge
of
vegetated
salt
marshes
and
encourage
the
use
of
methods
that
minimize
impacts
to
vegetated
habitats.

Responsible
Entities
HLR­
4.1
NYSDEC
(
lead)
through
contract
HLR­
4.2
NYSDEC
(
lead);
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
and
Riverhead;
PEP
Public
Education
and
Outreach
program;
and
shellfishermen
Peconic
Estuary
Program
CCMP
C
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37
Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
2,
3,
4,
6,
and
7.

The
protection
from
draining,
filling,
and
dredging
of
all
wetlands
by
section
404
of
the
Clean
Water
Act
and
tidal
wetlands
by
Article
25
of
the
NYS
ECL
has
been
very
successful.
It
is
important
that
no
matter
what
additional
preservation
and
restoration
activities
are
undertaken
to
increase
the
quality
and
quantity
of
the
wetland
resources
in
the
Peconic
Estuary
System,
these
existing
programs
must
remain
intact
and
continue
to
be
supported
by
the
public
and
elected
officials.
These
programs
represent
the
most
fundamental
level
of
protection
that
these
habitats
have.

In
the
past,
tidal
wetlands
were
extensively
ditched
in
order
to
facilitate
the
drainage
of
the
wetlands
at
low
tide.
The
purpose
of
this
was
to
minimize
the
amount
of
standing
water
in
the
marsh,
which
could
be
used
as
mosquito
breeding
areas.
However,
these
ditches
caused
excessive
drainage
of
tidal
wetlands
at
low
tide,
disturbing
the
natural
functioning
of
the
marsh,
which
supports
a
wide
variety
of
other
species
in
the
standing
pools
of
water
which
are
left
on
the
marsh
at
low
tide.
Although
diminution
of
standing
water
was
thought
to
reduce
the
populations
of
mosquitoes,
it
is
now
thought
that
the
pools
actually
provide
habitat
for
small
finfish
(
killifish)
which
eat
mosquito
larvae.
Over
the
past
few
years,
Suffolk
County
Vector
Control
(
SCVC)
has
discontinued
its
practice
of
creating
new
ditches
and
implementing
Open
Mash
Water
Management
to
restore
marshes
to
their
former
State
and
control
mosquito
populations.
This
policy
should
be
supported.
Additionally,
the
PEP
encourages
better
coordination
among
SCVC
and
all
other
agencies
and
towns
for
maintenance
of
existing
ditches
and
planning
of
mosquito
control
practices
in
wetlands.

Steps
HLR­
5.1
Ensure
continued
protection
of
freshwater
and
tidal
wetlands
through
the
implementation
and
enforcement
of
current
regulations
under
the
Federal
Clean
Water
Act
and
the
State
Wetlands
Protection
Programs,
local
government
regulations
and
local
land
use
practices.

HLR­
5.2
Review
existing
tidal
wetlands
protection
policies
to
determine
if
they
provide
for
maintenance
of
tidal
wetlands
with
respect
to
future
sea­
level
rise.

HLR­
5.3
Maintain
and
enforce
the
policy
of
creating
no
new
mosquito
ditches
in
tidal
wetlands
and
establish
a
policy
for
not
re­
opening
ditches
that
have
filled­
in
by
natural
processes.

HLR­
5.4
Ensure
that
SCVC
works
cooperatively
with
all
government
agencies,
East
End
towns
and
local
conservation
organizations
in
the
planning
of
wetland
mosquito
ditch
maintenance
and
pesticide
spraying.
HLR­
5
Implement,
Enforce,
and
Encourage
the
Continuation
of
Current
Policies
and
Regulations
Protective
of
Wetlands.
Peconic
Estuary
Program
CCMP
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Responsible
Entities
HLR­
5.1
NYSDEC
(
lead),
USACE,
East
End
Towns
HLR­
5.2
PEP­
Natural
Resources
Subcommittee
through
contractor
HLR­
5.3
SCVC
(
lead),
NYSDEC,
EPA,
SCDHS,
NYSDOS,
East
End
Towns
HLR­
5.4
SCVC
(
lead),
SCDHS,
EPA,
NYSDEC,
East
End
Towns
Peconic
Estuary
Program
CCMP
C
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39
Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
2,
3,
5,
6,
and
8.

Eelgrass
beds
are
an
important
marine
habitat
for
finfish
and
invertebrates
which
use
them
for
foraging,
shelter
and
nursery
areas.
Unfortunately,
many
of
the
eelgrass
beds
in
Peconic
Estuary
have
been
declining
and
the
causal
factors
responsible
for
this
decline
remain
somewhat
elusive.
The
remaining
eelgrass
beds
therefore,
should
be
protected
from
direct
human
threats
such
as:
propeller
scarring
and
anchor
dragging,
while
further
research
on
the
factors
contributing
to
the
health
of
eelgrass
beds
in
the
Peconics
should
be
encouraged
for
future
management
recommendations.
The
NYS
Tidal
Wetlands
Act
(
NYS
ECL,
Article
25)
gives
the
NYSDEC
authority
over
lands
under
tidal
waters
to
a
depth
of
six
feet
below
mean
low
water.
This
means
that
eelgrass
located
in
water
of
six
feet
or
less
are
protected
from
activities
such
as
excavation,
dumping,
erection
of
pilings
or
any
other
activity
that
may
substantially
impair
or
alter
natural
conditions.
Eelgrass
located
at
a
depth
of
six
feet
below
mean
low
water
also
are
protected
by
NYS
Use
and
Protection
of
Waters
(
NYS
ECL,
Article
15,
Title
5)
for
activities
involving
excavation
and
placement
of
fill
and
docks
and
moorings.
However,
because
eelgrass
beds
have
not
been
thoroughly
mapped
and
sometimes
may
not
be
visible
with
the
naked
eye,
they
could
be
overlooked
during
a
permit
application
review.

Steps
HLR­
6.1
Evaluate
the
effectiveness
of
current
policies
in
preserving
eelgrass
habitat
and
Priority
develop
ways
to
provide
increased
protection
for
all
extant
eelgrass.

HLR­
6.2
Monitor
and
protect
extant
eelgrass
(
Zostera
marina)
beds,
and
restore
degraded
eelgrass
beds.

HLR­
6.3
Evaluate
anchor
dragging,
propeller
scarring,
dredging
and
other
known
impacts
to
extant
eelgrass
beds
in
the
Peconic
Estuary
and
develop
recommendations
to
reduce
them.

HLR­
6.4
Hold
a
workshop
to
evaluate
the
factors
that
regulate
the
health
and
extent
of
eelgrass
beds
in
the
Peconic
Estuary
and
develop
management
recommendations
based
on
these
findings.

Responsible
Entities
HLR­
6.1
NYSDEC
(
lead)
through
contract
HLR­
6.2
NYSDEC
(
lead),
Cornell
Cooperative
Extension,
PEP­
Natural
Resources
Subcommittee,
and
PEP
HRWG
HLR­
6.3
NYSDEC
and
Habitat
Restoration
Workgroup
(
co­
leads)
through
contract
HLR­
6.4
NYSDEC,
PEP­
NRSC,
and
PEP
HRWG
(
co­
leads)
HLR­
6
Evaluate
the
Effectiveness
of
Current
Policies
in
Preserving
Eelgrass
Habitat
and
Develop
Ways
to
Provide
Increased
Protection
for
all
Extant
Eelgrass.
Peconic
Estuary
Program
CCMP
C
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Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
2,
4,
and
7.

Areas
where
resources
are
under
stress
or
no
longer
exist
need
to
be
identified
for
restoration.
To
ensure
a
comprehensive
and
coordinated
approach
to
restoration
activities,
the
PEP
advocates
formulating
an
overall
strategy
for
restoration:
an
estuary­
wide
Habitat
Restoration
Plan
(
HRP).

The
PEP
has
committed
to
the
formation
of
a
Habitat
Restoration
Work
Group
(
HRWG)
which
will
articulate
the
overall
goals
of
restoration
in
the
Peconic
Estuary,
identify
and
prioritize
the
types
of
habitats
in
need
of
restoration,
identify
the
specific
locations
in
the
Peconic
Estuary
where
restoration
of
these
habitat
types
is
feasible,
and
develop
a
process
and
criteria
for
project
selection
as
well
as
prioritization
of
selected
sites.

Not
all
estuarine,
intertidal,
or
terrestrial
habitats
found
in
the
Peconic
watershed
are
in
need
of
restoration,
are
considered
important
to
restore,
or
can
be
successfully
restored
given
current
levels
of
knowledge
and
technology.
As
the
first
step
in
developing
the
restoration
plan,
the
HRWG
will
develop
a
list
of
the
habitats
it
considers
most
important
for
restoration.
A
draft
list
has
already
been
developed
and
will
be
discussed
and
reviewed
prior
to
acceptance
into
the
final
plan.
These
habitats
currently
include:

 
Coastal
Grasslands;

 
Beaches
and
Dunes;

 
Riverine
Migratory
Corridors
and
Habitat;

 
Tidal
Wetlands;

 
Non­
tidal
Freshwater
Wetlands;

 
Submerged
Aquatic
Vegetation;

 
Estuarine
Embayments;

 
Coastal
Forest
Communities;
and,

 
Intertidal
Flats.

The
next
step
in
the
development
of
an
overall
restoration
plan
is
the
assessment
of
the
current
quantity
of
identified
priority
habitats.
Information
collected
for
this
inventory
would
include
the
quantity
of
habitat,
the
subjective
condition
in
which
it
exists,
whether
it
is
in
need
of
restoration,
and
what
level
of
restoration
can
be
achieved.
In
some
cases,
there
have
been
inventories
done
on
particular
lands
for
certain
types
of
habitat
(
e.
g.,
Town
of
Southampton­
owned
properties
have
been
identified
which
once
were
estuarine
wetlands
and
could
be
restored).
The
HRWG
will
compile
inventories
that
have
been
done
and
will
solicit
additional
site
nominations
from
Federal,
state,
and
local
governments
and
interest
groups.

The
third
step
in
the
HRP
creation
process
is
the
development
of
criteria
for
the
selection
of
restoration
sites.
There
are
a
number
of
factors
which
must
be
considered
when
selecting
sites
to
be
restored,
including:
1)
the
general
level
of
knowledge
about
the
specific
habitat
type;
2)
the
history
of
success
of
restorations
of
each
habitat
type;
and
3)
historical
information
for
each
site,
including
HLR­
7
Develop
and
Implement
an
Estuary­
Wide
Habitat
Restoration
Plan
(
HRP).
Peconic
Estuary
Program
CCMP
C
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causes
of
loss
or
degradation
of
the
habitat
and
the
current
status
of
those
stressors.
Other
factors
to
be
considered
in
site
selection
are
cost
and
ease
of
restoration,
community
acceptance
of
restoration,
and
surrounding
land
uses,
all
of
which
affect
the
likelihood
of
success.
To
assist
in
the
final
selection
of
restoration
sites,
information
about
ongoing
and
completed
restoration
projects
needs
to
be
compiled
and
assessed
as
to
cost,
success,
and
other
parameters.
Restoration
projects
that
are
completed
or
ongoing
include
tidal
wetland
restorations
at
a
variety
of
locations,
a
freshwater
wetland
restoration
in
Southold
(
e.
g.,
Cassidy
Preserve),
and
a
maritime
grassland
restoration
at
Orient
Point.

The
HRWG
will
encourage
municipalities
to
develop
plans
for
identified
restoration
opportunities
and
will
assist
municipalities
who
have
completed
restoration
planning
in
obtaining
funding
and
implementing
their
restoration
projects.
The
PEP
HRWG
and
its
member
agencies
will
develop
the
HRP
and
a
variety
of
planning
efforts
associated
with
it,
but
it
will
be
up
to
local
governments
and
other
groups
to
implement
restoration
projects
through
the
NYS
Clean
Water/
Clean
Air
Bond
Act
and
with
other
funds
(
e.
g.,
Suffolk
County
1/
4%
sales
tax).
Because
projects
that
are
eligible
for
NYS
Bond
Act
funds
must
involve
actual
implementation
of
habitat
restoration
projects,
Bond
Act
funds
cannot
be
spent
on
planning
or
other
activities
done
in
preparation
for
implementation.
Therefore,
the
NYSDOS
has
targeted
the
EPF
funds
over
which
it
has
jurisdiction
towards
inventory
and
planning
projects
in
order
to
complement
the
Bond
Act
funds.
Local
governments
that
have
the
desire
to
restore
habitats
but
have
not
yet
developed
plans
may
use
these
funds
for
that
initial
work.

There
are
already
existing
habitat
inventories
and
sites
targeted
for
habitat
restoration
by
groups
participating
in
the
PEP
HRWG.
If
these
efforts
meet
the
criteria
being
developed
by
the
HRWG,
they
should
not
be
held
up
by
the
development
of
the
entire
Habitat
Restoration
Plan,
but
should
be
allowed
to
move
forward
for
funding.
These
projects
should
be
reviewed
and
discussed
by
the
HRWG
with
regard
to
the
priority
habitat
list
and
the
monitoring
criteria
to
be
developed.
Based
on
these
discussions,
recommendations
for
funding
under
the
NYS
Bond
Act
should
be
prepared
for
forwarding
to
NYSDEC
Bond
Act
staff.
Not
all
of
these
projects
will
be
able
to
be
funded
through
the
Bond
Act,
so
other
sources
of
restoration
funds
should
also
be
sought
and
application
should
be
encouraged.

Steps
HLR­
7.1
Develop
and
implement
an
estuary­
wide
Habitat
Restoration
Plan
(
HRP).
Priority
HLR­
7.2
Identify
and
list
priority
habitat
types
for
the
HRP.

HLR­
7.3
Inventory
and
prioritize
a
list
of
restoration
projects
for
which
planning
is
underway
and
Priority
recommend
these
for
"
fast­
tracking"
towards
Bond
Act
funding.

HLR­
7.4
Inventory
and
list
restoration
opportunities
in
the
PEP
area
and
estimate
costs.

HLR­
7.5
Develop
and
include
in
the
HRP
criteria
for
selection
of
restoration
sites.

HLR­
7.6
Inventory
and
list
completed,
ongoing,
and
proposed
restoration
projects
for
inclusion
in
the
HRP.
Include
all
restoration
sites
on
GIS
maps.

HLR­
7.7
Develop
and
include
in
the
HRP
a
list
of
funding
sources
available
for
habitat
restoration
in
the
PEP
area.
Peconic
Estuary
Program
CCMP
C
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HLR­
7.8
Develop
model
guidelines
for
habitat
restoration
planning
for
use
by
municipalities
in
applying
for
Environmental
Protection
Fund
(
EPF)
monies.

Responsible
Entities
HLR­
7.1
PEP
HRWG
(
lead)

HLR­
7.2
PEP
HRWG
(
lead)

HLR­
7.3
NYSDOS
(
lead),
NYSDEC,
and
PEP
HRWG
HLR­
7.4
PEP
HRWG
(
lead)
and
East
End
Towns
HLR­
7.5
PEP
HRWG
(
lead)

HLR­
7.6
PEP
HRWG
(
lead)

HLR­
7.7
PEP
HRWG
(
lead)

HLR­
7.8
NYSDEC
and
NYSDOS
(
co­
leads);
PEP
HRWG;
EPA;
Towns;
CCE
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
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O
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4­
43
Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
3,
4,
6,
7,
and
8.

Tidal
wetlands,
beaches,
and
submerged
aquatic
vegetation
are
three
priority
habitats
designated
for
restoration
by
the
PEP
HRWG.
A
number
of
effective
actions
can
be
taken
by
the
HRWG
and
others
to
ensure
that
restoration
plans
are
created
and
implemented
for
these
important
habitats.

Tidal
wetlands
have
been
altered
by
mosquito
ditching
and
the
growth
of
the
invasive
species
Phragmites
australis.
Mosquito
ditches
cause
excessive
drainage
of
tidal
wetlands
at
low
tide.
Although
the
diminution
of
standing
water
was
thought
to
reduce
the
populations
of
mosquitoes,
it
is
now
thought
that
those
pools
actually
provide
habitat
for
small
finfish
which
eat
mosquito
larvae.
In
addition,
the
ditches
allowed
pathogens
contained
in
the
water
to
enter
the
system
and
be
taken
up
by
shellfish.
Damming
or
otherwise
maintaining
the
water
on
the
marsh
allows
time
for
the
pathogens
to
die
off
before
entering
the
estuary
(
see
Chapter
5).
These
ditches
should
be
dammed
or
modified,
through
a
series
of
practices
known
as
Open
Marsh
Water
Management
(
OMWM),
so
as
to
restore
the
marshes
to
a
condition
similar
to
that
which
existed
prior
to
ditching.

Tidal
wetlands
and
beaches
have
been
negatively
impacted
by
the
construction
of
hard
shoreline
structures
and
the
removal
of
native
plants.
Restoration
of
tidal
wetlands
and
beaches
could
be
accomplished
through
the
removal
of
hard
shoreline
structures
and
regrading
and
planting
of
the
areas
with
wetland
or
beach
plants.

Eelgrass
beds
are
declining
in
the
Peconic
Estuary.
Exact
causes
are
not
known,
but
it
is
believed
that
the
beds
have
been
impacted
by
the
effects
of
the
Brown
Tide
as
well
as
poor
water
quality
conditions,
including
high
levels
of
nitrogen
and
suspended
sediment
and
possibly
terrestrial
applications
of
pesticides
and
herbicides.
Actions
to
implement
this
additional
goal
of
protecting,
restoring,
and
enhancing
eelgrass
habitat
supports
the
overall
vision
of
what
the
CCMP
hopes
to
achieve
with
water
quality,
habitat,
and
living
resources.

Not
all
habitat
restoration
projects
require
large
amounts
of
funding
and
highly
technical
work
plans
in
order
to
mitigate
the
impacts
of
stress
and
encourage
the
return
of
plant
and
animal
communities.
Many
areas
are
only
slightly
degraded
and
can
be
restored
with
the
aid
of
relatively
untrained
individuals.
Examples
include
dune
restoration
through
the
planting
of
beach
grasses;
Phragmites
australis
and
other
exotic
or
nuisance
species
removal
by
physically
cutting
or
digging
out
the
plants
in
areas
of
minimal
invasion
and
replanting
with
native
species;
or
simply
removing
garbage
and
trash
from
beaches,
wetlands,
and
clogged
waterways.
Some
of
these
efforts
have
already
been
organized
and,
if
possible,
should
be
expanded.
Citizen
restoration
projects
should
be
identified
and
local
groups
should
be
encouraged
to
work
with
technical
experts
to
implement
restoration
and
postrestoration
monitoring.
This
kind
of
effort
not
only
saves
money,
but
also
fosters
a
sense
of
stewardship
and
caring
for
the
environment
in
the
public.
Therefore,
three
steps
should
be
taken:
1)
identify
simple
restoration
actions
appropriate
for
local
volunteers;
2)
identify
and
contact
appropriate
local
groups
to
participate;
and
3)
develop
an
outreach
effort
to
solicit
additional
projects
and
volunteers.
HLR­
8
Develop
and
Implement
Specific
Restoration
Projects.
Peconic
Estuary
Program
CCMP
C
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44
Steps
HLR­
8.1
Encourage
cooperation
among
governmental
agencies
to
plan
and
implement
Open
Marsh
Water
Management
(
OMWM)
to
manage
tidal
wetlands
with
grid
ditches
for
mosquito
control
with
the
goal
of
also
restoring
more
natural
conditions.

HLR­
8.2
Develop
recommendations
in
the
PEP
Habitat
Restoration
Plan
for
control
of
Phragmites
australis
by
restoration
of
natural
processes
such
as
removal
or
modification
of
flowrestriction
devices,
removal
of
hardened
shorelines,
and
revegetation
of
bay
and
creek
shorelines
or
by
other
means.

HLR­
8.3
Develop
a
quantitative
goal
for
eelgrass
restoration
based
on
ongoing
monitoring
and
Priority
mapping
efforts.

HLR­
8.4
Identify
and
prioritize
locations
where
restoration
of
eelgrass
is
most
feasible
based
on
water
quality
and
environmental
criteria
which
are
being
developed
for
eelgrass
in
the
Peconic
Estuary
System
and
elsewhere
in
its
range.

HLR­
8.5
Develop
and/
or
utilize
cooperative
programs
with
the
public
for
simple,
local
habitat
improvements
and
enhancements.

Responsible
Entities
HLR­
8.1
Cornell
Cooperative
Extension
(
CCE),
SCVC,
USFWS,
East
Hampton
Department
of
Natural
Resources,
and
NYSDEC
(
co­
leads),
PEP
HLR­
8.2
PEP
HRWG
(
lead)
through
contractor
HLR­
8.3
PEP
HRWG
(
lead),
NYSDEC,
SCDHS,
CCE,
DOS,
Towns
HLR­
8.4
PEP
HRWG
(
lead),
PEP,
NYSDEC,
and
NYSDOS
HLR­
8.5
PEP
HRWG
(
lead),
NY
Sea
Grant,
and
Cornell
Cooperative
Extension
Peconic
Estuary
Program
CCMP
C
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45
Addresses
Habitat
and
Living
Resources
Management
Objective
8.

Restoration
activities
have
been
conducted
in
the
past
which
may
not
have
actually
resulted
in
a
longterm
recovery
of
the
targeted
habitat.
These
projects
were
frequently
done
with
little
or
no
follow­
up
monitoring,
an
activity
that
might
have
helped
determine
if
the
restored
habitat
was
able
to
maintain
itself
or
if
the
conditions
causing
loss
or
degradation
of
the
habitat
still
existed,
leading
to
the
failure
of
the
restoration.
If
restored
areas
are
monitored,
factors
affecting
the
success
of
the
project
over
the
long
term
can
be
identified
and
steps
can
be
taken
to
mitigate
or
"
correct"
the
restoration
so
that
the
habitat
can
flourish.
It
is
important
to
develop
sets
of
criteria
or
guidelines
for
restoration
monitoring
for
each
priority
habitat
type
that
are
relatively
easy
to
measure,
can
be
tailored
to
projects
of
differing
conditions
and
goals,
and
employed
by
groups
of
various
levels
of
technical
expertise.
The
above
facts
have
been
recognized
by
the
Habitat
Restoration
Committee
of
the
Long
Island
Sound
Study,
by
the
NYSDOS
Coastal
Resources
Program,
and
by
the
NYSDEC,
particularly
with
respect
to
the
NYS
Clean
Water/
Clean
Air
Bond
Act
Aquatic
Habitat
Restoration
projects
to
be
funded.
The
PEP
HRWG
can
work
with
all
of
these
entities
to
develop
a
set
of
criteria
for
each
habitat
type.

Monitoring
data
and
other
information
collected
from
restoration
projects
are
most
useful
if
collected
in
a
standardized
fashion,
stored
in
a
central
repository,
and
made
accessible
to
managers,
interested
groups,
academic
researchers,
and
other
programs
conducting
and
evaluating
restoration.
Project
information
not
collected
and
stored
in
this
manner
may
be
lost
over
time
as
a
result
of
staff
turnover
or
student
graduation,
among
other
factors.
Also,
lack
of
access
to
information
from
prior
projects
may
hinder
regional
planning
efforts
and
result
in
the
repetition
of
mistakes.
Therefore,
the
PEP
should
develop
an
appropriate
collection
procedure
and
storage
format
for
restoration
project
information,
and
identify
a
location
for
a
long­
term
repository
of
such
information
for
the
PEP
area.

Steps
HLR­
9.1
Develop
and
implement
procedures
to
track
and
evaluate
restoration
efforts
using
success
criteria
and
monitoring
protocols
in
the
PEP
area.

HLR­
9.2
Develop
procedures
for
the
management
and
storage
of
habitat
restoration
project
and
monitoring
information
for
the
Peconic
Estuary.

HLR­
9.3
Identify
a
regional
set
of
reference
sites
to
assist
in
habitat
restoration
evaluation
and
monitoring
and
provide
a
framework
for
long­
term
habitat
and
living
resources
research
and
monitoring.

Responsible
Entities
HLR­
9.1
PEP
HRWG
(
lead)

HLR­
9.2
PEP
HRWG
(
lead)
and
PEP
HLR­
9.3
PEP
HRWG
and
PEP
Natural
Resources
Subcommittee
HLR­
9
Monitor
and
Evaluate
the
Success
of
Restoration
Efforts.
Peconic
Estuary
Program
CCMP
C
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46
Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
2,
5,
6,
7,
and
8.

Historically,
the
Peconic
Estuary
has
supported
successful
shellfish
aquaculture.
Aquaculture
activities
can
vary
widely
in
scale
and
therefore,
in
the
potential
impacts
they
may
have
on
the
environment.
In
an
estuarine
system
such
as
the
Peconic
Estuary,
which
is
relatively
shallow
and
fairly
enclosed,
especially
west
of
Shelter
Island,
it
is
important
to
determine
the
amount
and
type
of
aquaculture
that
should
be
permitted
without
causing
adverse
impacts
to
the
entire
estuary
or
to
local
embayments.
An
estuary­
wide
aquaculture
plan
could
be
used
to
develop
guidelines
and
criteria
for
aquaculture
operations,
identify
suitable
areas
where
aquaculturing
can
be
employed,
develop
monitoring
protocols,
and
control
the
commercial
culture
of
non­
indigenous
and
imported
species.

The
NYSDEC
has
responsibility
for
developing
and
enforcing
State­
wide
aquaculture
policy,
however,
Suffolk
County
has
been
given
certain
specific
rights
to
develop
such
policies
in
the
Peconic
Estuary.
An
overall
plan
has
not
yet
been
developed,
but
could
be
facilitated
through
input
from
the
PEP
and
other
interested
groups.
For
this
reason,
it
is
important
to
begin
to
develop
a
comprehensive
aquaculture
policy
for
the
Peconic
Estuary
Program
by
sponsoring
a
workshop
to
which
all
interested
parties
are
invited
so
that
all
of
the
concerns
can
be
discussed
and
incorporated
into
the
estuary­
wide
aquaculture
plan.
At
this
workshop,
the
development
of
guidelines
or
criteria
for
aquaculture
can
be
initiated
based
on
the
different
kinds
of
operations
which
currently
exist
and
which
may
be
proposed
for
this
body
of
water.
These
criteria
will
include
scale
of
operation,
methods
of
culturing,
amount
and
type
of
inputs
into
the
environment,
genotypes
and
species
used,
location,
and
amount
and
type
of
artificial
structure
to
be
used.

Depending
on
the
nature,
scale,
and
intensity
of
the
operation,
aquaculture
activities
in
natural
waters
can
have
a
significant
impact
on
local
water
quality,
living
resources,
and
habitats.
For
example,
small­
scale
shellfish
culturing,
which
is
a
common
type
of
culturing
that
exists
in
the
Peconic
Estuary,
is
probably
associated
with
lesser
impacts
to
the
estuary
than
large­
scale
fish
farms.
Shellfish
culturing
can
also
be
beneficial
to
water
quality
through
their
filtering
of
particles,
however,
they
should
not
be
located
in
naturally
productive
shellfish
or
finfish
areas
(
e.
g.,
eelgrass
beds,
finfish
spawning/
nursery
areas,
etc.).
In
order
to
ensure
that
neither
water
quality
nor
the
natural
communities
of
organisms
will
be
adversely
impacted,
aquaculture
sites
should
be
carefully
selected,
the
use
of
culture
stocks
should
be
regulated,
and
water
quality
monitoring
should
be
conducted
for
a
variety
of
parameters.

Location
of
Facilities
The
habitat,
food
sources,
and
general
health
and
behavior
of
species
such
as
sea
turtles
and
marine
mammals,
and
habitats
that
are
important
to
the
recruitment
of
natural
stocks
of
finfish
and
shellfish
could
be
impacted
by
aquaculture
facilities.
Based
on
existing
information
on
the
ways
in
which
species
of
concern
use
the
estuary
system,
it
should
be
possible
to
identify
embayments
or
other
areas
where
large­
scale
culturing
or
grow­
out
operations
and
associated
activities
may
be
detrimental
to
these
species
and
therefore,
avoided.
For
example,
one
concern
is
the
potential
impact
of
culturing
operations,
such
as
fish
pens,
on
the
interaction
between
spider
crabs
populations
and
sea
turtles.
Kemp's
ridley
sea
turtles
feed
primarily
on
spider
crabs.
If
either
spider
crabs
or
sea
turtles
are
attracted
to
aquaculture
operations,
there
is
a
potential
for
adverse
interactions
between
the
cultured
organisms,
the
structure
or
materials
of
the
operation,
and
the
species
of
concern.
Conversely,
if
HLR­
10
Develop
an
Aquaculture
Plan
for
the
Peconic
Estuary.
Peconic
Estuary
Program
CCMP
C
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47
spider
crabs
are
driven
from
an
area
by
the
presence
of
aquaculture
activities,
this
could
potentially
have
either
an
adverse
or
positive
impact
on
the
turtles.
Seals
are
another
concern.
Seals
may
be
attracted
to
fish
pens
because
of
the
proximity
to
their
haul­
out
areas
and
because
of
their
attraction
to
concentrations
of
finfish.
If
this
happens,
there
is
the
potential
for
adverse
interactions
between
the
structure
and
materials
associated
with
the
aquaculture
and
these
animals.
To
date,
there
have
been
no
known
or
reported
takes
of
marine
mammals
at
the
net
pens
located
off
Plum
Island;
whereas
at
net
pens
off
the
coast
of
Washington
and
British
Columbia
there
have
been
major
incidents.
The
impacts
of
the
presence
of
net
pens
off
Plum
Island
are
not
known
on
the
population
dynamics
of
marine
mammals.
The
CNRAs
identified
by
the
PEP
need
to
be
surveyed
to
assess
potential
impacts
to
marine
organisms
and
habitats
from
existing
and
future
aquaculture
activities.

Culture
Stocks
Research
has
been
done
on
the
genetic
differences
between
local
populations
and
stocks
of
the
same
species.
Often,
local
populations
are
better
adapted
to
local
conditions
and
prey
species
which
makes
them
better
able
to
function
in
the
local
ecosystem.
In
order
to
minimize
concerns
about
the
impact
of
culture
stocks
on
natural
waters
and
maximize
their
successful
culture,
all
aquaculture
operations
should
try
to
use
culture
stock
taken
from
the
Peconic
Estuary
rather
than
from
other
areas
of
the
country.
This
is
the
case
for
certain
shellfish
seeding
operations.
Other
stock
may
be
necessary
if
the
Peconic
Estuary
System
stock
is
not
available.
However,
a
State
importation
permit
is
required
of
all
products
used
for
aquaculture
that
are
brought
in
from
another
State.
Shellfish
stock
only
from
certain
locations
north
of
New
York
are
acceptable
for
importation
into
New
York.

Another
concern
about
importing
organisms
into
the
Peconic
Estuary
System
for
the
purpose
of
culturing
them
commercially
is
the
parasites
or
diseases
that
may
be
brought
in
with
them.
These
pests
may
be
transmitted
to
wild
populations
if
not
detected
in
the
cultured
animals
soon
enough.
As
part
of
developing
an
aquaculture
plan
for
the
entire
system,
a
plan
of
action
for
dealing
with
unforeseen
outbreaks
should
be
developed.
NYSDEC
should
maintain
the
policy
of
not
allowing
the
importation
of
southern
shellfish.

The
transplanting
of
shellfish
into
Peconic
Estuary
waters
for
cleansing
presents
a
similar
concern.
New
York's
shellfish
transplant
program
has
been
administered
by
the
NYSDEC
Bureau
of
Marine
Resources,
Shellfisheries
Section
since
1964.
The
primary
goals
of
the
transplant
program
are
to
protect
public
health
and
provide
a
long­
term
opportunity
for
utilization
of
shellfish
resources
which
are
presently
unusable
due
to
coliform
contamination
(
see
Chapter
5).
In
this
program,
shellfish
are
placed
in
certified
waters
for
cleansing
and
reharvested
after
21
days.
Some
of
these
transfers
are
carried
out
within
the
estuary
itself,
but
a
large
segment
of
the
New
York
transplant
program
involves
the
transfer
of
hard
clams
from
Raritan
Bay
in
New
York
Harbor
to
the
clean
near
shore
waters
of
the
Peconic
Estuary
System.
It
is
generally
believed
that
the
potential
difference
between
shellfish
in
both
bodies
of
water
in
terms
of
genetics,
disease,
or
parasites
is
negligible;
therefore,
no
monitoring
of
the
harvested
shellfish
is
done.
Also,
there
have
been
no
reported
diseases
or
parasites
in
hard
clams
in
New
York
waters.
With
the
occurrence
of
oyster
diseases
such
as
Perkinsus
marina
(
dermo)
and
Haplosporidium
nelsoni
(
MSX)
in
other
waters,
however,
it
may
be
useful
to
monitor
for
these
and
other
known
parasites
in
oysters
in
order
to
determine
if
they
may
be
transferred
to
the
Peconic
Estuary
should
a
transplant
program
for
oysters
commence
(
although
dermo
has
already
been
documented
in
the
Peconics
[
summer
1997]
and
MSX
may
already
exist
there
as
well).
Peconic
Estuary
Program
CCMP
C
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48
Non­
Indigenous
Species
There
are
many
documented
cases
of
non­
indigenous
species
(
finfish,
shellfish,
ad
other
invertebrates)
introduced
into
natural
waters
for
culturing
and
subsequently
released
either
accidentally
or
intentionally
beyond
the
culturing
facility
(
though,
there
are
no
documented
cases
in
New
York).
In
many
of
these
cases,
the
species
quickly
outcompete
and
outnumber
indigenous
populations,
causing
irreparable
damage
to
the
local
ecosystem.
There
are
already
non­
indigenous
species
in
the
Peconic
Estuary
System
(
e.
g.,
the
marine
macroalga
Codium
fragile)
whose
impact
on
the
environment
is
unknown.
The
NYSDEC
does
not
permit
the
importation
or
introduction
of
nonindigenous
species
for
aquaculture
whether
they
are
proposed
to
be
maintained
in
an
upland
facility
or
in
marine
waters.
It
is
important
that
NYSDEC
continue
to
prohibit
the
introduction
of
exotic
species
and
require
indigenous
genotypes
for
aquaculture.
If
non­
indigenous
species
are
maintained
on
land
in
tanks,
measures
should
be
taken
to
prevent
the
introduction
of
these
species
into
the
wild
as
well
as
into
surface
water
discharges
containing
waste
or
disease.

Monitoring
Reduction
of
water
quality
associated
with
culturing,
particularly
that
of
large­
scale
finfish
culture,
has
been
documented
in
other
areas
throughout
the
world.
In
order
to
maintain
high
water
quality
in
the
Peconic
Estuary,
ambient
monitoring
(
by
the
permittee
or
by
others)
should
be
implemented
when
aquaculture
permits
are
granted.
Examples
of
water
quality
parameters
which
have
been
incorporated
in
these
permits
include
dissolved
oxygen,
nitrogen
compounds,
total
suspended
solids,
and
chemicals
found
in
conjunction
with
food
for
the
cultured
organisms
(
e.
g.,
antibiotics).
Biological
parameters
which
are
measured
include
chlorophyll
a,
changes
in
adjacent
benthic
populations
and
interactions
with
turtles,
marine
mammals,
finfish,
and
large
mobile
epifauna
(
e.
g.,
crabs,
whelks).
A
protocol
for
monitoring
of
aquaculture
sites
should
be
matched
to
the
scale,
location
and
type
of
culturing
operation
(
e.
g.,
finfish
vs.
shellfish).
For
example,
the
one
net
pen
finfish
operation
off
Plum
Island
does
have
a
water
and
sediment
quality
monitoring
program
and
a
marine
mammal
and
avian
reporting
requirement.
This
net
pen
operation
also
conducts
daily
monitoring
of
dissolved
oxygen
inside
and
outside
the
pens
to
ensure
good
water
quality
for
the
caged
farm
fish.
Complementary
monitoring
by
an
independent
agency
or
entity
could
be
conducted
if
funded.

Steps
HLR­
10.1
Assist
in
the
development
and
implementation
of
an
estuary­
wide
aquaculture
plan.
Priority
Include
criteria
regarding
scale,
location,
assessment,
monitoring,
and
methodologies
of
shellfish
and
finfish
aquaculture
which
would
be
ecologically
beneficial
and
would
help
sustain
aquaculture
as
a
beneficial
estuarine
use
when
performed
in
a
manner
that
is
sensitive
to
the
natural
conditions,
productivity
and
ecology
of
the
Peconic
Estuary.

HLR­
10.2
Identify
suitable
areas
for
shellfish
and
finfish
aquaculture
activities
that
are
compatible
with
the
water
quality
and
habitat
protection
objectives
in
the
CCMP
to
ensure
that
a
balance
is
maintained
between
cultivated
and
wild
stocks,
and
include
in
the
estuary­
wide
aquaculture
plan.

HLR­
10.3
Investigate
the
need
to
require
monitoring
of
imported
cultured
organisms
and
intrastate
transplant
of
shellfish
for
disease
and
parasites
and
determine
if
a
requirement
should
be
established
to
certify
that
they
are
disease
free.
Peconic
Estuary
Program
CCMP
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HLR­
10.4
Continue
to
support
the
prohibition
of
commercial
culture
or
introduction
of
nonindigenous
species
in
New
York's
waters
and
require
that
all
aquaculture
operations
in
the
estuary
use
indigenous
genotypes.

HLR­
10.5
Develop
water
quality
and
natural
resource
monitoring
protocols
for
existing
and
future
shellfish
and
finfish
aquaculture
projects
Responsible
Entities
HLR­
10.1
Organize
workshop:
Suffolk
County
Planning
Department;
SCDHS
(
co­
leads);
NYSDEC;
PEP
­
Natural
Resources
Subcommittee;
NYSDOS;
NY
Sea
Grant;
NYSOGS;
USACE;
EPA;
NOAA/
NMFS;
Suffolk
County;
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
and
Riverhead;
villages;
Cornell
Cooperative
Extension;
fish
farmers;
other
groups;
and
individuals
interested
in
aquaculture;
Aquaculture
Plan:
Suffolk
County
with
input
from
PEP
and
other
stakeholders
(
NYSDEC,
Long
Island
Sound
Study,
and
New
York­
New
Jersey
Harbor
Estuary
Program)

HLR­
10.2
Suffolk
County
Planning
Department,
SCDHS,
NYSDEC
(
co­
leads),
NYSDOS,
USACE,
USFWS,
PEP­
Natural
Resources
Subcommittee,
and
Suffolk
County
Planning
Department
HLR­
10.3
Monitoring
assessment:
NYSDEC
(
lead);
Disease
and
parasite
screening:
PEP;
NYSDEC;
NYSDOS;
NYSOGS;
USACE;
EPA;
NOAA/
NMFS;
Suffolk
County;
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
and
Riverhead;
villages;
Cornell
Cooperative
Extension;
other
groups;
and
individuals
interested
in
aquaculture
(
co­
leads)

HLR­
10.4
NYSDEC
(
lead)
to
implement
legislation
and
NYS
legislature
HLR­
10.5
SCDHS,
NYSDEC
(
co­
leads),
USACE,
NYSDOS,
NYSOGS,
USFWS,
PEP,
NOAA,
and
fish
farmers
(
permittees)
Peconic
Estuary
Program
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Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
3,
4,
6,
and
8.

Unintentional
artificial
reefs
have
existed
as
long
as
humans
have
used
seagoing
vessels
and
lost
them
at
sea.
The
deliberate
placement
of
structures
in
the
water
for
the
purpose
of
attracting
finfish
is
a
more
recent
phenomenon.
It
is
clear
from
anecdotal
and
more
rigorous,
quantitative
research
that
these
areas
of
relief
do
indeed
attract
finfish,
some
of
which
use
the
structures
as
refuges
from
predators
or
for
breeding
and
feeding.
What
is
less
clear
are
the
impacts
of
these
structures
on
local
benthic
populations
and
regional
finfish
populations.
Topics
that
need
further
investigation,
either
through
literature
research
or
actual
studies,
include
the
following:

 
Benefits
of
the
structure
beyond
attracting
finfish
and
providing
"
good
fishing;"

 
Effects
on
finfish
stocks
(
i.
e.,
Do
the
reefs
concentrate
fish
into
a
small
area
and
then
cause
them
to
be
depleted
through
fishing
or
render
them
more
vulnerable
to
predators,
or
do
they
provide
additional
refuge
and
feeding
areas,
thus
increasing
populations
over
time?
Does
the
concentration
of
finfish
at
reef
sites
result
in
a
decrease
in
the
populations
elsewhere
or
result
in
a
shift
in
finfish
community
structure?);

 
Specific
effects
of
artificial
reefs
on
sea
turtle,
marine
mammals,
shark,
and
other
large
marine
species
populations;

 
The
potential
for
and
extent
of
habitat
and
species
displacement
and
a
determination
of
how
many
reefs
could
be
supported
in
the
estuary
without
causing
adverse
effects
such
as
those
mentioned
above;
and
 
A
definition
of
areas
where
artificial
reefs
should
not
be
located
due
to
the
presence
of
sensitive
species
or
habitats
of
concern,
and
areas
that
may
be
suitable
for
reef
structures
(
i.
e.,
are
consistent
with
the
water
quality
and
habitat
objectives
in
the
CCMP).

The
NYSDEC
Artificial
Reef
Plan
and
GEIS
was
prepared
in
the
late
1980s
and
approved
through
a
public
process
in
1991.
Since
that
time,
marine
mammal
use
of
the
system
has
been
increasing.
Since
all
artificial
reef
sites
require
a
full
evaluation
(
including
public
input
and
the
collection
of
relevant
information)
prior
to
decision
making,
special
attention
should
be
given
to
marine
mammal
and
sea
turtle
issues
and
addressed
in
a
pre­
placement/
siting
monitoring
program.
The
Reef
Plan
outlines
the
process
for
this
decision
making.

One
concern
related
to
sea
turtles
is
the
potential
impact
of
artificial
reefs
on
populations
of
spider
crabs.
Kemp's
ridley
sea
turtles
feed
primarily
on
spider
crabs.
If
either
spider
crabs
or
sea
turtles
are
attracted
to
artificial
reefs,
there
is
a
potential
for
adverse
interactions
between
the
reef
structure
or
materials
and
these
organisms.
Conversely,
if
spider
crabs
are
driven
from
an
area
by
the
presence
of
a
reef,
this
could
have
an
adverse
impact
on
the
turtles.
Seals
are
another
concern.
Seals
may
be
attracted
to
reefs
in
the
eastern
end
of
the
Peconics
because
of
the
proximity
to
their
haul­
out
areas
and
because
of
their
attraction
to
concentrations
of
finfish.
If
this
happens,
there
is
the
potential
for
adverse
interactions
between
the
reef
structure
and
materials
or
fishermen
and
these
animals.
Locations
where
these
interactions
might
occur
have
been
identified
by
some
researchers
and
these
HLR­
11
Determine
the
Suitability
of
Artificial
Reefs
in
the
Peconic
Estuary.
Peconic
Estuary
Program
CCMP
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51
sites
should
be
avoided
for
the
placement
of
artificial
reefs,
but
this
information
needs
to
be
documented.
These
potential
sites
include:

 
Orient
Harbor;

 
Waters
off
Plum
Island
and
Great
Gull
Island;

 
Waters
off
Jessups
Neck,
within
three­
quarters
of
a
mile
around
the
entire
peninsula;
and
 
Waters
off
shore
from
Three
Mile
Harbor
to
Accabonac
Harbor,
including
those
embayments.

At
least
one
site
recommended
for
reefs
in
the
Peconics
is
located
in
a
prime
feeding
area
for
Kemp's
ridley
sea
turtles
(
Orient
Harbor).
Presently,
an
evaluation
for
placement
of
a
demonstration
reef
is
proceeding
in
areas
to
the
east
(
where
there
is
an
unverified
wreck)
and
the
west
(
where
there
is
a
known
wreck)
off
Robin's
Island.
The
information
developed
from
this
evaluation
and
others
should
be
used
to
evaluate
potential
sites.
Sea
turtle
and
marine
mammal
monitoring
is
recommended
for
known
wrecks
and
natural
reef
areas
and
where
artificial
reefs
are
sited.

Steps
HLR­
11.1
Evaluate
the
use
of
natural
reefs,
wrecks,
artificial
reefs,
and
aquaculture
facilities
by
finfish,
sea
turtles,
diving
birds,
marine
mammals,
and
other
estuarine
organisms.
Develop
recommendations
to
minimize
the
impact
on
resources
by
these
structures.

HLR­
11.2
Determine
environmental
and
habitat
criteria
(
e.
g.,
productivity,
etc.)
for
site
selection
of
different
reef
structures,
and
evaluate
the
potential
for
the
extent
of
habitat
and
species
displacement
and
the
number
of
reefs
that
could
be
supported
in
the
estuary
without
causing
adverse
effects.

HLR­
11.3
Evaluate
the
potential
placement
of
artificial
reefs
in
known
sea
turtle
and
marine
mammal
feeding
areas
as
part
of
the
siting
process
outlined
in
the
NYSDEC
Artificial
Reef
Plan.

Responsible
Entities
HLR­
11.1
PEP
Natural
Resources
Subcommittee
(
lead)
(
long­
term
research
plan)
through
contractor
HLR­
11.2
PEP
Natural
Resources
Subcommittee
and
NYSDEC
(
co­
leads)

HLR­
11.3
NYSDEC
(
lead);
and
Towns
of
East
Hampton,
Southampton,
and
Southold
Peconic
Estuary
Program
CCMP
C
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52
Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
2,
3,
5,
6,
7,
and
8.

Habitat
degradation,
pollution,
overfishing,
and
improper
fishing
practices
can
all
lead
to
depletions
of
commercial
and
recreational
fish
and
shellfish
populations.
Data
collection
on
stocks
and
harvests,
regulation
of
fishing
and
shellfish
harvesting
practices,
habitat
protection,
and
pollution
prevention
are
all
needed
to
ensure
the
sustainable
use
of
these
stocks
by
humans.

Data
Collection
New
York
is
one
of
23
partners
in
the
Atlantic
Coastal
Cooperative
Statistics
Program.
The
goal
of
this
program
is
to
cooperatively
collect,
manage,
and
disseminate
fishery
statistical
data.
Data
on
commercial
fishing
are
compiled
by
NMFS.
A
certain
amount
of
information
is
also
periodically
compiled
and
analyzed
by
NYSDEC
fisheries
staff.
In
fact,
new
State
reporting
requirements
have
been
developed
which
will
require
commercial
fishermen
to
report
on
all
species
caught.
As
long
as
this
commercial
data
continues
to
be
collected
at
the
estuary
level,
this
increased
information
should
prove
useful
for
better
understanding
the
volume
and
distribution
of
landings
for
finfish
and
certain
crustacean
(
lobster)
and
shellfish
(
squid)
species
in
the
Peconic
Estuary.
For
recreational
fishing,
there
is
extensive
data
on
catch,
harvest,
and
discard
for
New
York,
but
it
is
not
available
specific
to
the
Peconics.
Better
information
on
both
of
these
types
of
fishing
at
the
estuary
level
would
enable
better
understanding
and
ultimately,
better
management
of
the
resources.

Fisheries
for
bait
and
for
shellfish,
such
as
conch,
have
existed
for
a
long
time.
Although
reliable
statistics
on
most
of
these
species
are
unavailable,
scientific
research
on
a
few
species
indicates
that
they
may
be
in
some
danger
of
being
depleted.
To
ascertain
the
stocks
of
bait
fish,
a
multi­
gear
and
temporal
study
of
bait
fish
populations
should
be
performed
on
a
variety
of
tributaries,
and
regulations
should
be
developed
to
prevent
overfishing
of
these
populations.
For
horseshoe
crabs,
NYSDEC
has
collected
harvest
data
informally
from
lobster
fishermen,
juvenile
anadromous
fish
seine
surveys,
and
the
Peconic
Trawl
Survey.
This
information
will
be
collected
under
the
proposed
Atlantic
Coastal
Cooperative
Statistical
Program
and
incorporated
into
the
Horseshoe
Crab
Fishery
Management
Plan
(
FMP)
(
approved
in
October
1998).
Based
on
the
recommendations
in
the
FMP,
NYSDEC
will
develop
appropriate
regulations
for
horseshoe
crabs.
Recently
adopted
regulations
for
horseshoe
crabs
include
a
25
percent
reduction
of
current
landings
coastwide
and
the
recommendation
that
additional
harvest
control
measures
be
considered
for
future
reductions.

Regulation
and
Management
Overfishing
of
finfish
stocks
that
are
highly
desirable
has
been
a
concern
for
decades.
Both
commercial
and
recreational
fishermen
contribute
to
this
problem.
Fishery
management
plans
and
fishery
regulations
have
been
designed
to
allow
for
sustainable
use
of
these
stocks
by
humans.
State
and
Federal
agencies,
including
NYSDEC
and
NMFS,
are
responsible
for
developing
plans
for
managing
coastal
migratory
finfish
stocks,
which
are
then
implemented
by
individual
States.
The
PEP
has
recognized
the
fact
that
many
of
the
species
of
finfish
taken
in
the
Peconic
Estuary
System
that
are
commercially
and
recreationally
valuable
are
migratory
in
nature
and,
therefore,
cannot
be
HLR­
12
Foster
Sustainable
Recreational
and
Commercial
Finfish
and
Shellfish
Uses
of
the
Peconic
Estuary
that
are
Compatible
with
Biodiversity
Protection.
Peconic
Estuary
Program
CCMP
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53
managed
by
efforts
exclusive
to
the
Peconic
Estuary.
Regulations
on
the
taking
of
these
fishes
are
promulgated
at
the
Federal
and
State
level
and
must
be
implemented
over
large
areas
by
the
appropriate
government
entities.
Therefore,
the
best
way
that
the
PEP
can
hope
to
protect
from
overfishing
the
coastal,
migratory
species
of
finfish
which
use
the
estuary
is
for
all
members
of
the
Management
Conference,
not
just
the
NYSDEC,
to
support
these
management
plans
and
regulations.
This
support
would
include
consistent
enforcement
of
regulations,
public
education
and
outreach
regarding
fishery
regulations
and
management
practices,
and
development
of
new
regulations
when
necessary
to
protect
the
sustainable
use
of
a
fishery
resource.

New
regulations
and
management
practices
may
be
warranted
to
protect
water
quality
and
to
protect
species
in
the
estuary
system
from
injury,
death,
and
overfishing.
Four
issues
proposed
for
action
include
management
of
fishing
gear,
implementation
of
BMPs
regarding
fish
waste,
regulations
for
fish
used
as
bait,
horseshoe
crabs,
and
whelks,
and
identification
and
regulation
of
spawner
sanctuaries.

Fishing
gear
can
result
in
permanent
injury
or
death
to
unintended
species.
For
example,
fishing
gear
which
is
lost
in
the
estuary
may
continue
to
"
ghost
fish"
for
a
long
period
of
time.
Pots,
traps,
fishing
lines,
and
nets
lost
during
storms
or
due
to
cut
lines
may
remain
in
the
water
column
or
on
the
bottom
in
a
functional
form.
Finfish
and
other
organisms
that
are
caught
by
this
gear
may
be
permanently
injured
trying
to
escape
or
may
not
escape
and
will
eventually
die.
In
addition,
certain
types
of
gear
may
be
very
effective
at
catching
not
only
the
target
species
but
other,
non­
target
species
which
may
be
injured
or
die
before
the
gear
is
retrieved
and
they
can
be
released.
Regulations
and
management
measures
should
be
implemented
that
will
reduce
injury
and
death
to
non­
target
species.

The
waste
generated
by
fishermen
from
cleaning
fish
is
often
discarded
back
into
the
water
in
the
mistaken
belief
that,
because
it
is
biodegradable
and
came
from
the
estuary,
it
is
acceptable
to
return
it
there.
In
fact,
this
material
attracts
scavengers,
both
aquatic
and
terrestrial,
and
adds
to
the
organic
matter
already
decaying
in
the
sheltered
embayments
where
marinas
are
usually
located.
A
number
of
simple
practices
can
be
implemented
to
minimize
this
problem,
including:

 
Establishing
fish­
cleaning
areas
with
proper
waste
receptacles;

 
Developing
and
implementing
rules
governing
the
conduct
and
location
of
fish­
cleaning
stations;

 
Implementing
fish
composting
where
appropriate;
and
 
Educating
boaters
and
fishermen
regarding
the
importance
of
proper
fish­
cleaning
procedures.

Research
on
hard
clams
in
the
Great
South
Bay
of
Long
Island
has
indicated
that
the
hydrographic
regime
associated
with
certain
tributaries
provides
prime
habitat
for
shellfish
reproduction.
These
areas
usually
contain
concentrations
of
coliform
bacteria
introduced
from
stormwater
runoff
and
are
uncertified
for
shellfish
harvesting
due
to
coliform
contamination.
Because
shellfish
in
these
areas
are
not
routinely
harvested,
the
populations
are
often
larger
and
the
reproductive
output
higher
than
in
other
areas
of
the
estuary
system.
Thus,
these
areas
may
be
supplying
a
disproportionate
share
of
larval
hard
clams
to
the
Great
South
Bay.
It
is
not
clear
if
there
are
any
areas
in
the
Peconic
Estuary
system
which
function
similarly.
This
should
be
studied
because
if
similar
de
facto
spawner
sanctuaries
exist
in
the
Peconic
Estuary,
some
harvesting
restrictions
should
be
considered,
particularly
if
efforts
to
improve
water
quality
and
reduce
pathogen
contamination
are
successful
and
these
areas
could
be
re­
opened
to
shellfishing.
Certified
areas
should
also
be
examined
for
potential
Peconic
Estuary
Program
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designations
as
spawner
sanctuaries.
Spawner
sanctuaries
for
scallops
are
viewed
by
NYSDEC
as
having
more
potential
to
succeed
in
the
Peconic
Estuary
System.

Habitat
Protection
and
Pollution
Prevention
A
variety
of
habitats
are
important
to
different
finfish
species
that
use
the
Peconic
Estuary
System.
A
number
of
coastal
migratory
species
use
the
system
as
spawning,
nursery,
or
feeding
grounds.
These
include
weakfish,
tautog,
winter
flounder,
scup,
bluefish,
butterfish,
and
summer
flounder.
Habitats
which
are
of
importance
to
these
species
for
a
variety
of
reasons
include
shallow
subtidal
areas,
both
vegetated
(
eelgrass)
and
unvegetated,
deep
subtidal
areas
(
sandy
and
muddy
substrate),
and
intertidal
salt
marshes
(
feeding
over
both
vegetated
Spartina
beds
and
unvegetated
flats).
These
habitats
should
be
identified,
protected,
and
restored
to
enhance
shellfish
and
fish
stocks.
Principal
threats
to
these
include:
physical
and
chemical
impacts
from
shoreline
hardening
structures;
physical
and
chemical
inputs
from
runoff;
and
physical,
chemical
and
biological
impacts
to
eelgrass
beds.

Steps
HLR­
12.1
Collect
better
statistical
data
on
commercial
and
recreational
fishing
landings
and
by­
Priority
catch
specific
to
the
Peconic
Estuary
System.

HLR­
12.2
Identify,
protect,
and
restore
key
shellfish
and
finfish
spawning,
nursery,
and
feeding
Priority
habitats
in
the
Peconic
Estuary
to
enhance
shellfish
and
fish
stocks
and
incorporate
this
data
into
the
on­
going
Essential
Fish
Habitat
work
being
conducted
under
the
Atlantic
States
Marine
Fisheries
Commission
(
ASMFC).

HLR­
12.3
Support
the
Atlantic
Coastal
Cooperative
Statistics
Program.

HLR­
12.4
Support
the
fishery
management
plans
which
have
been
and
are
being
developed
by
the
Mid­
Atlantic
Fishery
Management
Council
(
MAFMC)
and
the
ASMFC.

HLR­
12.5
Ensure
the
enforcement
of
existing
regulations
on
both
commercial
and
recreational
fisheries.

HLR­
12.6
Support
NMFS
Essential
Fish
Habitat
Designations
within
the
Peconic
Estuary.

HLR­
12.7
Develop
a
public
education
program
about
the
value
of
fish
and
fishing
and
the
importance
of
commercial
and
recreational
fishing
regulations
and
compliance
with
the
regulations.

HLR­
12.8
Support
the
prevention,
or
at
least
minimization,
of
the
effects
on
finfish
and
non­
target
species
by
lost
or
incorrectly­
designed
fishing
gear.
Measures
to
be
supported
include:
(
1)
developing
a
program
to
encourage
commercial
and
recreational
fishermen
to
retrieve
and
properly
dispose
of
fishing
line,
nets,
traps,
pots,
and
other
gear;
(
2)
work
with
the
AMI
to
develop
a
campaign
for
dockside
recovery
and
recycling
programs;
(
3)
support
implementation
of
fishery
regulations
requiring
escape
vents
and
degradable
panels
in
fish
and
lobster
pots;
(
4)
implementing
fishery
regulations
requiring
minimum
mesh
size
for
gill,
fyke,
and
otter
trawl
nets;
and
(
5)
promoting
the
use
of
fishing
gears
that
minimize
by­
catch
and
discard
(
e.
g.,
pound
nets).
Peconic
Estuary
Program
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HLR­
12.9
Implement
CZARA
section
6217
BMPs
regarding
fish
waste
at
marinas
and
on
docks.
Develop
public
education
materials
for
distribution
at
marinas,
bait
and
tackle
shops,
and
other
related
businesses
detailing
these
BMPs.

HLR­
12.10
Expand
the
monitoring
and
analysis
of
the
NYSDEC
finfish
trawl
survey
to
the
east
of
Shelter
Island
and
coordinate
with
PEP
Living
Resources
Research,
Monitoring,
Assessment
Plan.

HLR­
12.11
Examine
the
role
of
areas
uncertified
for
shellfishing
as
"
spawner
sanctuaries"
for
shellfish
species.

HLR­
12.12
On
a
biennial
cycle,
perform
deep­
and
shallow­
water
shellfish
abundance
surveys.

Responsible
Entities
HLR­
12.1
NOAA/
NMFS
and
NYSDEC
(
co­
leads)

HLR­
12.2
PEP,
NOAA/
NMFS,
ASMFC,
New
York
Sea
Grant
Institute,
NYSDEC,
and
local
universities
and
colleges
HLR­
12.3
NMFS,
NYSDEC,
and
PEP
(
co­
leads)

HLR­
12.4
NYSDEC,
PEP
(
co­
leads),
ASMFC,
NMFS,
and
MAFMC
HLR­
12.5
NYSDEC
Division
of
Law
Enforcement
(
lead),
Suffolk
County
Marine
Police,
and
town
bay
constables
HLR­
12.6
PEP­
MC,
NYSDEC,
and
NMFS.

HLR­
12.7
PEP
Public
Education
and
Outreach
program
(
lead),
NYSDEC,
Sea
Grant,
CCE
­
Marine
Program,
AMI,
and
marina
and
fishing
business­
owners
HLR­
12.8
NMFS,
NYSDEC,
NYS
Sea
Grant
(
co­
leads),
CCE,
AMI,
and
commercial
and
recreational
fishing
community
HLR­
12.9
PEP
Public
Education
and
Outreach
program
(
lead),
AMI,
marina
owners,
other
business
owners,
NYSDEC,
Sea
Grant,
and
CCE
­
Marine
Program
HLR­
12.10
NYSDEC
(
lead)
and
PEP
Natural
Resources
Subcommittee
HLR­
12.11
PEP
Natural
Resources
Subcommittee
(
lead),
NYSDEC,
and
CCE
HLR­
12.12
PEP
through
contractor
Peconic
Estuary
Program
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Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
2,
3,
6,
7,
and
8.

Shorebird
nests
and
chicks
on
open
beaches
are
vulnerable
to
disturbance,
injury,
and
death
from
vehicles,
humans,
and
unleashed
dogs,
predators
such
as
foxes,
crows,
raccoons,
gulls,
and
cats,
and
flooding.
However,
many
of
these
impacts
can
be
reduced
through
careful
habitat
management
and
public
education.
For
example,
research
and
monitoring
has
shown
that
shorebird
chicks
and
eggs
are
extremely
vulnerable
to
off­
road
vehicles
and
noise
from
motorized
watercraft
near
or
within
their
nesting
and
feeding
habitat.
Vehicular
disturbance
can
lead
to
abandonment
of
nests,
injury
or
death
of
eggs
and
chicks,
or
reduced
ability
to
feed,
leading
to
malnourishment.
Seasonally
restricting
the
use
of
vehicles
and
watercraft
on
or
in
the
vicinity
of
nesting
and
feeding
shorebirds
can
aid
in
the
recovery
of
these
species.
Therefore,
the
current
county
and
town
practice
of
selling
beach­
driving
permits
may
not
be
compatible
with
a
management
goal
of
protecting
critical
nesting
and
feeding
habitat
of
rare
shorebirds.

Plovers
and
terns
are
so
vulnerable
to
disturbance
that
they
need
annual
management.
Since
it
is
unreasonable
to
ban
the
public
from
beaches,
signs
and
fences
should
be
placed
around
nesting
and
feeding
habitat
to
protect
the
birds
during
the
breeding
season.
Since
the
plovers
begin
nesting
in
mid
to
late
April,
every
effort
should
be
made
to
find
and
fence
each
pair's
early
season
nest
to
ensure
a
high
rate
of
fledglings
before
the
Fourth
of
July.
Fencing
and
posting
also
protects
the
landowner
from
a
"
taking"
under
the
Federal
Endangered
Species
Act.
Terns
that
are
protected
by
New
York
State
need
their
nesting
habitat
protected
from
mid­
May
to
mid­
August.
Existing
state
and
local
programs
generally
are
underfunded
and
understaffed
to
carry
out
the
recommended
fencing
and
monitoring.

The
USFWS
has
developed
guidelines
to
manage
recreational
activities
in
piping
plover
breeding
habitat.
Compliance
with
these
guidelines
will
assist
in
the
recovery
of
threatened
and
endangered
species
and
conservation
of
other
coastal
species.
Implementing
these
guidelines
will
also
ensure
that
violations
of
Section
9
of
the
Endangered
Species
Act
are
avoided.
The
guidelines
provide
a
variety
of
management
options
intended
to
prevent
mortality,
harm,
and/
or
harassment
of
piping
plovers
and
their
eggs
due
to
recreational
activities.

Management
is
best
accomplished
when
the
cause
for
bird
mortality
is
known
and
qualified
with
documentation
so
that
the
management
actions
can
be
targeted
to
site
specific
threats.
Therefore,
intensive
monitoring
and
threat
documentation
is
very
important.

Steps
HLR­
13.1
Strengthen
existing
municipal
shorebird
(
terns
and
plovers)
management
programs
to
Priority
ensure
timely
fencing
and
erection
of
enclosures,
adequate
monitoring
and
reporting,
and
management
of
recreation
and
other
activities
within
nesting
and
feeding
habitat.
Implement
the
1997
Suffolk
County
Department
of
Parks,
Recreation
and
Conservation
Piping
Plover
Protection
Program
and
the
NYSDEC
Bureau
of
Wildlife
1998
Action
Plan
for
Piping
Plover
Conservation
in
New
York.
HLR­
13
Protect
Nesting
and
Feeding
Habitat
of
Shorebirds.
Peconic
Estuary
Program
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HLR­
13.2
Restrict
the
use
of
off­
road
vehicles
and
small
watercraft
in
shorebird
nesting
areas
during
breeding
season
(
April
 
August).

HLR­
13.3
Consult
with
the
USFWS
to
comply
with
Federal
guidelines
for
managing
recreational
activities
in
piping
plover
breeding
habitat.

HLR­
13.4
Document
threats
to
nesting
shorebirds
(
plovers
and
terns)
such
as
off­
road
vehicles,
predation,
and
recreation,
and
develop
and
implement
measures
that
lead
to
higher
productivity
and
larger
nesting
populations.

Responsible
Entities
HLR­
13.1
NYSDEC;
Suffolk
County
Parks
Department;
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
and
Riverhead;
villages;
Trustees;
The
Nature
Conservancy;
and
USFWS
(
co­
leads)

HLR­
13.2
OPRHP,
Suffolk
County
Parks
Department;
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
and
Riverhead;
villages;
and
NYSDEC
for
DEC­
owned
properties
(
co­
leads)

HLR­
13.3
Beach
managers
including
Federal
(
USFWS),
State,
Suffolk
County,
towns,
and
property
owners
(
co­
leads)

HLR­
13.4
East
End
towns
and
NYSDEC
Peconic
Estuary
Program
CCMP
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Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
3,
4,
6,
7,
and
8.

The
Kemp's
ridley,
loggerhead,
and
green
sea
turtles
use
the
Peconic
Estuary
as
important
developmental
habitat
when
they
are
juveniles.
Leatherback
turtles
are
found
to
a
much
lesser
extent
in
the
estuary.
All
of
these
species
of
turtles
are
Federally­
listed
as
either
endangered
or
threatened.
Therefore,
any
activities
that
kill,
injure,
or
significantly
disturb
the
behavior
of
these
organisms
are
of
concern.

Sea
turtles
are
most
frequently
sighted
in
Southold
Bay,
Orient
Harbor,
Noyack
Bays,
the
waters
from
Accabonac
Harbor
to
Napeague
Harbor,
including
the
embayments,
and
the
waters
off
Plum
Island,
Great
Gull
Island,
Gardiners
Island,
and
Jessup's
Neck.
Current
activities
that
may
directly
or
indirectly
kill,
injure,
or
disturb
turtles
include
boating
and
dredging.
Activities
in
the
system
which
are
not
of
concern
yet,
but
which
have
the
potential
to
expand
and
result
in
more
frequent
turtle
encounters,
are
large­
scale,
intensive
aquaculture
projects
or
relatively
large­
scale,
poorly­
designed
artificial
reefs.
All
the
current
activities
and
all
proposed
activities
in
these
areas
should
be
reviewed
with
the
impact
on
sea
turtles
in
mind.

Under
New
York
State
Environmental
Conservation
Law
Article
11,
Section
0107,
it
is
illegal
to
injure
or
cause
the
death
of
harbor
seals.
It
is
also
illegal
under
this
law
to
buy,
sell,
transport,
or
have
possession
of
these
animals.
The
law
was
implemented
a
number
of
years
ago
when
the
harbor
seal
was
the
only
species
of
pinniped
found
in
New
York
waters.
Currently,
there
are
five
species
of
seals
that
are
found
in
these
waters,
of
which
three
have
become
fairly
common.
In
order
to
protect
these
species,
as
well
as
other
marine
mammals,
such
as
the
bottlenose
dolphin
and
the
harbor
porpoise,
this
law
should
be
expanded.

Steps
HLR­
14.1
Review
uses
of
areas
which
have
been
identified
as
sea
turtle
and
marine
mammal
feeding
areas
and
consider
what
restrictions
may
be
necessary
to
be
more
protective
of
these
species
and
their
food
resources.

HLR­
14.2
Evaluate
the
expansion
of
existing
laws
to
ensure
that
all
species
of
seals
as
well
as
other
marine
mammals
are
protected
from
intentional
injury
or
death.

HLR­
14.3
Expand
New
York
State
law
protecting
harbor
seals
(
ECL
Article
11,
Section
0107)
to
include
all
species
of
seals
in
NYS
marine
waters.

Responsible
Entities
HLR­
14.1
NYS
agencies
(
e.
g.,
NYSDEC,
NYSDOS,
NYS
Office
of
Parks,
Recreation
and
Historic
Preservation,
NYS
Office
of
General
Services)
(
co­
leads),
Suffolk
County,
and
Towns
HLR­
14.2
NYS
agencies
(
e.
g.,
NYSDEC,
NYSDOS,
NYS
Office
of
Parks,
Recreation
and
Historic
Preservation,
NYS
Office
of
General
Services)
(
co­
leads),
SCDHS,
and
towns
HLR­
14.3
New
York
State
Legislature
and
NYSDEC
(
co­
leads)
HLR­
14
Protect
Sea
Turtles
and
Marine
Mammals.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
F
O
U
R
4­
59
Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
2,
3,
4,
6,
7,
and
8.

Measures
are
needed
to
counteract
the
effects
of
increasing
human
populations
and
development
of
the
lands
and
waters
of
the
watershed
surrounding
the
estuary.
The
pressure
on
the
natural
system,
if
not
controlled
or
mitigated,
will
result
in
replacement
or
loss
of
natural
habitats
(
conversion
to
lawns
and
gardens,
hardening
of
the
shoreline
resulting
in
lost
wetlands,
increased
siltation
and
lowered
salinity
from
runoff);
increased
introduction
of
toxic
chemicals
and
excess
nutrients
to
surface
and
ground
waters
as
a
result
of
increases
in
impervious
surface
areas
and
other
inputs
(
pesticides,
herbicides,
household
chemicals,
septic
systems,
fertilizers);
and
displacement
of
wildlife
(
shorebirds,
diamondback
terrapins,
small
mammals,
indigenous
plant
communities).
With
proper
planning
and
management,
residents
and
visitors
will
be
able
to
continue
to
use
and
enjoy
the
many
resources
the
estuary
has
to
offer
for
generations
to
come;
the
finfishery
and
shellfishery
resources
of
the
estuary
can
also
be
sustained
and
improve
as
viable
economic
resources.
Otherwise,
the
estuary
risks
becoming
unproductive
ecologically
and
economically.

Planning
Coordinated
land
use
planning
and
comprehensive
planning
on
a
local
level
can
be
used
to
ensure
protection
of
natural
resources
and
habitats
from
cumulative
impacts.
A
master
plan,
especially
when
developed
in
conjunction
with
those
of
other
towns,
is
a
powerful
tool
for
managing
the
way
in
which
an
area
is
developed.
The
East
End
of
Long
Island
is
under
increasing
pressure
for
development.
It
will
require
careful
planning
and
uniform
implementation
to
ensure
that
increases
in
population
do
not
overwhelm
the
natural
resources
that
make
the
East
End
such
a
desirable
place
to
live.
The
development
of
a
master
plan
in
each
town
and
minimization
of
variances
allowed
are
good
measures
for
achieving
such
control.
Towards
this
action,
the
Towns
of
East
Hampton,
Southold,
and
Southampton
are
in
the
process
of
developing
Local
Waterfront
Revitalization
Plans.
The
Villages
of
Greenport
and
Sag
Harbor
have
already
adopted
such
plans.
These
types
of
plans
can
be
used
to
address
the
need
for
public
access
and
the
impacts
associated
with
public
demands
for
open
space.
Providing
well­
sited
and
well­
planned
public
access
points
protects
habitat
and
meets
the
public's
demand
while
building
a
constituency
for
enhanced
protection
of
natural
habitat
and
species
populations.
Planning
is
needed
to
ensure
that
access
points
are
coupled
with
the
right
kind
of
space
to
accommodate
different
uses:
places
to
fish,
places
to
swim,
places
close
to
wildlife
habitat
for
observation,
safe
places
for
boating
including
support
facilities,
and
places
to
walk
along
the
water.
People
must
be
able
to
enjoy
and
appreciate
a
clean
estuary
for
there
to
be
continuing
support
for
further
investments
to
improve
water
quality
and
coastal
habitats.
PEP
supports
maintaining
a
balance
between
the
needs
and
opportunities
for
public
access
and
the
requirements
for
sustaining
living
resources.

One
local
plan
that
has
been
used
successfully
in
the
estuary
is
the
Harbor
Protection
Overlay
District
(
HPOD).
The
Town
of
East
Hampton
created
the
HPOD
to
address
developments
on
waterfront
property.
The
HPOD
imposes
restrictions
on
newly­
developed
or
redeveloped
waterfront
property.
A
number
of
these
restrictions
are
particularly
useful
in
the
protection
of
living
resources,
such
as
HLR­
15
Utilize
Land
Use
Planning,
BMPs,
and
Other
Management
Measures
to
Reduce
the
Negative
Impacts
of
Human
Uses
and
Development
on
the
Estuary
System.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
F
O
U
R
4­
60
requirements
that
the
shoreline
be
maintained
with
a
natural
buffer
made
up
of
native
vegetation.
The
PEP
encourages
other
towns
to
adopt
similar
planning
measures.

Regulations
already
exist
that
protect
natural
resources
of
the
estuary
from
human
impacts
(
e.
g.,
NYS
freshwater
and
tidal
wetland
regulations
that
require
minimum
setbacks
for
house
and
sanitary
systems
and
vegetated
buffer
zones).
Statewide
plans
are
also
useful
tools
for
protecting
estuary
resources.
New
York
has
developed
a
State
Coastal
Nonpoint
Management
Plan
in
response
to
CZARA
Section
6217.
This
plan
addresses
all
of
the
categories
of
nonpoint
source
pollution
which
have
been
identified
as
being
of
concern
in
the
Peconic
Estuary
System
and
recommends
BMPs
or
management
measures
for
controlling
sources
of
nonpoint
pollution
in
coastal
waters.
Many
of
these
BMPs
are
protective
of
habitat
and
living
resources.
The
PEP
should
work
with
local
governments
and
other
agencies
to
implement
BMPs
and
encourage
or
require
land
owners
to
adopt
BMPs.

Another
plan
that
is
protective
of
the
Peconic
Estuary
is
the
Areawide
Contingency
Plan
for
dealing
with
large
oil
spills.
This
plan,
which
was
developed
by
the
U.
S.
Coast
Guard
(
USCG),
in
conjunction
with
other
Federal
and
State
agencies,
is
periodically
revised
and
updated.
The
review
period
provides
an
opportunity
for
the
PEP
to
contribute
information
with
regard
to
critical
areas
and
species
of
concern
in
the
estuary
such
as
waterfowl
(
ducks
and
geese),
waterbirds
(
herons,
terns,
etc.),
sea
turtles,
and
marine
mammals.
In
addition,
this
plan
could
be
a
conduit
for
including
PEP
stakeholders
in
clean­
up
efforts
for
large
spills.
At
this
time,
there
are
no
trained
wildlife
rehabilitators
to
care
for
the
species
most
at
risk
from
a
large­
scale
oil
spill.
In
order
to
be
prepared
for
this
contingency,
local
rehabilitators
should
be
encouraged
to
take
training
in
handling
oiled
wildlife.
The
NYSDEC
and
USCG
could
then
include
them
in
the
clean­
up
effort
for
a
large
spill.

The
use
of
town
councils
or
planning
boards
for
reviewing
actions
that
affect
public
lands
and
open
space
is
another
tool
for
minimizing
cumulative
impacts
of
development
and
population
growth.
Currently,
the
Town
of
Southampton
has
a
Conservation
Advisory
Board;
the
Towns
of
East
Hampton,
Southold,
and
Shelter
Island
have
Conservation
Advisory
Councils.
State
legislation
exists
which
enables
towns
to
increase
the
status
of
these
councils
in
order
to
provide
them
with
a
role
in
reviewing
Town
Board
actions.
Any
action
that
may
be
taken
by
a
Board,
which
would
have
an
effect
on
the
overall
open
space
of
a
town,
is
reviewed
by
the
Conservation
Advisory
Board
and
appropriate
recommendations
are
made.
Such
reviews
may
provide
the
Town
Board
with
important
information
on
the
impacts
of
individual
actions
on
the
entire
inventory
of
open
space
and
its
management
in
the
town.

All
of
these
planning
and
management
efforts
will
not
be
successful
if
they
are
not
conducted
in
a
coordinated
manner.
One
way
to
ensure
that
these
protection
and
conservation
efforts
are
implemented
in
a
coordinated
manner
is
to
develop
a
group
such
as
the
Protected
Lands
Council,
which
has
been
established
for
the
management
of
the
Pine
Barrens.
The
Council
includes
all
groups
that
manage
the
Pine
Barrens
for
preservation
and
ensure
that
uses
are
managed
equitably.
The
Council
fosters
communication
and
cooperation
among
the
managers
in
order
to
use
staff
and
financial
resources
more
efficiently.
It
may
be
possible
to
expand
this
group
to
include
the
management
of
lands
throughout
the
Peconic
River
and
estuary
watershed.
Alternatively,
it
may
be
more
feasible
to
establish
a
similar
group
for
the
estuary
that
includes
different
entities,
since
the
PEP
CCMP
and
the
Pine
Barrens
Plan
have
different
goals.
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
F
O
U
R
4­
61
Steps
HLR­
15.1
Each
town
should
develop
a
master
or
comprehensive
management
plan,
coordinated
Priority
with
plans
of
other
towns
that
increases
the
level
of
protection
of
natural
resources
and
habitats
and
accounts
for
cumulative
impacts.

HLR­
15.2
Increase
public
access
to
the
estuary
consistent
with
other
ecosystem
objectives.
Priority
HLR­
15.3
Develop
and
implement
a
Harbor
Protection
Overlay
District
such
as
that
developed
by
the
Town
of
East
Hampton
and
include
it
in
the
master
plan
for
each
town.

HLR­
15.4
Develop
implementation
mechanisms
for
all
measures
required
by
Section
6217(
g)
of
CZARA
that
are
applicable
to
the
Peconic
Estuary.
These
measures
would
include
BMPs
for
the
use
of
natural
vegetation,
minimization
of
impervious
surfaces,
safe
and
reasonable
use
of
lawn,
garden,
and
household
chemicals,
and
minimization
of
stormwater
runoff.
Incorporate
these
BMPs
into
the
site
plan
requirements
for
all
newlydeveloped
and
redeveloped
property,
particularly
along
the
shoreline.

HLR­
15.5
Use
the
Protected
Lands
Council
of
the
Central
Pine
Barrens
Comprehensive
Land
Use
Plan
as
a
model
for
developing
a
similar
coalition
of
public
agencies
and
conservation
organizations
to
address
common
issues
of
concern
throughout
the
estuary.

HLR­
15.6
Encourage
towns
with
existing
Conservation
Advisory
Councils
or
planning
staff,
to
be
given
the
responsibility
as
Conservation
Advisory
or
Planning
Boards
to
review
proposed
Town
Board
actions
as
they
affect
public
lands
and
open
space
concerns.

HLR­
15.7
Review
and
provide
comments
to
NYSDEC
on
any
revisions
to
the
Statewide
Oil
Spill
Areawide
Contingency
Plan
for
the
Peconic
Estuary
relating
to
waterfowl,
marine
mammals,
and
sea
turtles
and
their
rehabilitation
if
oiled.
Develop
and
distribute
information
on
reporting
and
responding
to
small­
scale
spills.

HLR­
15.8
Develop
regulations
for
new
marinas
or
expansion
of
existing
marinas
which
include
the
following
(
from
CZARA
section
6217):
(
1)
assessment
of
water
quality
conditions
during
and
after
construction;
(
2)
site
and
design
such
that
tides
and/
or
currents
will
aid
in
the
flushing
of
the
site
or
renew
its
water
regularly;
(
3)
site
and
design
to
protect
against
adverse
effects
on
shellfish
resources,
wetlands,
submerged
aquatic
vegetation,
or
other
important
riparian
and
aquatic
habitat
areas
as
designated
by
local,
State,
or
Federal
governments;
(
4)
designate
and
enforce
no­
wake
zones
and
ensure
that
shoreline
areas
are
stabilized
effectively
by
vegetative
means;
and
(
5)
require
effective
stormwater
runoff
control
measures
to
reduce
sediment
and
toxic
inputs.

Responsible
Entities
HLR­
15.1
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
and
Riverhead;
and
NYSDOS
(
co­
leads);
EPA,
NYSDEC,
SCDHS
HLR­
15.2
All
Federal,
state,
and
local
governmental
agencies
in
the
PEP
watershed
(
co­
leads);
NYSDEC
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
F
O
U
R
4­
62
HLR­
15.3
NYSDOS
(
lead);
Towns
of
Southampton,
Southold,
Shelter
Island,
and
Riverhead
HLR­
15.4
NYSDEC,
NYSDOS,
PEP
Education
and
Outreach
Program
(
co­
leads),
Suffolk
County
Soil
and
Water
Conservation
District,
SCDHS,
USDA
NRCS,
CCE,
NY
Sea
Grant,
Peconic
BayKeeper,
SCDHS
HLR­
15.5
PEP
and
Pine
Barrens
Commission
and
Protected
Lands
Council
(
co­
leads);
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
Riverhead;
NYSDEC;
SCDHS
HLR­
15.6
Towns
of
East
Hampton,
Southold,
Shelter
Island,
and
Riverhead
(
co­
leads)

HLR­
15.7
PEP
Natural
Resources
Subcommittee
in
conjunction
with
the
USCG,
NYSDEC,
USFWS
(
co­
leads);
Rehabilitation:
local
wildlife
rehabilitators
(
licensed);
Education:
PEP
Public
Education
and
Outreach
program
in
conjunction
with
the
USCF,
NYSDEC,
and
USFWS;
BMPs:
NYSDOS;
AMI;
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island;
and
Riverhead;
and
villages
HLR­
15.8
NYSDEC
(
lead);
SCDHS;
EPA;
PEP;
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
and
Riverhead;
AMI;
and
private
marina
owners
Peconic
Estuary
Program
CCMP
C
H
A
P
T
E
R
F
O
U
R
4­
63
Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
2,
3,
5,
6,
7,
and
8.

Although
humans
have
lived
around
and
worked
in
the
Peconic
Estuary
for
thousands
of
years,
a
relatively
small
amount
of
scientific
research
has
been
performed
on
the
living
resources
of
this
system.
To
understand
the
impacts
of
humans
and
their
activities
on
this
system,
there
must
be
a
better
understanding
of
how
the
estuary
functions
ecologically.
This
understanding
can
only
be
achieved
through
a
focused
research,
monitoring,
and
assessment
effort
(
RM&
A).

Monitoring
involves
the
multi­
year
collection
of
data
on
living
resources
and
water
quality
to
understand
natural
variability
of
populations
over
time
as
well
as
changes
in
those
populations
which
result
from
human
influences.
Monitoring
certain
sensitive
species
or
communities
as
overall
indicators
of
ecosystem
health
can
be
a
valuable
tool
in
keeping
track
of
conditions
which
may
stress
a
system.
Data
from
monitoring
programs
can
provide
an
"
early
warning"
about
the
declining
health
of
the
estuary.
Monitoring
living
resources
is
needed
for
the
estuary
system.

As
part
of
the
process
of
developing
this
CCMP,
the
PEP
identified
and
performed
a
number
of
priority
characterization
projects.
Many
of
the
important
questions
about
the
system
could
not
be
answered,
however,
due
to
time
and
funding
constraints.
The
PEP
now
needs
to
identify
and
prioritize
all
of
the
remaining
research
and
monitoring
needs
and
develop
an
RM&
A
Program.
The
RM&
A
Program
will
define
the
critical
research
questions
that
need
to
be
answered,
facilitate
coordination
among
various
new
and
ongoing
research,
monitoring,
and
assessment
programs,
and
identify
private
and
public
sources
of
funding.
The
RM&
A
Program
would
outline
monitoring
needs,
agencies,
and
organizations
responsible
for
conducting
monitoring
activities,
funding
sources,
and
methods
for
coordination
with
ongoing
programs.
The
development
of
integrated
water
quality
and
living
resource
indicators
should
also
be
included
in
the
RM&
A
Program.
The
PEP
sponsored
a
workshop
in
1998
involving
scientists
and
participants
of
the
PEP
Management
Conference
to
develop
a
framework
for
the
RM&
A
Program.

Topics
already
identified
by
the
PEP
Natural
Resources
Subcommittee
for
inclusion
in
the
Program
poses
questions
regarding
finfish
spawning,
larval
development,
and
recruitment
to
the
fishery;
population
dynamics
of
the
benthic
communities
of
the
system;
distribution,
abundance,
and
growth,
including
habitat
use
and
preference,
by
juvenile
and
forage
fish;
and
the
links
among
these
different
components
of
the
food
web.

One
of
the
monitoring
needs
identified
by
the
PEP
includes
monitoring
eelgrass
by
aerial
photographic
interpretation,
appropriate
groundtruthing,
periodic
mapping,
and
other
surveillance
techniques
to
adequately
assess
trends
in
eelgrass
distribution,
abundance
and
overall
health.
Given
the
recent
decline
in
eelgrass
beds
over
the
last
decade,
a
long­
term
commitment
to
eelgrass
monitoring
is
essential
to
provide
adequate
management,
preservation,
and
restoration
measures.
HLR­
16
Develop
and
Implement
a
Living
Resources
Research,
Monitoring,
and
Assessment
Program.
Peconic
Estuary
Program
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Additional
research,
monitoring,
and
assessment
needs
identified
by
the
PEP
include
the
following:

1)
impacts
of
macroalgae
and
toxic
contaminants
on
eelgrass
distribution
and
abundance;

2)
distribution,
abundance,
habitat
preferences,
and
life
stage
requirements
of
forage
fish
species,
horseshoe
crabs,
slipper
shells,
bay
scallops
and
hard
clams;

3)
critical
spawning
habitats
for
local
populations
of
winter
founder;

4)
basic
food
web
ecology;

5)
benthic
habitat
mapping;

6)
assessing
and
monitoring
the
impacts
of
shoreline
hardening
on
habitat
and
living
resources;
and,

7)
effects
of
sea
level
rise
on
saltmarsh
distributions
and
shallow
water
habitats.

Information
sharing,
coordination
of
research
and
monitoring
efforts,
and
funding
and
incentives
for
increased
research
and
monitoring
are
needed
to
ensure
that
research,
monitoring,
and
assessment
activities
within
the
Peconic
Estuary
System
are
successful.

Dissemination
of
research
and
monitoring
information
is
essential
to
evaluate
progress
made
in
restoration
and
conservation
efforts
and
develop
improved
methods
for
research,
monitoring,
and
stewardship
of
our
important
natural
resources.
A
biennial
conference
would
provide
an
opportunity
for
scientists
to
meet
together
with
managers
and
the
public
to
review
and
discuss
findings.
By
creating
an
accessible
database
of
natural
resources,
data
would
be
available
in
a
standard,
meaningful
format
that
could
be
used
by
managers,
researchers,
and
stewards
of
the
Peconic
Estuary.

Although
the
Peconic
Bays
are
an
excellent
estuarine
laboratory
for
basic
and
applied
research
by
universities
(
e.
g.,
SUNY
Stony
Brook),
colleges
(
e.
g.,
LIU­
Southampton
College),
institutions
(
e.
g.,
Brookhaven
National
Laboratory),
and
public
and
private
schools,
very
little
basic
and
applied
research
takes
place
here.
Necessary
incentives
to
encourage
researchers
to
focus
their
scientific
inquiries
here
need
to
be
identified,
developed,
and
promoted.
Establishing
a
research
center/
scientific
platform
and
targeting
funding
are
two
incentives
which
can
support
cutting
edge
marine
research
and
monitoring.

Other
National
Estuary
Programs
have
embarked
on
research
projects,
which
have
resulted
in
significant
findings
about
marine
systems
that
are
applicable
to
many
estuaries.
The
PEP
should
participate
in
coordinated
research
and
information
exchange
with
other
National
Estuary
Programs.

Steps
HLR­
16.1
Develop
and
implement
a
research
program
for
the
Peconic
Estuary
and
its
watershed
to
Priority
investigate
natural
processes,
impairments,
and
links
to
water
quality,
maintenance
of
systems
and
species,
and
effects
of
recreation
and
pollution
on
biodiversity,
among
other
research
needs.
Investigate
and
seek
funding
sources
for
supporting
implementation
of
the
program
(
e.
g.,
National
Estuarine
Research
Reserve
Systems)
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Estuary
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HLR­
16.2
Develop
a
long­
term
program
for
monitoring
and
assessment
of
living
resources
in
the
Priority
Peconic
Estuary
that
is
coordinated
with
the
development
of
a
research
plan
and
ongoing
research
and
monitoring
efforts.

HLR­
16.3
Support
research
on
the
interactions
between
eelgrass
and
the
dominant
macroalgae
species
in
the
Peconic
Estuary
to
determine
impacts
of
macroalgae
on
eelgrass
distribution
and
abundance.

HLR­
16.4
Perform
research
and
monitoring
of
forage
fish
species,
horseshoe
crabs,
and
conch
in
the
Peconic
Estuary
to
understand
their
distribution
(
temporal
and
spatial),
abundance,
habitat
preferences,
and
different
life
stage
requirements
to
develop
management
strategies.

HLR­
16.5
Perform
research
on
the
ecology
of
food
sources
of
sea
turtles
to
evaluate
the
importance
of
the
Peconic
Estuary
to
them
and
potential
threats
to
these
endangered
and
threatened
species.

HLR­
16.6
Research
the
lethal,
sublethal,
and
synergistic
effects
of
elevated
nutrients,
toxic
chemicals,
and
Brown
Tide
on
the
reproduction
and
behavior
of
finfish
and
invertebrate
species.

HLR­
16.7
Determine
the
effects
of
navigational
dredging
on
shallow
water
communities
and
the
recovery
time
of
benthic
communities
exposed
to
dredging.

HLR­
16.8
Ensure
implementation
of
adequate
mapping
and
monitoring
programs
to
track
trends
in
the
extent
and
quality
of
eelgrass,
and
to
evaluate
progress
towards
reaching
restoration
goals.

HLR­
16.9
Establish
a
scientific
panel
to
review
research,
monitoring,
and
assessment
data,
and
to
offer
guidance
in
management
of
the
habitats
and
living
resources
in
the
Peconics.

HLR­
16.10
Organize
an
annual
or
biennial
conference
to
report
research,
monitoring,
and
assessment
results
to
the
public
and
guide
management
decisions.

HLR­
16.11
Establish
and
maintain
an
accessible
database
of
natural
resources
in
the
Peconic
Estuary.

HLR­
16.12
Promote
research
and
monitoring
opportunities
in
the
Peconic
Estuary
to
local
schools,
colleges,
universities,
and
institutes
by
establishing
funding
and
scientific
platforms
and
other
incentives
to
facilitate
basic
and
applied
marine
research.

HLR­
16.13
Seek
opportunities
to
link
research
and
monitoring
in
the
Peconic
Estuary
System
to
related
estuaries
and
regional
studies.

HLR­
16.14
Support
priorities
listed
in
the
Living
Resources
Research,
Monitoring,
and
Assessment
Plan
including
research
on
ecosystem
productivity
and
ecosystem
structure,
bioindicators,
and
effects
of
global
climate
change
on
wetlands.
Peconic
Estuary
Program
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Responsible
Entities
HLR­
16.1
Plan
development
and
coordination:
PEP
Natural
Resources
Subcommittee
and
the
Marine
Conservation
Planner
(
co­
leads)
in
consultation
with
other
members
of
the
PEP
Management
Conference
and
technical
experts;
Plan
implementation:
PEP
Management
Conference,
NYSDEC,
NYSDOS,
New
York
Sea
Grant
Institute,
and
SCDHS
(
co­
leads)

HLR­
16.2
Monitoring
plan:
PEP
Natural
Resources
Subcommittee
and
Marine
Conservation
Planner
(
co­
leads)
in
conjunction
with
NYSDEC;
SCDHS;
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
and
Riverhead;
Plan
implementation:
PEP
in
conjunction
with
NYSDEC
(
co­
leads);
SCDHS;
Towns
of
East
Hampton,
Southampton,
Southold,
Shelter
Island,
and
Riverhead;
Cornell
Cooperative
Extension;
local
universities
and
colleges;
and
NY
Sea
Grant
HLR­
16.3
Plan
development:
PEP
Natural
Resources
Subcommittee
and
the
Marine
Conservation
Planner
(
co­
leads)
in
consultation
with
other
members
of
the
PEP
Management
Conference
and
technical
experts;
Plan
implementation:
PEP
Management
Conference,
NYSDEC,
NYSDOS,
New
York
Sea
Grant
Institute,
and
SCDHS
(
co­
leads)

HLR­
16.4
PEP
Natural
Resources
Subcommittee,
NYSDEC,
Marine
Conservation
Planner
(
coleads
and
technical
experts
through
the
PEP
long­
term
research
plan
HLR­
16.5
PEP
Natural
Resources
Subcommittee
(
lead)
and
technical
experts
through
the
PEP
longterm
research
plan
HLR­
16.6
PEP
Natural
Resources
Subcommittee
(
lead)
and
technical
experts
through
the
PEP
longterm
research
plan,
NY
Sea
Grant
HLR­
16.7
PEP
Natural
Resources
Subcommittee
(
lead)
and
technical
experts
to
define
specific
research
questions,
USACE,
SCDPW,
and
NYSDEC
HLR­
16.8
PEP
Natural
Resources
Subcommittee
(
lead)
and
PEP
Management
Council
(
co­
leads)

HLR­
16.9
PEP
Natural
Resources
Subcommittee
(
lead)

HLR­
16.10
PEP
Natural
Resources
Subcommittee
in
conjunction
with
EPA,
NYSDEC
(
co­
leads),
SCDHS,
and
local
universities
and
colleges
HLR­
16.11
PEP
Natural
Resources
Subcommittee
(
lead)

HLR­
16.12
PEP,
NY
Sea
Grant,
EPA
(
co­
leads),
NOAA,
NYS
Marine
Educators
Association
(
MEA),
and
Cornell
Cooperative
Extension
­
Marine
Program
HLR­
16.13
Association
of
NEPs,
EPA,
PEP
(
co­
leads),
NY
Sea
Grant,
and
NOAA
HLR­
16.14
PEP
Natural
Resources
Subcommittee
Peconic
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Program
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Addresses
Habitat
and
Living
Resources
Management
Objectives
1,
2,
3,
4,
and
8.

Grazer
and
filter­
feeding
organisms,
such
as
zooplankton,
clams,
scallops,
menhaden,
and
sponges,
are
vital
to
the
estuary
ecosystem.
Filter
feeders,
particularly
shellfish,
filter
large
volumes
of
bay
water
over
relatively
short
time
periods.
They
can
affect
water
quality
and
exert
significant
influence
on
the
size,
type,
and
abundance
of
phytoplankton.
Conversely,
changes
in
phytoplankton
species
composition
can
affect
the
diversity
and
abundance
of
grazers
and
filter­
feeders.
For
example,
preliminary
Brown
Tide
research
findings
by
Caron
and
Lonsdale
have
resulted
in
a
working
hypothesis
that
reduced
shellfish
populations
prior
to
the
first
Brown
Tide
in
the
Peconics
may
have
led
to
significant
reduction
in
grazing
pressure
on
phytoplankton,
thereby
allowing
the
onset
of
Brown
Tide.
Brown
Tide,
changes
in
the
nutrient
regime,
and
harvesting
of
shellfish
and
finfish
can
shift
the
abundance,
diversity,
and
temporal
and
spatial
distribution
of
grazers
and
filter­
feeders.
Understanding
the
food
web
dynamics
and
"
top­
down"
control
of
productivity
can
therefore,
be
equally
important
to
the
management
of
the
Peconic
Estuary
as
that
of
nutrient
cycling
("
bottom­
up").
A
working
group
is
needed
to
examine
these
issues
more
closely
and
evaluate
the
relationship
between
filter­
feeders
and
water
quality,
as
well
as
to
link
other
PEP
efforts
and
to
identify
potential
management
applications.

The
work
group
should
include
Brown
Tide
researchers,
shellfish
and
fishery
scientists,
marine
ecologists,
baymen,
aquaculturists,
water
quality
modelers,
resource
managers
and
regulators.

Issues:

1)
Understanding
the
relationship
of
grazer
and
filter­
feeder
diversity
and
abundance
with
phytoplankton
diversity
and
abundance;

2)
How
to
enhance
shellfish
and
finfish
stocks
to
accommodate
harvesting
while
also
maintaining
sufficient
populations
that
are
adequate
to
fulfill
ecological
functions;
and
3)
Need
for
collaboration
between
related
Peconic
Estuary
efforts,
such
as
the
Brown
Tide
Research
Initiative
(
BTRI),
water
quality
modeling,
estuary­
wide
aquaculture
plan
work
group,
and
finfish
monitoring.

Steps
HLR­
17.1
Review
appropriate
scientific
literature,
identify
information
gaps,
and
develop
research
recommendations
regarding
how
shellfish,
finfish
and
other
"
top­
down"
predators
influence
water
quality
and
the
planktonic
community.

HLR­
17.2
Develop
research,
monitoring,
and
assessment
needs
for
quantifying
food
web
dynamics.

HLR­
17.3
Develop
food
web
sub­
models
to
be
included
in
the
nutrient
model
to
evaluate
the
sensitivity
of
productivity
to
anthropogenic
changes
in
nutrient
supply.
HLR­
17
Establish
a
Working
Group
to
Examine
the
Role
of
Grazers
and
Filter
Feeding
Organisms
in
Influencing
Water
Quality
and
Productivity,
and
to
Better
Understand
the
Food
Web
Dynamics
and
to
Develop
Management
Applications.
Peconic
Estuary
Program
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HLR­
17.4
Consult
with
the
BTRI
and
the
estuary­
wide
aquaculture
plan
work
group
to
develop
management
recommendations
for
"
top­
down"
regulation
of
water
quality
and
Brown
Tide
in
the
Peconic
Estuary.

HLR­
17.5
Facilitate
communication
among
BTRI,
water
quality
managers
and
the
estuary­
wide
aquaculture
plan
work
group.

Responsible
Entities
HLR­
17.1
PEP
Natural
Resources
Subcommittee
(
lead)
through
contractor
HLR­
17.2
PEP
Natural
Resources
Subcommittee
(
lead)
and
marine
conservation
planner
HLR­
17.3
PEP
Natural
Resources
Subcommittee
through
contractor
(
lead)
in
consultation
with
other
members
of
the
PEP
Management
Conference
and
technical
experts
HLR­
17.4
PEP
Natural
Resources
Subcommittee
(
lead)
in
consultation
with
other
members
of
the
PEP
Management
Conference
and
technical
experts;
NYSDEC,
NYSDOS,
New
York
Sea
Grant
Institute,
SCDHS,
BTRI
researchers,
SUNY
Stony
Brook,
Cornell,
and
commercial
aquaculture
facilities
in
the
Peconics
HLR­
17.5
PEP
Natural
Resources
Subcommittee
(
lead)
in
consultation
with
other
members
of
the
PEP
Management
Conference
and
technical
experts;
NYSDEC,
NYSDOS,
New
York
Sea
Grant
Institute,
SCDHS,
BTRI
researchers,
SUNY
Stony
Brook,
Cornell,
and
commercial
aquaculture
facilities
in
the
Peconics
BENEFITS
OF
THE
MANAGEMENT
ACTIONS
Implementation
of
these
management
actions
will
greatly
benefit
the
Peconic
Estuary
by
protecting
rare
and
endangered
species,
enhancing
ecological
communities
throughout
the
system,
restoring
degraded
habitats
to
increase
biodiversity,
protecting
high
quality
areas
where
there
are
concentrations
of
exemplary
examples
of
natural
communities,
improving
our
understanding
and
assessment
of
impacts
on
natural
resources,
and
providing
sustainable
commercial
and
recreational
fisheries.
These
management
recommendations
also
include
important
actions
that
can
be
taken
to
mitigate
stress
by
minimizing
impacts
to
living
resources
and
habitats
crucial
to
their
survival.

The
estuary
is
on
the
brink
of
being
seriously
impacted
by
overuse.
By
setting
management
actions
that
foster
commercial
and
recreational
use
that
is
sustainable
and
compatible
with
protection
of
biodiversity,
stakeholders
can
ensure
an
important
balance
between
preservation
and
the
wise
use
of
the
bays'
natural
resources.
EAI's
Economic
Value
Assessment
and
Finance
Plan
may
contain
quantifiable
benefits
to
highlight
these
claims.
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Estuary
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COSTS
OF
THE
MANAGEMENT
ACTIONS
The
individual
cost
for
each
management
action
is
provided
in
Table
4­
1.

The
total
cost
of
all
new
actions
proposed
for
the
Habitat
and
Living
Resources
management
in
this
chapter
is
$
9,088,750
in
one­
time
costs
and
$
1,881,250
annually.
(
See
"
Action
Costs"
in
Chapter
1
for
an
explanation
of
how
these
costs
were
determined.)

HABITAT
AND
LIVING
RESOURCES
ACTIONS
SUMMARY
TABLE
Table
4­
1
provides
the
following
summary
information
about
each
of
the
actions
presented
in
this
chapter.
Priority
Habitat
and
Living
Resources
steps
are
also
identified
in
the
table.
These
priorities
were
decided
by
the
PEP
Natural
Resources
Subcommittee.

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
in
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
a
expanded
explanation
of
base
programs
and
action
costs.
C
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A
P
T
E
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F
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U
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4­
70
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
1
Use
Critical
Natural
Resource
Areas
(
CNRAS)
to
Develop
and
Implement
Management
Strategies
to
Protect
High
Quality
Habitats
and
Concentrations
of
Species
of
Special
Emphasis.
(
Objectives
1,
2,
3,
6,
7,
and
8)

HLR­
1.1
Priority
Collect
and
interpret
natural
resource,
water
quality,
and
land
use
data
sets.
Use
GIS
technology
to
finalize
a
comprehensive
inventory
of
species,
natural
communities
and
water
quality,
refine
maps
(
including
development
of
maps
of
each
CNRA),
and
evaluate
individual
and
cumulative
threats
within
each
CNRA.
NYSDEC,
The
Nature
Conservatory
(
co­
leads)
with
towns
and
USFWS
assistance
Post­
CCMP
$
150,000
for
contractor
assistance
NYSDEC
 
1.0
FTE
TNC
 
1.0
FTE
Towns
 
0.1
FTE
USFWS
 
0.2
FTE
R
HLR­
1.2
Priority
Finalize
CNRA
boundaries
and
adopt
CNRAs
by
appropriate
levels
of
government.
NYSDEC;
The
Nature
Conservancy
(
co­
leads);
PEP
Natural
Resources
Subcommittee;
Towns
of
East
Hampton,
Southampton,

Southold,
Shelter
Island,

Riverhead,
and
Brookhaven;

NYSDEC;
OPRHP;
Suffolk
County
Parks
Department;

USFWS;
NYSDOS
Post­
CCMP
NYSDEC
 
0.3
FTE
SCDHS
 
0.3
FTE
PEP
 
0.3
FTE
TNC
 
0.3
FTE
USFWS
 
0.3
FTE
Towns
 
0.2
FTE
each
SC
Parks
 
0.3
FTE
R
Table
continued
next
page
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
C
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A
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F
O
U
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4­
71
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
1.3
Priority
Develop
management
recommendations
and
plans
to
protect
CNRAs
in
each
town
in
coordination
with
existing
Federal,

State,
county,
and
municipal
programs
that
address
individual
and
potential
cumulative
impacts
including
but
not
limited
to
docks,

shoreline
stabilization
structures,

dredging,
marinas,
artificial
reefs,

fish
farms,
shellfish
culture,
fishing,

pesticides,
golf
courses,
motorized
personal
watercraft,
swimming
pools,
sewage
treatment
and
disposal,
building
and
adjacent
upland
development,
and
clearing
of
vegetation.
NYSDEC,
The
Nature
Conservancy
(
co­
leads)
to
assist
local
governments
in
coordination
with
PEP
Management
Conference,

EPA,
SCDHS
.
Post­
Completion
of
HLR­
1.1
and
HLR­
1.2
EPA
 
0.05
FTE
NYSDEC
 
0.9
FTE
SCDHS
 
0.5
FTE
TNC
 
0.5
FTE
Towns
 
1.0
FTE
each
R
HLR­
1.4
Priority
Protect
the
CNRAs
through
land
acquisition
and
other
protection
tools
(
e.
g.,
clearing
restrictions,

setback
requirements,
zoning,

Transfer
of
Development
Rights)

principally
within
the
areas
themselves
and
including
essential
watershed
buffers
(
see
Chapter
7).
NYSDEC;
NYS
Office
of
Parks,
Recreation
and
Historic
Preservation;
Suffolk
County
Planning
Department;

Towns
of
East
Hampton,

Southampton,
Southold,

Shelter
Island,
Riverhead,

and
Brookhaven
Ongoing
(
Significant
funding
has
been
allocated
for
acquisition
estuary­
wide.
See
Chapters
7
and
9.
C/
O
Table
continued
next
page
C
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A
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F
O
U
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4­
72
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
1.5
Prohibit
the
installation
of
new
shoreline
hardening
structures
within
CNRAs.
Investigate
ecologically
enhancing,
innovative
designs
to
replace
or
use
as
an
alternative
to
hard
structures.
Prohibit
installation:
Towns
of
East
Hampton,

Southampton,
Southold,

Shelter
Island,
Riverhead,

villages,
NYSDEC;

Investigate
new
designs:

NYSDEC,
TNC,
EPA,

SCDHS,
Peconic
BayKeeper
Subsequent
to
completion
of
HLR­
1.2
Prohibit
installation:
Base
Program;
Investigate
new
designs:
$
50,000
EPA
 
0.1
FTE
NYSDEC
 
0.8
FTE
SCDHS
 
0.5
FTE
TNC
 
0.5
FTE
Towns
 
0.5
FTE
each
Peconic
BayKeeper
 
0.2
FTE
R
HLR­
1.6
Coordinate
PEP
recommendations
for
CNRAs
with
the
NYSDOS
Significant
Coastal
Fish
and
Wildlife
Habitat
Program
and
Local
Waterfront
Revitalization
Plan
Programs.
NYSDOS
(
lead),
NYSDEC,

PEP
Natural
Resources
Subcommittee
Fall
1999
NYSDEC
 
0.1
FTE
PEP
 
0.1
FTE
NYSDOS
 
0.2
FTE
C/
O
HLR­
1.7
Encourage
increased
use
of
the
NYSDOS
Significant
Coastal
Fish
and
Wildlife
Habitat
Program
guidelines
by
appropriate
Federal,
State,
county,

and
municipal
agencies.
NYSDOS
(
lead),
NYSDEC,

Towns,
USACE,
USFWS,

NMFS
Ongoing
NYSDOS
 
0.2
FTE
NYSDEC
 
0.1
FTE
C/
O
HLR­
1.8
Examine
the
possibility
of
establishing
marine
reserves
(
e.
g.,
protect
eelgrass
beds)
within
the
CNRAs.
PEP
Natural
Resources
Subcommittee,
EPA,

NYSDEC,
SCDHS
Post­
CCMP
EPA
 
0.05
FTE
NYSDEC
 
0.05
FTE
SCDHS
 
0.05
FTE
PEP
 
0.05
FTE
R
HLR­
1.9
Discourage
expansion
of
existing
marinas
and
the
creation
of
new
ones
within
the
PEP
CNRAs.
The
marina
expansion
and
creation
issue
will
be
further
evaluated
as
part
of
a
comprehensive
strategy
dealing
with
shoreline
hardening,
marinas,
docks,

and
public
access
(
see
HLR­
1.3).
Contingent
upon
adoption
of
CNRAs
(
see
HLR­
1.2)
Post­
completion
of
HLR­
1.2
Base
Program
R
Table
continued
on
next
page
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
C
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A
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T
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F
O
U
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4­
73
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
2
Manage
Shoreline
Stabilization,
Docks,
Piers,
and
Flow
Restriction
Structures
to
Reduce
or
Prevent
Additional
Hardening
and
Encourage
Restoration
of
Hardened
Shorelines
to
a
Natural
State.
(
Objectives
1,
3,
4,
6,
7,
and
8)

HLR­
2.1
Priority
Quantify
and
map
all
hardened
shoreline,
docks
and
piers,
and
flow­
restriction
structures
in
the
Peconic
Estuary
and
assess
the
overall
impacts
of
stabilization
structures
on
natural
resources.

Develop
recommendations
to
promote
alternative
shoreline
management
and
incentives
for
maintaining
and
restoring
natural
shorelines.
Contract
with
Cornell
and
USFWS
Develop
recommendations:

NYSDEC,
EPA,
SCDHS,

NYSDOS,
Towns
Due:
Spring
2001
Post­
CCMP
($
65,000
NEP
funds
allocated)

Develop
recommendations:

NYSDEC
 
0.2
FTE
EPA
 
0.1
FTE
SCDHS
 
0.1
FTE
NYSDOS
 
0.2
FTE
Towns
 
0.1
FTE
each
C/
O
R
HLR­
2.2
Review
existing
regulations
for
shoreline
hardening
structures
at
all
levels
of
government,
encourage
consistent
policies
and
strengthen
regulations
where
appropriate.
PEP­
Natural
Resources
subcommittee
through
contractor
Post­
CCMP
$
50,000
R
HLR­
2.3
Priority
Establish
and
enforce
a
policy
of
no
net
increase"
of
hardened
shoreline
in
the
Peconic
Estuary
and,
if
possible,
a
net
decrease
in
hardened
shoreline.
Use
HLR­
1
and
HLR­
2
as
a
mechanism
to
establish
this
strategy.
PEP
Management
Conference
(
lead);
NYSDEC;

Towns
of
East
Hampton,

Southampton,
Southold,

Shelter
Island,
Riverhead;

villages;
NYSDOS;
USACE;

PEP,
SCDHS,
EPA
Post­
CCMP
Establishing
the
policy
could
be
done
with
Base
program
funds
but
implementation
of
such
a
policy
could
be
substantial
EPA
 
0.3
FTE
NYSDEC
 
0.3
FTE
SCDHS
 
0.3
FTE
PEP
 
0.3
FTE
Towns
 
0.3
FTE
NYSDOS
 
0.3
FTE
R
Table
continued
next
page
C
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A
P
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E
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F
O
U
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4­
74
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
2.4
Priority
Develop
a
variety
of
financial
incentives
and
programs
to
encourage
property
owners
to
remove
or
modify
hardened
shoreline
structures
and
replace
them
with
natural
vegetation
and
other
vegetated
(
bioengineered)

alternatives
to
restore
the
natural
shoreline
of
the
estuary.
Peconic
BayKeeper
(
lead);

Towns
of
East
Hampton,

Southampton,
Southold,

Shelter
Island,
Riverhead;

villages;
HRWG;
NYSDEC;

SCDHS;
PEP
Post­
CCMP
NYSDEC
 
0.1
FTE
SCDHS
 
0.1
FTE
PEP
 
0.1
FTE
Towns
 
0.2
FTE
each
Peconic
BayKeeper
 
0.3
FTE
R
HLR­
3
Assess
the
Impacts
of
Dredging
Activities
on
Habitat
and
Natural
Resources
and
Develop
Recommendations
and
Guidelines
for
Reducing
those
Impacts.
(
Objectives
1,
2,
3,
6,
and
7)

HLR­
3.1
Priority
Hold
a
"
Dredging
Summit"
for
the
Peconic
Estuary
System
to
address
specific
concerns
(
i.
e.,
impacts
on
shorebird
nesting,
demersal
fish
eggs,
benthic
communities,
and
the
potential
release
of
contaminants)

and
develop
dredging
guidance
on
an
embayment­
specific
basis
and
for
identified
CNRAs.
Integrate
dredging
guidance
into
existing
regulatory
programs.
NYSDEC
(
lead)
through
contractor;
USACE;

NYSDOS;
SCDPW;
EPA;

SCDHS;
Towns
of
East
Hampton,
Southampton,

Southold,
Shelter
Island,

Riverhead;
other
interested
stakeholders
Post­
CCMP
Dredging
Summit:
$
15,000
Develop
Guidance:

NYSDEC
 
0.4
FTE
NYSDOS
 
0.2
FTE
SCDHS
 
0.2
FTE
EPA
 
0.1
FTE
R
R
Table
continued
next
page
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
C
H
A
P
T
E
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F
O
U
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4­
75
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
3.2
Priority
Assess
navigational
dredging
in
tidal
creeks
and
embayments
(
utilizing
Suffolk
County's
Generic
Environmental
Impact
Statement)

for
damages
or
impacts
to
eelgrass
beds
and
other
habitats
and
develop
permit
conditions
to
minimize
impacts
that
potentially
could
result
in
habitat
loss
and
degradation.

Determine
if
navigational
dredging
locally
impairs
water
quality
to
the
point
of
precluding
restoration
of
eelgrass.
PEP
through
contractor,

NYSDEC,
DOS,
SCDHS
Post­
CCMP
Assessment:
$
50,000
Determination:

NYSDEC
 
0.2
FTE
NYSDOS
 
0.2
FTE
SCDHS
 
0.2
FTE
R
R
HLR­
3.3
Determine
the
need
for
frequency
of
maintenance
dredging
and
develop
recommendations
to
reduce
runoff
and
erosion
in
creeks
to
reduce
the
need
for
maintenance
dredging.
Frequency
of
dredging:

SCDPW
(
lead);

Runoff
recommendations:

NYSDEC,
NYSDOS
(
co­
leads);
PEP,
SCDHS
Post­
CCMP
Frequency
of
dredging:
Base
Program
Runoff
recommendation:

NYSDEC
 
0.1
FTE
SCDHS
 
0.1
FTE
PEP
 
0.2
FTE
R
R
Table
continued
on
next
page
C
H
A
P
T
E
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F
O
U
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4­
76
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
4
Examine
and
Promote
Methods
of
Shellfish
Harvesting
that
are
Most
Compatible
with
Establishment
and
Growth
of
Eelgrass
Beds
and
Vegetated
Salt
Marshes.
(
Objectives
1,
3,
5,
6,
and
8)

HLR­
4.1
Examine
methods
of
harvesting
clams,
scallops,
and
other
shellfish
and
determine
which
are
most
compatible
with
eelgrass
establishment
and
growth.
Develop
recommendations
for
harvesting
methods,
frequency,
and
timing
which
will
allow
recovery
of
eelgrass
throughout
the
estuary
and
enhance
shellfish
productivity.
NYSDEC
(
lead)
through
contract
Post­
CCMP
$
50,000
for
contractor
support
NYSDEC
 
0.3
FTE
R
HLR­
4.2
Discourage
harvesting
of
shellfish
at
the
edge
of
vegetated
salt
marshes
and
encourage
the
use
of
methods
that
minimize
impacts
to
vegetated
habitats.
NYSDEC
(
lead);
Towns
of
East
Hampton,
Southampton,

Southold,
Shelter
Island,

Riverhead;
PEP
Public
Education
and
Outreach
program;
shellfishermen
Post­
CCMP
Base
program
and
$
10,000
for
education
and
outreach
NYSDEC
 
0.2
FTE
PEP
 
0.2
FTE
R
HLR­
5
Implement,
Enforce,
and
Encourage
the
Continuation
of
Current
Policies
and
Regulations
Protective
of
Wetlands.

(
Objectives
1,
2,
3,
4,
6,
and
7)

HLR­
5.1
Ensure
continued
protection
of
freshwater
and
tidal
wetlands
through
the
implementation
and
enforcement
of
current
regulations
under
the
Federal
Clean
Water
Act
and
the
State
Wetlands
Protection
Programs,
local
government
regulations
and
local
land
use
practices.
NYSDEC
(
lead),
ACOE,

East
End
Towns
Ongoing
Base
program
Enhance
existing
programs
NYSDEC
 
2.0
FTE/
yr
C/
O
R
Table
continued
on
next
page
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
C
H
A
P
T
E
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F
O
U
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4­
77
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
5.2
Review
existing
tidal
wetlands
protection
policies
to
determine
if
they
provide
for
maintenance
of
tidal
wetlands
with
respect
to
future
sea­
level
rise.
PEP
 
Natural
Resources
Subcommittee
through
contractor
Post­
CCMP
$
25,000
R
HLR­
5.3
Maintain
and
enforce
the
policy
of
creating
no
new
mosquito
ditches
in
tidal
wetlands
and
establish
a
policy
for
not
re­
opening
ditches
that
have
filled­
in
by
natural
processes.
SCVC
(
lead),
NYSDEC,

EPA,
SCDHS,
NYSDOS,

East
End
Towns
Ongoing
EPA
 
0.1
FTE
NYSDEC
 
0.2
FTE
SCDHS
 
0.2
FTE
PEP
 
0.2
FTE
SCVC
 
0.3
FTE
Towns
 
0.1
FTE
each
C/
O
HLR­
5.4
Ensure
that
SCVC
works
cooperatively
with
all
government
agencies,
East
End
towns
and
local
conservation
organizations
in
the
planning
of
wetland
mosquito
ditch
maintenance
and
pesticide
spraying.
SCVC
(
lead),
SCDHS,

NYSDOS,
EPA,
NYSDEC,

East
End
Towns
Post­
CCMP
EPA
 
0.1
FTE
NYSDEC
 
0.1
FTE
SCDHS
 
0.1
FTE
PEP
 
0.1
FTE
SCVC
 
0.1
FTE
R
HLR­
6
Evaluate
the
Effectiveness
of
Current
Policies
in
Preserving
Eelgrass
Habitat
and
Develop
Ways
to
Provide
Increased
Protection
for
all
Extant
Eelgrass.
(
Objectives
1,
2,
3,
5,
6,
and
8)

HLR­
6.1
Priority
Evaluate
the
effectiveness
of
current
policies
in
preserving
eelgrass
habitat
and
develop
ways
to
provide
increased
protection
for
all
extant
eelgrass.
NYSDEC
(
lead)
through
contract
Ongoing
$
25,000
R
HLR­
6.2
Monitor
and
protect
extant
eelgrass
(
Zostera
marina)
beds,
and
restore
degraded
eelgrass
beds.
NYSDEC,
(
lead),
Cornell
Cooperative
Extension,
PEP­

Natural
Resources
Subcommittee
PEP­
HRWG
Ongoing
(
Monitor:
$
75,000
biennially,

included
in
Environmental
Monitoring
Plan.)

Protect
and
Restore:
to
be
determined
C/
O
R
Table
continued
on
next
page
C
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4­
78
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
6.3
Evaluate
anchor
dragging,
propeller
scarring,
dredging
and
other
known
impacts
to
extant
eelgrass
beds
in
the
Peconic
Estuary
and
develop
recommendations
to
reduce
them.
NYSDEC,
Habitat
Restoration
Workgroup
(

coleads
through
contract
Post­
CCMP
Evaluation
through
contractor:
$
50,000
Develop
recommendations:

NYSDEC
 
0.2
FTE
R
HLR­
6.4
Hold
a
workshop
to
evaluate
the
factors
that
regulate
the
health
and
extent
of
eelgrass
beds
in
the
Peconic
Estuary
and
develop
management
recommendations
based
on
these
findings.
NYSDEC,
PEP­
NRSC,
PEP
HRWG
(
co­
leads)
Post­
CCMP
Workshop
costs:
$
10,000
Develop
recommendations:

NYSDEC
 
0.4
FTE
R
R
HLR­
7
Develop
and
Implement
an
Estuary­
Wide
Habitat
Restoration
Plan
(
HRP).
(
Objectives
1,
2,
4,
and
7)

HLR­
7.1
Priority
Develop
and
implement
an
estuarywide
Habitat
Restoration
Plan
(
HRP).
PEP
HRWG
(
lead)
Initiate
in
Fall
1998,

complete
in
2001
Costs
for
implementation
in
PEP
Habitat
Restoration
Plan
NYSDEC
 
0.1
FTE/
yr
SCDHS
 
0.1
FTE/
yr
PEP
 
0.1
FTE/
yr
Towns
 
0.1
FTE
each/
yr
Cornell
 
0.2
FTE/
yr
NYSDOS
 
0.2
FTE/
yr
C/
O
HLR­
7.2
Identify
and
list
priority
habitat
types
for
the
HRP.
PEP
HRWG
(
lead)
Completed
Included
in
HLR­
7.1
C/
O
HLR­
7.3
Priority
Inventory
and
prioritize
a
list
of
restoration
projects
for
which
planning
is
underway
and
recommend
these
for
"
fast­
tracking"

towards
Bond
Act
funding.
NYSDOS
(
lead),
NYSDEC,

PEP
HRWG
Annually,
prior
to
Spring
announcement
of
available
funds
Included
in
HLR­
7.1
C/
O
HLR­
7.4
Inventory
and
list
restoration
opportunities
in
the
PEP
area
and
estimate
costs.
PEP
HRWG
(
lead),
East
End
Towns
Completed
Included
in
HLR­
7.1
C/
O
Table
continued
on
next
page
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
C
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A
P
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E
R
F
O
U
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4­
79
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
7.5
Develop
and
include
in
the
HRP
criteria
for
selection
of
restoration
sites.
PEP
HRWG
(
lead)
Completed
Included
in
HLR­
7.1
C/
O
HLR­
7.6
Inventory
and
list
completed,

ongoing,
and
proposed
restoration
projects
for
inclusion
in
the
HRP.

Include
all
restoration
sites
on
GIS
maps.
PEP
HRWG
(
lead)
Completed
Included
in
HLR­
7.1
C/
O
HLR­
7.7
Develop
and
include
in
the
HRP
a
list
of
funding
sources
available
for
habitat
restoration
in
the
PEP
area.
PEP
HRWG
(
lead)
Completed
Included
in
HLR­
7.1
C/
O
HLR­
7.8
Develop
model
guidelines
for
habitat
restoration
planning
for
use
by
municipalities
in
applying
for
EPF
monies.
NYSDOS,
NYSDEC
(

coleads
PEP
HRWG,
EPA,

Towns,
CCE
2001
EPA
 
0.1
FTE
PEP
 
0.1
FTE
Towns
 
0.1
FTE
each
Cornell
 
0.2
FTE
NYSDOS
 
0.2
FTE
C/
N
HLR­
8
Develop
and
Implement
Specific
Restoration
Projects.
(
Objectives
1,
3,
4,
6,
7,
and
8)

HLR­
8.1
Encourage
cooperation
among
governmental
agencies
to
plan
and
Implement
Open
Marsh
Water
Management
(
OMWM)
to
manage
tidal
wetlands
with
grid
ditches
for
mosquito
control
with
the
goal
of
also
restoring
more
natural
conditions.
Cornell
Cooperative
Extension,
SCVC,
USFWS,

East
Hampton
Department
of
Natural
Resources,
NYSDEC
(
co­
leads),
PEP
Post­
CCMP
NYSDEC
 
0.1
FTE
PEP
 
0.1
FTE
Cornell
 
0.3
FTE
SCVC
 
0.3
FTE
USFWS
 
0.3
FTE
Towns
 
0.2
FTE
each
R
Table
continued
on
next
page
C
H
A
P
T
E
R
F
O
U
R
4­
80
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
8.2
Develop
recommendations
in
the
PEP
Habitat
Restoration
Plan
for
control
of
Phragmites
australis
by
restoration
of
natural
processes
such
as
removal
or
modification
of
flowrestriction
devices,
removal
of
hardened
shorelines,
and
revegetation
of
bay
and
creek
shorelines
or
by
other
means.
PEP
HRWG
(
lead)
through
contractor
2001
Base
Program
and
$
10,000
for
contractor
C
HLR­
8.3
Priority
Develop
a
quantitative
goal
for
eelgrass
restoration
based
on
ongoing
monitoring
and
mapping
efforts.
PEP
HRWG
(
lead),

NYSDEC,
SCDHS,
CCE,

DOS,
Towns
2001
NYSDEC
 
0.05
FTE
SCDHS
 
0.05
FTE
PEP
 
0.1
FTE
Towns
 
0.05
FTE
each
Cornell
 
0.2
FTE
NYSDOS
 
0.2
FTE
C/
N
HLR­
8.4
Identify
and
prioritize
locations
where
restoration
of
eelgrass
is
most
feasible
based
on
water
quality
and
environmental
criteria
which
are
being
developed
for
eelgrass
in
the
Peconic
Estuary
System
and
elsewhere
in
its
range.
PEP
HRWG
(
lead),
PEP,

NYSDEC,
NYSDOS
2001
Included
in
HLR­
8.3
C/
N
HLR­
8.5
Develop
and/
or
utilize
cooperative
programs
with
the
public
for
simple,

local
habitat
improvements
and
enhancements.
PEP
HRWG
(
lead),
NY
Sea
Grant,
Cornell
Cooperative
Extension
Post­
CCMP
$
25,000
per
year
R
HLR­
9
Monitor
and
Evaluate
the
Success
of
Restoration
Efforts.
(
Objective
8)

HLR­
9.1
Develop
and
implement
procedures
to
track
and
evaluate
restoration
efforts
using
success
criteria
and
monitoring
protocols
in
the
PEP
area.
PEP
HRWG
(
lead)
Post­
CCMP
HRWG
 
0.2
FTE
R
Table
continued
on
next
page
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
C
H
A
P
T
E
R
F
O
U
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4­
81
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
9.2
Develop
procedures
for
the
management
and
storage
of
habitat
restoration
project
and
monitoring
information
for
the
Peconic
Estuary.
PEP
HRWG
(
lead),
PEP
HRWG
 
0.2
FTE
R
HLR­
9.3
Identify
a
regional
set
of
reference
sites
to
assist
in
habitat
restoration
evaluation
and
monitoring
and
provide
a
framework
for
long­
term
habitat
and
living
resources
research
and
monitoring.
PEP
HRWG,
PEP
Natural
Resources
Subcommittee
2001
Included
in
HLR­
8.3
C/
N
HLR­
10
Develop
an
Aquaculture
Plan
for
the
Peconic
Estuary.
(
Objectives
1,2,
5,
6,
7,
and
8)

HLR­

10.1
Priority
Assist
in
the
development
and
implementation
of
an
estuary­
wide
aquaculture
plan.
Include
criteria
regarding
scale,
location,

assessment,
monitoring,
and
methodologies
of
shellfish
and
finfish
aquaculture
which
would
be
ecologically
beneficial
and
would
help
sustain
aquaculture
as
a
beneficial
estuarine
use
when
performed
in
a
manner
that
is
sensitive
to
the
natural
conditions,

productivity
and
ecology
of
the
Peconic
Estuary.
Organize
workshop:
Suffolk
County
Planning
Department;

SCDHS
(
co­
leads);
NYSDEC;

PEP
 
Natural
Resources
Subcommittee;
NYSDOS;
NY
Sea
Grant;
NYSOGS;
USACE;

EPA;
NOAA/
NMFS;
Suffolk
County;
Towns
of
East
Hampton,
Southampton,

Southold,
Shelter
Island,

Riverhead;
villages;
Cornell
Cooperative
Extension;
fish
farmers;
other
groups
and
individuals
interested
in
aquaculture;
Aquaculture
Plan:

Suffolk
County
with
input
from
PEP
and
other
stakeholders
(
NYSDEC,
Long
Island
Sound
Study,
New
York­
New
Jersey
Harbor
Estuary
Program)
Post­
CCMP
Plan:
within
one
year
of
workshop
Workshop:
$
5,000
Plan:

EPA
 
0.2
FTE
NYSDEC
 
1.0
FTE
S.
C.
 
1.0
FTE
R
Table
continued
on
next
page
C
H
A
P
T
E
R
F
O
U
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4­
82
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
10.2
Identify
suitable
areas
for
shellfish
and
finfish
aquaculture
activities
that
are
compatible
with
the
water
quality
and
habitat
protection
objectives
in
the
CCMP
to
ensure
that
a
balance
is
maintained
between
cultivated
and
wild
stocks
and
include
in
the
estuary­
wide
aquaculture
plan.
Suffolk
County
Planning
Department,
SCDHS,

NYSDEC
(
co­
leads),

NYSDOS,
USACE,

USFWS,
PEP­
Natural
Resources
Subcommittee
Post­
CCMP
$
500,000
for
a
survey
Enhance
existing
programs:

NYSDEC
 
0.5
FTE/
yr
SCDHS
 
0.5
FTE/
yr
R
R
HLR­
10.3
Investigate
the
need
to
require
monitoring
of
imported
cultured
organisms
and
intrastate
transplant
of
shellfish
for
disease
and
parasites
and
determine
if
a
requirement
should
be
established
to
certify
that
they
are
disease
free.
Monitoring
assessment:

NYSDEC
(
lead);
Disease
and
parasite
screening:
PEP;

NYSDEC;
NYSDOS;

NYSOGS;
USACE;
EPA;

NOAA/
NMFS;
Suffolk
County,
Towns
of
East
Hampton,
Southampton,

Southold,
Shelter
Island,

Riverhead;
villages,
Cornell
Cooperative
Extension;

other
groups
and
individuals
interested
in
aquaculture
(
co­
leads)
Post­
CCMP
$
50,000
per
year
Enhance
existing
programs:

NYSDEC
 
1.0
FTE/
yr
R
R
HLR­
10.4
Continue
to
support
the
prohibition
of
commercial
culture
or
introduction
of
non­
indigenous
species
in
New
York's
waters
and
require
that
all
aquaculture
operations
in
the
estuary
use
indigenous
genotypes.
NYSDEC
(
lead)
to
implement
legislation,
NYS
legislature
Ongoing
Base
Program
Enhance
existing
programs:

NYSDEC
 
1.0
FTE/
yr
C/
O
R
Table
continued
on
next
page
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
C
H
A
P
T
E
R
F
O
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4­
83
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
10.5
Develop
water
quality
and
natural
resource
monitoring
protocols
for
existing
and
future
shellfish
and
finfish
aquaculture
projects.
SCDHS,
NYSDEC
(
co­
leads),
USACE,

NYSDOS,
NYSOGS,

USFWS,
PEP,
NOAA,
fish
farmers
(
permittees)
Post­
CCMP
Enhance
existing
programs:

NYSDEC
 
1.0
FTE
SCDHS
 
1.0
FTE
R
HLR­
11
Determine
the
suitability
of
Artificial
Reefs
in
the
Peconic
Estuary.
(
Objectives
1,
3,
4,
6,
and
8)

HLR­
11.1
Evaluate
the
use
of
natural
reefs,

wrecks,
artificial
reefs,
and
aquaculture
facilities
by
finfish,
sea
turtles,
diving
birds,
marine
mammals,
and
other
estuarine
organisms.
Develop
recommendations
to
minimize
the
impact
on
resources
by
these
structures.
PEP
Natural
Resources
Subcommittee
(
lead)
(

longterm
research
plan)
through
contractor
Post­
CCMP
$
100,000
through
contractor
R
HLR­
11.2
Determine
environmental
and
habitat
criteria
(
e.
g.,
productivity,

etc.)
for
site
selection
of
different
reef
structures,
and
evaluate
the
potential
for
the
extent
of
habitat
and
species
displacement
and
the
number
of
reefs
that
could
be
supported
in
the
estuary
without
causing
adverse
effects.
PEP
Natural
Resources
Subcommittee
&
NYSDEC
(
co­
leads)
Post­
CCMP
$
100,000
through
contractor
R
HLR­
11.3
Evaluate
the
potential
placement
of
artificial
reefs
in
known
sea
turtle
and
marine
mammal
feeding
areas
as
part
of
the
siting
process
outlined
in
the
NYSDEC
Artificial
Reef
Plan.
NYSDEC
(
lead);
Towns
of
East
Hampton,
Southampton,

Southold
Post­
CCMP
$
50,000
through
contractor
R
Table
continued
on
next
page
C
H
A
P
T
E
R
F
O
U
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4­
84
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
12
Foster
Sustainable
Recreational
and
Commercial
Finfish
and
Shellfish
Uses
of
the
Peconic
Estuary
that
are
Compatible
with
Biodiversity
Protection.
(
Objectives
1,
2,
3,
5,
6,
7,
and
8)

HLR­
12.1
Priority
Collect
better
statistical
data
on
commercial
and
recreational
fishing
landings
and
by­
catch
specific
to
the
Peconic
Estuary
System.
NOAA/
NMFS,
NYSDEC
(
co­
leads)
Post­
CCMP
Enhance
existing
programs:

NYSDEC
 
2.0
FTE/
yr
R
HLR­
12.2
Priority
Identify,
protect,
and
restore
key
shellfish
and
finfish
spawning,

nursery,
and
feeding
habitats
in
the
Peconic
Estuary
to
enhance
shellfish
and
fish
stocks
and
incorporate
this
data
into
the
ongoing
Essential
Fish
Habitat
work
being
conducted
under
the
Atlantic
States
Marine
Fisheries
Commission
(
ASMFC).
PEP,
NOAA/
NMFS,

ASMFC,
New
York
Sea
Grant
Institute,
NYSDEC,

local
universities
and
colleges
Post­
CCMP
$
100,000
R
HLR­
12.3
Support
the
Atlantic
Coastal
Cooperative
Statistics
Program.
NMFS,
NYSDEC,
PEP
(
co­
leads)
Ongoing
Base
Programs
C/
N
HLR­
12.4
Support
the
fishery
management
plans
which
have
been
and
are
being
developed
by
the
Mid­

Atlantic
Fishery
Management
Council
(
MAFMC)
and
the
ASMFC.
NYSDEC,
PEP
(
co­
leads),

ASMFC,
NMFS,
MAFMC
Ongoing
Base
Programs
C/
O
HLR­
12.5
Ensure
the
enforcement
of
existing
regulations
on
both
commercial
and
recreational
fisheries.
NYSDEC
Division
of
Law
Enforcement
(
lead),
Suffolk
County
Marine
Police,
town
bay
constables
Ongoing
Base
Program
Enhance
existing
programs:

NYSDEC
 
2.0
FTE
/
yr
C/
O
R
HLR­
12.6
Support
NMFS
Essential
Fish
Habitat
Designations
within
the
Peconic
Estuary.
PEP
 
MC,
NYSDEC,

NMFS
Ongoing
Base
Program
NYSDEC
 
0.1
FTE
/
yr
C/
O
Table
continued
on
next
page
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
C
H
A
P
T
E
R
F
O
U
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4­
85
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
12.7
Develop
a
public
education
program
about
the
value
of
fish
and
fishing
and
the
importance
of
commercial
and
recreational
fishing
regulations
and
compliance
with
the
regulations.
PEP
Public
Education
and
Outreach
program
(
lead),

NYSDEC,
Sea
Grant,
Cornell
Cooperative
Extension
­

Marine
Program,
AMI,

marina
and
fishing
businessowners
Post­
CCMP
$
15,000
R
HLR­
12.8
Support
the
prevention,
or
at
least
minimization,
of
effects
on
finfish
and
non­
target
species
by
lost
or
incorrectly
designed
fishing
gear.

Measures
to
be
supported
include:

(
1)
developing
a
program
to
encourage
commercial
and
recreational
fishermen
to
retrieve
and
properly
dispose
of
fishing
line,

nets,
traps,
pots,
and
other
gear;
(
2)

work
with
the
AMI
to
develop
a
campaign
for
dockside
recovery
and
recycling
programs;
(
3)
support
implementation
of
fishery
regulations
requiring
escape
vents
and
degradable
panels
in
fish
and
lobster
pots;
(
4)
implementing
fishery
regulations
requiring
minimum
mesh
size
for
gill,
fyke,

and
otter
trawl
nets;
and
(
5)

promoting
the
use
of
fishing
gears
that
minimize
by­
catch
and
discard
(
e.
g.,
pound
nets).
NMFS,
NYSDEC,
NYS
Sea
Grant
(
co­
leads),
CCE,
AMI,

commercial
and
recreational
fishing
community
Post­
CCMP
Base
Program
and
additional
funding
(
to
be
determined)

for
outreach
and
education
Enhance
existing
programs:

NYSDEC
 
2.0
FTE/
yr
Cornell
 
0.1
FTE/
yr
C/
N
R
Table
continued
on
next
page
C
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86
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
12.9
Implement
CZARA
Section
6217
BMPs
regarding
fish
waste
at
marinas
and
on
docks.
Develop
public
education
materials
for
distribution
at
marinas,
bait
and
tackle
shops,
and
other
related
businesses
detailing
these
BMPs.
PEP
Public
Education
and
Outreach
program
(
lead),

AMI,
marina
owners,
other
business
owners,
NYSDEC,

Sea
Grant,
Cornell
Cooperative
Extension
 
Marine
Program
Post­
CCMP
$
15,000
for
education
and
outreach
materials
R
HLR­
12.10
Expand
the
monitoring
and
analysis
of
the
NYSDEC
finfish
trawl
survey
to
the
east
of
Shelter
Island
and
coordinate
with
the
PEP
Living
Resources
Research,
Monitoring,

and
Assessment
Plan.
NYSDEC
(
lead),
PEP
Natural
Resources
Subcommittee
Post­
CCMP
(
Included
in
Environmental
Monitoring
Plan:

Start­
up:
$
500,000
Annually:
$
300,000
R
HLR­
12.11
Examine
the
role
of
areas
uncertified
for
shellfishing
as
"
spawner
sanctuaries"
for
shellfish
species.
PEP
Natural
Resources
Subcommittee
(
lead),

NYSDEC,
Cornell
Cooperative
Extension
Post­
CCMP
$
50,000
R
HLR­
12.12
On
a
biennial
cycle,
perform
deep­

and
shallow­
water
shellfish
abundance
surveys.
PEP
through
contractor
Post­
CCMP
$
150,000
R
Table
continued
next
page
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
C
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Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
13
Protect
Nesting
and
Feeding
Habitat
of
Shorebirds.
(
Objectives
1,
2,
3,
6,
7,
and
8)

HLR­
13.1
Priority
Strengthen
existing
municipal
shorebird
(
terns
and
plovers)

management
programs
to
ensure
timely
fencing
and
erection
of
enclosures,
adequate
monitoring
and
reporting,
and
management
of
recreation
and
other
activities
within
nesting
and
feeding
habitat.

Implement
the
1997
Suffolk
County
Department
of
Parks,
Recreation
and
Conservation
Piping
Plover
Protection
Program
and
the
NYSDEC
Bureau
of
Wildlife
1998
Action
Plan
for
Piping
Plover
Conservation
in
New
York.
NYSDEC;
Suffolk
County
Parks
Department;
Towns
of
East
Hampton,
Southampton,

Southold,
Shelter
Island,
and
Riverhead;
villages;
Trustees;

The
Nature
Conservancy;

USFWS
(
co­
leads)
Ongoing
and
Post­
CCMP
Base
Program
Enhance
existing
programs:

NYSDEC
 
1.0
FTE/
yr
TNC
 
1.0
FTE/
yr
Towns
 
0.3
FTE
each/
yr
C/
O
R
HLR­
13.2
Restrict
the
use
of
off­
road
vehicles
and
small
watercraft
in
shorebird
nesting
areas
during
breeding
season
(
April
 
August).
OPRHP;
Suffolk
County
Parks
Department;
Towns
of
East
Hampton,
Southampton,

Southold,
Shelter
Island,
and
Riverhead;
villages;

NYSDEC
for
DEC­
owned
properties
(
co­
leads)
Ongoing
and
Post­
CCMP
Enhance
existing
programs:

Towns
 
0.3
each/
yr
R
HLR­
13.3
Consult
with
the
USFWS
to
comply
with
Federal
guidelines
for
managing
recreational
activities
in
piping
plover
breeding
habitat.
Beach
managers
including
Federal
(
USFWS),
state,

Suffolk
County,
the
towns,

property
owners
(
co­
leads)
Ongoing
and
Post­
CCMP
Base
Program
USFWS
 
0.2
FTE/
yr
C/
O
Table
continued
next
page
C
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F
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U
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4­
88
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
13.4
Document
threats
to
nesting
shorebirds
(
plovers
and
terns)
such
as
off­
road
vehicles,
predation,
and
recreation,
and
develop
and
implement
measures
that
lead
to
higher
productivity
and
larger
nesting
populations.
East
End
towns
and
NYSDEC
(
co­
leads)
Post­
CCMP
$
10,000
R
HLR­
14
Protect
Sea
Turtles
and
Marine
Mammals.
(
Objectives
1,
3,
4,
6,
7,
and
8)

HLR­
14.1
Review
uses
of
areas
which
have
been
identified
as
sea
turtle
feeding
and
marine
mammal
areas
and
consider
what
restrictions
may
be
necessary
to
be
more
protective
of
these
species
and
their
food
resources.
NYS
agencies
(
e.
g.,

NYSDEC,
NYSDOS,
NYS
Office
of
Parks,
Recreation
and
Historic
Preservation,

NYS
Office
of
General
Services)
(
co­
leads),

Suffolk
County,
towns
Post­
CCMP
Enhance
existing
programs:

NYSDEC
 
1.0
FTE
NYSDOS
 
0.2
FTE
Parks
 
0.2
FTE
SCDHS
 
0.2
FTE
Towns
 
0.1
FTE
each
R
HLR­
14.2
Evaluate
the
expansion
of
existing
laws
to
ensure
that
all
species
of
seals
as
well
as
other
marine
mammals
are
protected
from
intentional
injury
or
death.
NYS
agencies
(
e.
g.,
NYSDEC,
NYSDOS,

NYS
Office
of
Parks,

Recreation
and
Historic
Preservation,
NYS
Office
of
General
Services)

(
co­
leads),
SCDHS,
towns
Post­
CCMP
Included
in
HLR­
14.1
R
HLR­
14.3
Expand
New
York
State
law
protecting
harbor
seals
(
ECL
Article
11,
section
0107
to
include
all
species
of
seals
in
NYS
marine
waters.
New
York
State
Legislature,

NYSDEC
(
co­
leads)
Post­
CCMP
Included
in
HLR­
14.1
R
Table
continued
on
next
page
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
C
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A
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F
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4­
89
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
15
Utilize
Land
Use
Planning,
BMPs,
and
Other
Management
Measures
to
Reduce
the
Negative
Impacts
of
Human
Uses
and
Development
on
the
Estuary
System.
(
Objectives
1,
2,
3,
4,
6,
7,
and
8)

HLR­
15.1
Priority
Each
town
should
develop
a
master
or
comprehensive
management
plan,

coordinated
with
plans
of
other
towns
that
increases
the
level
of
protection
of
natural
resources
and
habitats
and
accounts
for
cumulative
impacts.
Towns
of
East
Hampton,

Southampton,
Southold,

Shelter
Island,
Riverhead;

NYSDOS
(
co­
leads),
EPA,

NYSDEC,
SCDHS
Post­
CCMP
Enhance
existing
programs:

NYSDEC
 
0.1
FTE
EPA
 
0.1
FTE
SCDHS
 
0.1
FTE
Towns
 
1.0
FTE
each
R
HLR­
15.2
Priority
Increase
public
access
to
the
estuary
consistent
with
other
ecosystem
objectives.
All
Federal,
state,
and
local
governmental
agencies
in
the
PEP
watershed
(
co­
leads);
NYSDEC
Post­
CCMP
Base
Program
and
sitespecific
costs
for
each
access
opportunity
to
be
determined
Enhance
existing
programs:

NYSDEC
 
1.0
FTE/
yr
C/
N
R
HLR­
15.3
Develop
and
implement
a
Harbor
Protection
Overlay
District
such
as
that
developed
by
the
Town
of
East
Hampton
and
include
it
in
the
master
plan
for
each
town.
NYSDOS
(
lead);
Towns
of
Southampton,
Southold,

Shelter
Island,
and
Riverhead
Post­
CCMP
$
50,000
per
town
Towns
 
1.0
FTE
each
R
Table
continued
on
next
page
C
H
A
P
T
E
R
F
O
U
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4­
90
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
15.4
Develop
implementation
mechanisms
for
all
measures
required
by
Section
6217(
g)
of
CZARA
that
are
applicable
to
the
Peconic
Estuary.
These
measures
would
include
BMPs
for
the
use
of
natural
vegetation,
minimization
of
impervious
surfaces,
safe
and
reasonable
use
of
lawn,
garden,
and
household
chemicals,
and
minimization
of
stormwater
runoff.

Incorporate
these
BMPs
into
the
site
plan
requirements
for
all
newlydeveloped
and
redeveloped
property,
particularly
along
the
shoreline.
NYSDEC,
NYSDOS,
PEP
Education
and
Outreach
Program
(
co­
leads),
Suffolk
County
Soil
and
Water
Conservation
District,

SCDHS,
USDA
NRCS,

Cornell
Cooperative
Extension,
NY
Sea
Grant,

Peconic
BayKeeper,
SCDHS
Post­
CCMP
Base
Program
Enhance
existing
programs:

NYSDEC
 
0.1
FTE
SCDHS
 
0.1
FTE
PEP
 
0.1
FTE
C/
N
R
HLR­
15.5
Use
the
Protected
Lands
Council
of
the
Central
Pine
Barrens
Comprehensive
Land
Use
Plan
as
a
model
for
developing
a
similar
coalition
of
public
agencies
and
conservation
organizations
to
address
common
issues
of
concern
throughout
the
estuary.
PEP;
Pine
Barrens
Commission
and
Protected
Lands
Council
(
co­
leads);

Towns
of
East
Hampton,

Southampton,
Southold,

Shelter
Island,
and
Riverhead;
NYSDEC;

SCDHS
Post­
CCMP
NYSDEC
 
0.05
FTE/
yr
SCDHS
 
0.05
FTE/
yr
Enhance
existing
programs:

Towns
 
0.5
FTE
each/
yr
C
R
HLR­
15.6
Encourage
towns
with
existing
Conservation
Advisory
Councils
or
planning
staff,
to
be
given
the
responsibility
as
Conservation
Advisory
or
Planning
Boards
to
review
proposed
Town
Board
actions
as
they
affect
public
lands
and
open
space
concerns.
Towns
of
East
Hampton,

Southold,
Shelter
Island,
and
Riverhead
(
co­
leads)
Post­
CCMP
Enhance
existing
programs:

Towns
 
0.5
FTE
each/
yr
R
Table
continued
on
next
page
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
C
H
A
P
T
E
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F
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U
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4­
91
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
15.7
Review
and
provide
comments
to
NYSDEC
on
any
revisions
to
the
Statewide
Oil
Spill
Areawide
Contingency
Plan
for
the
Peconic
Estuary
relating
to
waterfowl,

marine
mammals,
and
sea
turtles
and
their
rehabilitation
if
oiled.

Develop
and
distribute
information
on
reporting
and
responding
to
small­
scale
spills.
PEP
Natural
Resources
Subcommittee
in
conjunction
with
the
USCG,

NYSDEC,
USFWS
(
co­
leads);
Rehabilitation:

local
wildlife
rehabilitators
(
licensed);
Education:
PEP
Public
Education
and
Outreach
program
in
conjunction
with
the
USCF,

NYSDEC,
USFWS;
BMPs:

NYSDO;
AMI;
Towns
of
East
Hampton,

Southampton,
Southold,

Shelter
Island,
and
Riverhead;
villages
Post­
CCMP
Base
Program
NYSDEC
 
0.05
FTE/
yr
SCDHS
 
0.05
FTE/
yr
PEP
 
0.05
FTE/
yr
R
Table
continued
on
next
page
C
H
A
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F
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U
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4­
92
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
15.8
Develop
regulations
for
new
marinas
or
expansion
of
existing
marinas
which
include
the
following
(
from
CZARA
section
6217):
(
1)
assessment
of
water
quality
conditions
during
and
after
construction;
(
2)
site
and
design
such
that
tides
and/
or
currents
will
aid
in
the
flushing
of
the
site
or
renew
its
water
regularly;
(
3)
site
and
design
to
protect
against
adverse
effects
on
shellfish
resources,
wetlands,
submerged
aquatic
vegetation,
or
other
important
riparian
and
aquatic
habitat
areas
as
designated
by
local,
State,
or
Federal
governments;
(
4)
designate
and
enforce
no­
wake
zones
and
ensure
that
shoreline
areas
are
stabilized
effectively
by
vegetative
means;

and,
(
5)
require
effective
stormwater
runoff
control
measures
to
reduce
sediment
and
toxic
inputs.
NYSDEC
(
lead);
Suffolk
County;
DHS;
EPA;
PEP;

Towns
of
East
Hampton,

Southampton,
Southold,

Shelter
Island,
and
Riverhead;
AMI;
private
marina
owners.
Post­
CCMP
EPA
 
0.3
FTE
NYSDEC
 
0.5
FTE
SCDHS
 
0.3
FTE
PEP
 
0.3
FTE
Enhanced
Programs:

NYSDEC
 
1.0
FTE/
yr
R
R
Table
continued
on
next
page
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
C
H
A
P
T
E
R
F
O
U
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4­
93
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
16
Develop
and
Implement
a
Living
Resources
Research,
Monitoring,
and
Assessment
Program.
(
Objectives
1,
2,
3,
5,
6,
7,
and
8)

HLR­
16.1
Priority
Develop
and
implement
a
research
program
for
the
Peconic
Estuary
and
its
watershed
to
investigate
natural
processes,
impairments,

and
links
to
water
quality,

maintenance
of
systems
and
species,
and
effects
of
recreation
and
pollution
on
biodiversity,

among
other
research
needs.

Investigate
and
seek
funding
sources
for
supporting
implementation
of
the
program
(
e.
g.,
National
Estuarine
Research
Reserve
Systems).
Plan
development
and
coordination:
PEP
Natural
Resources
Subcommittee
and
the
Marine
Conservation
Planner
(
co­
leads)
in
consultation
with
other
members
of
the
PEP
Management
Conference
and
technical
experts;
Plan
implementation:
PEP
Management
Conference,

NYSDEC,
NYSDOS,
New
York
Sea
Grant
Institute,

SCDHS
(
co­
leads)
Plan
development
and
peerreview
2001
Plan
implementation:
After
the
plan
is
developed,

adopted,
and
funding
is
allocated.
Plan
development:
Base
Program
Plan
implementation:
$
3
million
over
3
to
5
years
NYSDEC
 
0.2
FTE/
yr
SCDHS
 
0.05
FTE/
yr
TNC
 
0.7
FTE/
yr
Plan
Dev.:

C/
N;
Implement.:

R
Table
continued
on
next
page
C
H
A
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F
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U
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4­
94
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
16.2
Priority
Develop
a
long­
term
program
for
monitoring
and
assessment
of
living
resources
in
the
Peconic
Estuary
that
is
coordinated
with
the
development
of
a
research
plan
and
ongoing
research
and
monitoring
efforts.
Monitoring
and
assessment
plan:
PEP
Natural
Resources
Subcommittee
and
Marine
Conservation
Planner
(
co­
leads)
in
conjunction
with
NYSDEC;
SCDHS;

Towns
of
East
Hampton,

Southampton,
Southold,

Shelter
Island,
and
Riverhead;
Plan
implementation:
PEP
in
conjunction
with
NYSDEC
(
co­
leads);
SCDHS;
Towns
of
East
Hampton,

Southampton,
Southold,

Shelter
Island,
and
Riverhead;
Cornell
Cooperative
Extension;

local
universities
and
colleges;
NY
Sea
Grant
Plan
development
and
peerreviewed
By
2001
Plan
implementation:
After
the
plan
is
developed,

adopted,
and
funding
is
allocated
Plan
development:
Base
Program
Plan
implementation:
To
be
determined.
Included
in
HLR­
16.1
C/
N
R
Table
continued
on
next
page
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
C
H
A
P
T
E
R
F
O
U
R
4­
95
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
16.3
Support
research
on
the
interactions
between
eelgrass
and
the
dominant
macroalgae
species
in
the
Peconic
Estuary
to
determine
impacts
of
macroalgae
on
eelgrass
distribution
and
abundance.
Plan
development:
PEP
Natural
Resources
Subcommittee
and
the
Marine
Conservation
Planner
(
co­
leads)
in
consultation
with
other
members
of
the
PEP
Management
Conference
and
technical
experts;
Plan
implementation:
PEP
Management
Conference,

NYSDEC,
NYSDOS,
New
York
Sea
Grant
Institute,

SCDHS
(
co­
leads)
Post­
CCMP
$
150,000
(
estimate)
R
HLR­
16.4
Perform
research
and
monitoring
of
forage
fish
species,
horseshoe
crabs,
and
conch
in
the
Peconic
Estuary
to
understand
their
distribution
(
temporal
and
spatial),

abundance,
habitat
preferences,

and
different
life
stage
requirements
to
develop
management
strategies.
PEP
Natural
Resources
Subcommittee,
NYSDEC,

Marine
Conservation
Planner
(
co­
leads),
technical
experts
through
the
PEP
long­
term
research
plan
Post­
CCMP
and
adoption
of
HLR­
16.1
$
500,000
(
estimate)
R
HLR­
16.5
Perform
research
on
the
ecology
of
food
sources
of
sea
turtles
to
evaluate
the
importance
of
the
Peconic
Estuary
to
them
and
potential
threats
to
these
endangered
and
threatened
species.
PEP
Natural
Resources
Subcommittee
(
lead)
and
technical
experts
through
the
PEP
long­
term
research
plan
Post­
CCMP
and
adoption
of
HLR­
16.1
$
75,000
through
contractor
R
Table
continued
next
page
C
H
A
P
T
E
R
F
O
U
R
4­
96
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­
16.6
Research
the
lethal,
sublethal,
and
synergistic
effects
of
elevated
nutrients,
toxic
chemicals,
and
Brown
Tide
on
the
reproduction
and
behavior
of
finfish
and
invertebrate
species.
PEP
Natural
Resources
Subcommittee
(
lead)
and
technical
experts
through
the
PEP
long­
term
research
plan,
NY
Sea
Grant
Post­
CCMP
and
adoption
of
HLR­
16.1
To
be
determined
R
HLR­
16.7
Determine
the
effects
of
navigational
dredging
on
shallow
water
communities
and
the
recovery
time
of
benthic
communities
exposed
to
dredging.
PEP
Natural
Resources
Subcommittee
(
lead)
and
technical
experts
to
define
specific
research
questions,

USACE,
Suffolk
County
SCDPW,
NYSDEC
Post­
CCMP
and
adoption
of
HLR­
16.1
To
be
determined
R
HLR­
16.8
Ensure
implementation
of
adequate
mapping
and
monitoring
programs
to
track
trends
in
the
extent
and
quality
of
eelgrass,
and
to
evaluate
progress
toward
reaching
restoration
goals.
PEP
Natural
Resources
Subcommittee,
PEP
Management
Council
(

coleads
Post­
CCMP
$
45,000
per
year
R
HLR­
16.9
Establish
a
scientific
panel
to
review
research,
monitoring
and
assessment
data,
and
to
offer
guidance
in
management
of
the
habitats
and
living
resources
in
the
Peconics.
PEP
Natural
Resources
Subcommittee
(
lead)
Post­
CCMP
and
adoption
of
HLR­
16.1
To
be
determined
R
HLR­

16.10
Organize
an
annual
or
biennial
conference
to
report
research,

monitoring,
and
assessment
results
to
the
public
and
guide
management
decisions.
PEP
Natural
Resources
Subcommittee
in
conjunction
with
EPA,

NYSDEC
(
co­
leads),

SCDHS,
local
universities
and
colleges
Post­
CCMP;
Biennial
$
10,000
per
conference
R
HLR­

16.11
Establish
and
maintain
an
accessible
database
of
natural
resources
in
the
Peconic
Estuary.
PEP
Natural
Resources
Subcommittee
(
lead)
Ongoing
NYSDEC
 
0.1
FTE/
yr
SCDHS
 
0.05
FTE/
yr
PEP
 
0.1
FTE/
yr
Enhance
existing
programs:

NYSDEC
 
0.5
FTE/
yr
C/
O
Table
continued
on
next
page
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
C
H
A
P
T
E
R
F
O
U
R
4­
97
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­

16.12
Promote
research
and
monitoring
opportunities
in
the
Peconic
Estuary
to
local
schools,
colleges,

universities,
and
institutes
by
establishing
funding
and
scientific
platforms
and
other
incentives
to
facilitate
basic
and
applied
marine
research.
PEP,
NY
Sea
Grant,
EPA
(
co­
leads),
NOAA,
NYS
Marine
Educators
Association
(
MEA),
Cornell
Cooperative
Extension
 
Marine
Program
Post­
CCMP
Funding
needs
for
research
center/
scientific
platform
to
be
determined
R
HLR­

16.13
Seek
opportunities
to
link
research
and
monitoring
in
the
Peconic
Estuary
Program
to
related
estuaries
and
regional
studies.
Association
of
NEPs,
EPA,

PEP
(
co­
leads),
NY
Sea
Grant,
NOAA
Post­
CCMP
NYSDEC
 
0.2
FTE/
yr
EPA
 
0.1
FTE/
yr
PEP
 
0.1
FTE/
yr
R
HLR­

16.14
Support
priorities
listed
in
the
Living
Resources
Research,

Monitoring,
and
Assessment
Plan
including
research
on
ecosystem
productivity
and
ecosystem
structure,
bioindicators,
and
effects
of
global
climate
change
on
wetlands.
PEP
Natural
Resources
Subcommittee
Ongoing
Base
Programs
C/
O
HLR­
17
Establish
a
Working
Group
to
Examine
the
Role
of
Grazers
and
Filter
Feeding
Organisms
in
Influencing
Water
Quality
and
Productivity,
and
to
Better
Understand
the
Food
Web
Dynamics
and
to
Develop
Management
Applications.
(
Objectives
1,
2,
3,
4,
and
8)

HLR­
17.1
Review
appropriate
scientific
literature,
identify
information
gaps,
and
develop
research
recommendations
regarding
how
shellfish,
finfish
and
other
"

topdown
predators
influence
water
quality
and
the
planktonic
community.
PEP
Natural
Resources
Subcommittee
(
lead)

through
contractor
Post­
CCMP
$
50,000
for
review
R
Table
continued
on
next
page
C
H
A
P
T
E
R
F
O
U
R
4­
98
Peconic
Estuary
Program
CCMP
Table
4­
1.
Habitat
and
Living
Resources
Management
Plan
Actions.
(
continued)

Action
Responsible
Entity
Timeframe
Cost
Status
HLR­

17.2
Develop
research,
monitoring
and
assessment
needs
for
quantifying
food
web
dynamics.
PEP
Natural
Resources
Subcommittee
(
lead)
and
marine
conservation
planner
Post­
CCMP
NYSDEC
 
0.1
FTE
TNC
 
0.5
FTE
PEP
 
0.2
FTE
R
HLR­

17.3
Develop
food
web
sub­
models
to
be
included
in
the
nutrient
model
to
evaluate
the
sensitivity
of
productivity
to
anthropogenic
changes
in
nutrient
supply.
PEP
Natural
Resources
Subcommittee
through
contractor
(
lead)
in
consultation
with
other
members
of
the
PEP
Management
Conference
and
technical
experts
Post­
CCMP
$
100,000
for
model
development
R
HLR­

17.4
Consult
with
the
BTRI
and
the
estuary­
wide
aquaculture
plan
work
group
to
develop
management
recommendations
for
"
top­
down"
regulation
of
water
quality
and
Brown
Tide
in
the
Peconic
Estuary.
PEP
Natural
Resources
Subcommittee
(
lead)
in
consultation
with
other
members
of
the
PEP
Management
Conference
and
technical
experts;
NYSDEC,

NYSDOS,
New
York
Sea
Grant
Institute,
SCDHS,
BTRI
researchers,
SUNY
Stony
Brook,
Cornell,
commercial
aquaculture
facilities
in
the
Peconics
Post­
CCMP
Enhance
existing
programs:

NYSDEC
 
0.2
FTE
EPA
 
0.2
FTE
SCDHS
 
0.2
FTE
R
HLR­

17.5
Facilitate
communication
among
BTRI,
water
quality
managers
and
the
estuary­
wideaquaculture
plan
work
group.
PEP
Natural
Resources
Subcommittee
(
lead)
in
consultation
with
other
members
of
the
PEP
Management
Conference
and
technical
experts;
NYSDEC,

NYSDOS,
New
York
Sea
Grant
Institute,
SCDHS,
BTRI
researchers,
SUNY
Stony
Brook,
Cornell,
and
commercial
aquaculture
facilities
in
the
Peconics
Post­
CCMP
Included
in
HLR­
17.4
R
Peconic
Estuary
Program
Draft
Final
CCMP
October
2000
Peconic
Estuary
Program
CCMP