Final Draft Determining the effects of freshwater releases
Senior Thesis-FINAL
1.
The
Health
Status
of
Disturbed
and
Undisturbed
Non-‐Saline
Estuaries:
A
CRAM-‐based
assessment
By,
Eria
E.
Garnica
Senior
Thesis
Dr.
Jeffery
A.
Foran
May
14,
2014
3.
3
Abstract
This
senior
project
analyzes
and
compares
two
perennial,
non-‐saline
estuaries
in
California
by
using
the
California
Rapid
Assessment
Method
for
Wetland
(CRAM)
to
signify
the
differences
between
undisturbed
and
disturbed
estuaries.
The
California
Rapid
Assessment
Method,
is
used
to
rapidly
assess
wetland
ecological
features
for
water
purification
and
influencing
wildlife
habitat.
These
four
attribute
are
used
to
comparatively
analyze
the
variation
between
disturbed
and
undisturbed
estuarine
wetlands.
CRAM
is
a
useful
reference
tool
to
evaluate
quick
results
for
the
health
status
of
California
Wetlands.
Introduction
Objective
Estuaries
are
valuable,
complex
ecosystems
that
filter
contaminants,
pollutants,
solids,
wastes,
pesticides,
and
other
urban
runoff.
They
also
stabilize
shorelines
from
erosion,
decrease
the
effects
of
coastal
storms,
and
increase
aquatic,
terrestrial
biodiversity.
Estuaries
are
significant
because
they
create
habitats
for
fish
and
wildlife,
including
threatened
or
endangered
species
listed.
Currently,
perennial
non-‐saline
estuaries
in
California
suffer
from
sea
level
rise,
salt-‐water
intrusion,
and
other
human
impacts.
Most
signs
of
human
disturbance
degrade
wetlands
services
and
functions,
particularly
fish
and
wildlife
habitats
(Parker
et
al
2011).
Today,
scientists
have
acknowledged
a
91%
loss
of
California
wetlands,
and
only
44,456
acres
of
estuaries
remain
(CA
State
of
Wetlands
Report
2010).
As
a
4.
4
result,
the
state
has
made
wetlands
restoration
a
priority
in
California.
The
California
Wetlands
Conservation
Policy
(executive
order
W-‐59-‐93)
explains
the
course
of
action
for
restoring,
monitoring,
and
protecting
California
wetlands
under
state
agencies,
public
and
private
partnerships,
and
the
federal
government
(Snow
2010).
Disturbed
and
undisturbed
wetlands
are
both
affected
by
sea
level
rise
increasing
salt-‐water
intrusion
into
the
freshwater
and
brackish
marshes.
Salt-‐water
intrusion
could
shift
the
wetland
composition
by
decreasing
freshwater
plant
species
to
salt
tolerant
plant
species.
Recent
studies
state
and
increase
in
sea
level
rise
results
a
shift
in
the
salinity
gradient,
and
a
dramatic
decrease
in
San
Francisco
Bay-‐Delta’s
tidal
marsh
biodiversity
(such
as,
Sarcocornia
pacifica,
Spartina
foliosa,
and
Distichlis
spicata),
(Mall
1969).
Also,
the
increase
in
carbon
dioxide
will
affect
soil
carbon
storage,
soil
nutrient
cycling,
plant
respiration,
rates
of
decomposition,
mycorrhizal
symbionts,
and
herbivory
(Parker
et
al
2011).
These
freshwater
estuarine
values
(wetland
composition
structure)
take
part
in
the
water
purification
cycle
(wetland
function).
The
ecological
processes
include
chemical,
physical,
and
biological
processes
that
all
take
part
in
the
water
purification
cycle
(Kadlec
1996).
In
addition
to
the
water
purification
cycle,
system
components
include
plants,
soils,
detritus,
bacteria,
protozoa,
water
levels,
depth,
temperature,
dissolved
oxygen,
and
pH
(Sherwood
et
al
1995).
This
project
will
analyze
and
compare
two
restored
CA
freshwater
estuaries
(Rush
Ranch
Estuary
and
Arroyo
Burro
Estuary)
and
their
health
status
by
using
the
California
Rapid
Assessment
Methods
(CRAM)
along
with
quantitative
5.
5
data
for
correlation.
Non-‐saline
estuaries
are
I
hypothesize
that
there
are
significant
differences
between
the
performance
standards
of
disturbed
and
undisturbed,
non-‐
saline
estuaries
located
in
California.
CRAM
is
a
cost-‐effective
way
to
rapidly
assess
the
health
status
of
California
wetlands.
CRAM,
uses
a
grading
rubric
with
a
series
of
four
scores
that
indicate
the
total
score
for
the
wetland
health
status.
This
method
assists
scientists
and
researchers
in
understanding
what
actions
need
to
be
addressed
to
improve
wetland
restoration.
The
California
Rapid
Assessment
Methods
for
wetlands
consists
of
three-‐
tiered
assessment
levels
from
the
California
Wetlands.
The
three-‐tiered
assessment
levels
correlate
one
another
by
showing
a
more
in-‐depth
contextual
understanding
of
the
overall
estuarine
wetland
condition
(Solek,
Stein,
and
Sutula
2011).
Level
One,
Landscape
Assessment,
consists
of
using
remote
sensing
data
and
field
surveys
in
an
inventory
database
that
is
created
by
the
California
State
Resources
Agency.
Level
two,
Rapid
Assessment,
includes
assessing
wetland
conditions
by
using
field
diagnostics
and
existing
data.
Level
three,
Intensive
Site
Assessment,
consists
of
data
that
validates
the
CRAM
results
along
with
exemplifying
the
condition.
Receiving
validation
on
the
CRAM
results
for
the
study
sites
is
a
very
important
analytical
step
to
assess
the
estuarine
wetland
health
status.
Approach
There
are
four
different
attributes
that
this
project
will
focus
on
to
score
the
perennial,
non-‐saline
estuaries:
buffer
and
landscape,
hydrology,
physical
structure,
and
biotic
structure.
Attribute
1:
Buffer
and
Landscape
includes
A:
an
evaluation
of
6.
6
the
landscape
context,
B:
Assessment
Area
and
buffer
width,
C:
buffer
condition.
Attribute
2:
Hydrology
includes
A:
water
source,
B:
hydroperiod,
C:
hydrologic
connectivity.
Attribute
3:
Physical
Structure
consists
of
A:
structural
patch
richness,
B:
topographic
complexity.
Attribute
4:
Biotic
Structure
A:
number
of
plant
layers.
B:
number
of
co-‐dominant
plant
species,
C:
invasive
plant
species,
D:
horizontal
interspersion,
E:
vertical
biotic
structure.
I
will
compare
disturbed
and
undisturbed
perennial,
non-‐saline
estuaries
in
California.
By
evaluating
the
CRAM
scores
for
each
freshwater
estuarine
marsh,
I
will
be
able
to
distinguish
the
differences
between
disturbed
and
undisturbed
estuaries.
I
predict
natural
estuaries
will
have
a
higher
CRAM
scores
because
they
have
fewer
environmental
impacts
disrupting
the
wildlife
habitat.
Significance
The
results
from
this
project
may
be
used
to
support
better
restoration
and
mitigation
planning
in
the
future.
The
Society
for
Ecological
Restoration
(SER)
states,
“Ecological
restoration
is
the
process
of
renewing
and
maintaining
ecosystem
health
(SER
Board
of
Directors,
1995).”
Ultimately,
this
method
can
be
a
cost-‐effective
way
to
rapidly
assess
the
health
status
of
California
wetlands.
7.
7
Methods
I
chose
two
perennial
non-‐saline
estuaries
as
my
samples
from
the
E-‐CRAM
state
database,
one
high
quality
and
one
low
quality
score.
I
evaluated
their
health
status
by
using
CRAM;
The
California
Rapid
Assessment
Method
for
Wetlands,
perennial
Estuarine
Wetlands
Field
book,
version
6.1.
The
scores
will
be
in
numeric
form
this
includes,
12/12,
9/12,
6/12,
or
3/12.
The
two
non-‐saline
estuaries
were
chosen
because
of
their
documented
CRAM
scores
that
are
based
on
high
and
low
quality
scores,
and
they
are
available
on
Eco-‐Atlas’s
website.
The
documented
CRAM
scores
clarify
problem
areas
of
the
non-‐saline
estuaries.
The
problem
areas
allow
scientists
to
analyze
their
significant
environmental
impacts,
disturbance
levels,
and
artificial
inputs.
This
project
focuses
on
comparing
the
differences
between
disturbed
and
undisturbed
estuaries
by
using
CRAM
to
distinguish
the
variation
in
their
health
status.
Undisturbed
and
disturbed
wetlands
are
comparatively
analyzed
from
their
ecological
processes,
system
components,
topographic
complexity
features,
and
what
they
are
mainly
intended
for.
Undisturbed
wetlands
are
the
perfect
reference
wetlands
that
are
used
to
compare
the
function
too
since
they
have
not
experienced
moderate
to
high
levels
of
degradation
(net
loss
in
abotic
factors).
I
conducted
this
California
Rapid
Assessment
Methods
with
a
professional
Senior
Wetland
Ecologist/Botanist,
Mr.
Russell
Huddleston.
Mr.
Huddleston
is
a
trained
professional
in
the
California
Rapid
Assessment
Methods
for
Wetlands
and
he
helped
me
with
assessing
and
receiving
accurate
data.
The
line
transects
extended
250
meters
north,
south,
west,
and
east
in
the
Assessment
Area
and
Buffer
8.
8
(figure
1).
All
line
transects
extended
the
250
meters
without
any
interruptions
by
unnatural
inputs
or
disturbances.
Two
sites
that
were
chosen
for
this
project
are:
Rush
Ranch
Estuary
and
Arroyo
Burro
Estuary.
Rush
Ranch
Estuary
is
located
Southern
Solano
County,
CA,
latitude
38.211529
and
-‐122.029459
longitude.
Rush
Ranch
Estuary
occurs
in
the
upper
western
portions
of
the
Suisun
Slough
(Vasey
et
al
2012).
This
tidal
marsh
is
located
within
the
San
Francisco
Bay.
The
Arroyo
Burro
Estuary
is
located
in
the
Santa
Barbara
Region
near
Mesa
Creek,
latitude
34.40473°N,
and
longitude
-‐
119.73982°W.
Down
below
in
map1
shows
the
locations
of
the
two
wetlands
used
for
this
senior
project.
Figure
1.
Two
CA
freshwater
estuarine
wetlands
(Google
Earth)
9.
9
Perennial
Estuarine
Wetlands:
Field
Book
ver.
6.1
I.
CRAM
Field
Book:
The
CRAM
field
book
includes
four
attribute
sections
that
make
up
the
grading
rubric
and
total
numeric
scores.
The
CRAM
scoring
sheet
for
perennial
estuarine
wetlands
is
located
after
the
four
attribute
terms.
Each
attribute
score
can
provide
significant
information
about
effects
or
environmental
impacts.
If
the
score
is
low,
one
can
analyze
the
reasoning
behind
the
low
score,
and
influences
that
could
result
in
environmental
impacts,
artificial
inputs,
or
newly
restored
plant
species.
By
using
the
CRAM
field
book,
scientists
can
rapidly
assess
individual
wetlands
and
rate
their
health
status.
II.
Buffer
and
Landscape:
The
buffer
and
landscape
attribute
section
consists
of
four
parts,
this
aquatic
area
abundance;
buffer
sub-‐metric
A:
percent
of
Assessment
Area
with
Buffer;
buffer
sub-‐metric
B:
average
buffer
width;
and
last
buffer
sub-‐metric
C:
buffer
condition.
All
these
sections
under
the
Buffer
and
Landscape
attribute
section
are
significant
towards
calculating
the
final
attribute
score.
The
aquatic
area
abundance
is
a
spatial
region
that
has
aquatic
corridors
(e.g.
rivers,
streams,
and
channels)
in
the
landscape.
Line
transects
are
scored
from
the
number
of
times
aquatic
corridors
are
crossed
by
line
transects.
The
buffer
sub-‐metric
A:
percent
of
AA
with
buffer
is
the
buffer
joining
the
Assessment
Area
(AA).
The
buffer
is
5
meters
wide
and
extends
along
the
perimeter
of
AA.
The
buffer
percent
is
how
long
the
line
transects
could
extend
without
interruption.
The
wetland
buffer
is
not
continuous
with
buffer
breaks:
golf
courses,
10.
10
commercial
developments,
fences,
intensive
agriculture,
parking
lots,
railroads,
residential
areas,
sound
walls,
sports
fields,
urbanized
parks,
pedestrian
side
walks
and
trails
(very
active),
bike
and
foot
trails
(not
very
active),
horse
trails,
natural
upland
habitats,
wild-‐land
parks,
land
and
pastures,
railroads
(only
2
trains
a
day),
swales
and
ditches,
and
vegetated
levees.
The
sub-‐metric
B:
average
buffer
width,
consists
of
required
measurements
for
the
buffer
width.
For
example,
if
the
buffer
width
is
5
meters
or
less
then
it
cannot
be
considered
a
buffer
width.
In
addition,
open
water
is
not
included
in
the
buffer
width
calculations.
The
sub-‐metric
C:
buffer
condition,
includes
the
disturbance
levels
along
with
plant
species.
The
three
categories
of
plant
species
include
California
natives,
non-‐
natives,
or
invasive
plant
species
in
the
buffer.
The
disturbance
levels
are
rated
by
soil
compactions,
level
of
human
disturbance,
and
the
presence
or
absence
of
a
buffer.
III.
Hydrology:
The
hydrology
attribute
section
consists
of
three
sections
that
make
up
the
total
hydrology
score,
such
as
water
source,
hydro-‐period,
and
hydrologic
connectivity.
Water
source
is
the
extent,
duration,
and
frequency
of
hydrologic
regimes
in
the
Assessment
Area.
Undisturbed
estuaries
are
recharged
naturally
by
precipitation,
tidal
inflows,
and
watershed
runoff.
Disturbed
estuaries
are
recharged
by
water
pumps,
and
the
hydrologic
dynamics
are
controlled
by
storm
drains,
weirs,
dams,
and
grade
control
structures.
11.
11
The
hydro-‐period
discuses
the
frequency
and
duration
period
of
water
saturation
and
inundation.
The
water
levels
in
undisturbed
estuaries
vary
through
out
the
year
because
of
the
four
seasons.
However,
disturbed
estuaries
may
be
affected
by
tide
gates,
culverts,
open
channels,
water
pumps,
rip-‐rap,
and
bridges.
The
hydrologic
connectivity
describes
the
water
flow
of
the
estuary.
The
water
flow
includes
inflows
and
out
flows
of
the
wetland.
The
restrictions
on
the
hydrologic
connectivity
consist
of
levees,
dikes,
and
road
grades..
IV.
Physical
Structure:
The
physical
structure
consists
of
two
sources
that
make
up
the
total
physical
structure
score.
The
two
sources
are
structural
patch
richness
and
topographic
complexity.
The
structural
patch
richness
includes
the
following
characteristics:
abundant
wrack
or
organic
debris
in
channel
or
on
floodplain,
animal
mounds
and
burrows,
bank
slumps
or
undercut
banks
in
channels,
debris
jams,
filamentous
macro-‐algae
and
algal
mats,
large
woody
debris,
non-‐vegetated
flats,
pools
on
floodplains,
plant
hummocks
or
sediment
mounds,
point
bars
and
in-‐channel
bars,
pools
or
depressions
in
channels,
secondary
channels,
shellfish
beds,
soil
cracks,
standing
snags,
and
submerged
vegetation.
Topographic
complexity
describes
how
complex
the
estuary
is.
The
topographic
complexity
characteristics
consist
of
micro
and
macro
topographic
relief,
elevation
gradients,
and
how
the
tidal
channels
are
formed.
The
topograghic
complexity
is
a
way
to
see
potential
for
restoration
work.
12.
12
V.
Biotic
Structure:
The
biotic
structure
consists
of
five
different
parts
that
make
up
the
total
score
for
the
attribute
section.
The
five
parts
are,
plant
community
sub-‐metric
A:
number
of
plant
layers,
plant
community
sub-‐metric
B:
number
of
Co-‐dominant
species,
plant
community
sub-‐metric
C:
percent
invasion,
horizontal
interspersion,
and
vertical
biotic
structure.
Under
the
plant
community
sub-‐metric
A,
includes
the
number
of
plant
layers
present
in
the
Assessment
Area.
The
number
of
plant
layers
must
consist
of
at
least
5%
cover
to
be
considered
a
plant
layer.
If
the
Assessment
Area
(AA)
holds
less
then
5%
plant
layers,
has
no
plant
layers,
or
has
artificial
inputs,
it
will
receive
a
“D”
score.
The
artificial
inputs
that
could
cause
a
“D”
score
are
rip-‐rap,
concrete,
or
newly
transplanted
plants.
Sub-‐metric
B:
number
of
Co-‐dominant
species
is
the
percent
cover
of
a
plant
species
that
only
constitutes
10%
in
the
AA.
In
section
sub-‐metric
C:
percent
invasion
is
for
invasive
plant
organisms
in
plant
layers.
The
last
two
features
in
the
grading
rubric
are
horizontal
interspersion
and
vertical
biotic
structure.
The
horizontal
interspersion
is
an
overview
of
the
AA
including
vegetation
layers.
The
vertical
biotic
structure
is
an
interspersion
and
complexity
of
plant
layers.
The
results
will
consist
of
the
“scoring
sheet:
perennial
estuarine
wetlands”
for
the
two
non-‐saline
estuaries
(Rush
Ranch
and
Arroyo
Burro).
Each
attribute
section
is
a
component
of
a
functional
assessment
that
estimates
the
whole
landscape
context
of
the
wetland.
The
results
will
include
numeric
scores
that
will
13.
13
focus
on
problem
areas.
The
scores
will
give
relevance
toward
explaining
the
health
status
and
performance
standards
for
each
estuarine
wetland.
The
health
status
will
determine
the
difference
between
these
two
perennial
freshwater
marshlands.
By
using
the
scores
as
a
guide,
one
can
refer
to
the
environmental
effects
and
artificial
inputs
that
could
alter
the
wetland
composition
and
its
function.
For
example,
a
low
score
under
the
hydrology
section
can
indicate
unnatural
inputs
or
human
disturbance.
In
addition,
the
problem
areas
will
be
supported
by
quantitative
data
to
correlate
the
California
Rapid
Assessment
Method
scores.
Results
The
results
show
a
distinct
difference
in
two
attributes,
hydrology
and
biotic
structure
while
the
other
two
attributes
did
not
show
enough
variation
(Graph
1).
The
graphical
approach
was
used
to
show
variation
between
the
two
estuaries
and
their
attributes
(Graph
1)
furthermore
the
two
estuaries
were
compared
with
California
non-‐saline
estuaries
by
their
total
CRAM
scores
(Graph
2).
The
results
also
included
information
on
the
biodiversity
that
occurs
at
Rush
Ranch
(Table
3),
and
newly
restored
plant
species
that
were
transplanted
in
the
Arroyo
Burro
Estuary
streambed
(Table
4).
CRAM
Scores
The
scoring
for
Rush
Ranch
estuary
has
two
different
scores
that
consist
of
documented
scores
from
Eco-‐Atlas
and
my
own
scores
that
I
conducted
with
Mr.
Huddleston
a
trained
professional
in
the
California
Rapid
Assessment
Methods
for
14.
14
Wetlands
(CRAM
field
book
2013).
The
scores
for
Arroyo
Burro
Estuary
are
documents
from
the
Eco-‐Atlas.
However
there
is
a
lack
of
information
in
regards
to
specific
locations
of
the
Assessment
Area
(AA)
and
Buffer
during
the
CRAM.
With
out
a
map
showing
the
location
of
the
AA
and
Buffer
it
would
be
difficult
to
spot
the
problem
areas.
Buffer
and
Landscape
Context
Attribute
Aquatic
Area
Abundance:
Rush
Ranch
Estuary
scored
a
“12/12”
while
Arroyo
Burro
Estuary
scored
a
“9/12”
(Table
1).
Not
enough
variation
between
the
two
study
sites
for
this
attribute.
Rush
Ranch
has
rich
aquatic
corridors
(Figure
2
and
3).
However,
Arroyo
Burro
Estuary
had
a
higher
score
than
predicted
because
it
is
surrounded
by
urbanization
and
lacks
aquatic
corridors
(Figure
4).
There
is
no
documented
maps
showing
the
Assessment
Area
or
Buffer,
and
trying
to
indicate
if
the
line
transects
crossed
aquatic
corridors
is
an
issue.
Attribute
Percent
of
Assessment
Area
with
Buffer:
Rush
Ranch
Estuary
received
“12/12”
while
Arroyo
Burro
Estuary
received
“9/12”
(Table
1).
There
is
no
variation
between
the
two
estuaries.
Attribute
Average
Buffer
Width:
Rush
Ranch
Estuary
scored
a
“12/12”
compared
to
Arroyo
Burro
“9/12”
(Table
1).
The
results
showed
no
variation
between
the
two
study
sites.
Attribute
Buffer
Condition:
Rush
Ranch
Estuary
resulted
a
“12/12”
while
Arroyo
Burro
Estuary
scored
a
“9/12”
(Table).
There
was
not
enough
difference
between
the
two
estuaries.
Results
have
shown
that
this
attribute
along
with
the
other
physical
structure
attributes,
show
no
importance
of
the
buffer
condition,
15.
15
percent,
width,
or
aquatic
abundance
areas.
Since,
an
undisturbed
wetland
can
have
no
difference
in
buffer
scores
compared
to
a
highly
disturbed
wetland.
Results,
specifies
the
dependence
on
mapping
the
buffer
and
assessment
area
location
in
the
study
site.
Hydrology
Attribute
Hydrologic
Connectivity:
Rush
Ranch
Estuary
received
a
“12/12”
compared
to
Arroyo
Burro
Estuary
“6/12”
because
of
unnatural
inputs
(such
as
levees,
dikes,
and
road
grades)
that
count
for
50-‐90%
of
the
wetland
in
the
Assessment
Area
(Graph
1
and
table
1).
The
results
demonstrated
a
difference
between
the
two
estuaries
in
the
hydrologic
connectivity.
The
changes
that
were
made
to
restore
the
Arroyo
Burro
Estuary’s
streambed
included
an
open
new
channel,
slope,
levees,
vegetation,
dikes,
and
removal
of
a
300ft.
concrete
culver
that
all
contribute
into
lowering
the
hydrology
score
(URS
2014).
While
Rush
Ranch
Estuary
has
several
secondary
and
primary
tidal
channels
resulting
in
a
rich
aquatic
corridors
(Figure
2
and
3).
Attribute
Hydro-‐Period:
Rush
Ranch
Estuary
scored
a
“12/12”
while
Arroyo
Burro
Estuary
received
an
“12/12.”
There
is
no
difference
between
the
two
study
sites
in
this
attribute
section.
The
hydro-‐period
score
for
Arroyo
Burro
Estuary
was
higher
than
predicted
however,
this
shows
great
streambed
restoration
planning.
The
first
year
of
monitoring
the
Arroyo
Burro
Estuary,
have
shown
a
57%
of
abundance
in
California
native
plant
cover,
and
a
80%
survival
rate
for
newly
restored
plants
species
(native
and
non-‐native
plant
species)
(Kisner
2007).
Since
there
was
an
increase
in
relative
abundance
it
results
in
a
high
score
for
the
hydro-‐
16.
16
period
attribute.
Changes
in
channel
morphology,
drainage
network
density,
and
the
relative
abundance
of
plants
could
raise
the
hydro-‐period
attribute
score
(CRAM
dictionary
2013).
Attribute
Water
Source:
Rush
Ranch
scored
a
“12/12”
while
Arroyo
Burro
scored
a
“6/12”.
These
scores
specify
a
difference
between
the
two
estuarine
wetlands.
Arroyo
Burro
Estuary
consists
of
urban
runoff,
direct
irrigation,
storm
drains,
and
regulated
water
releases
controlled
by
a
large
reservoir
within
2km
upstream
of
the
Assessment
Area
(CRAM
field
book
2013).
Recent
studies
have
shown
fecal
coliform
concentrations
in
the
Arroyo
Burro
watershed,
Vs
=4/17E-‐6
for
the
average
settling
velocity
of
fine
grain
sediments,
sediment
resuspension
rate
Rt=
0
kg/m2s
summer
versus
5.49E-‐4
kg/m2s
winter,
and
total
suspended
solids
concentration
TSS=
0.3
kg/m3s
summer
and
1.5
kg/m3s
winter
(Steets
et
al
2003).
The
Arroyo
Burro
Estuary
is
under
the
“Water
Quality
Limited
segments
in
the
Clean
Water
Act
Section
303-‐(d)
List”
and
Arroyo
Burro
was
reported
in
1999
as
4E6
and
8E6
MPN/m3
while
the
“California’s
Single
Sample
Standard
for
fecal
coliforms
in
recreational
water
regions
should
not
exceed
4E6
MPN/m3
”(Sercu
et
al
2008).
Other
studies
sampled
the
pH
and
dissolved
oxygen
levels
of
Arroyo
Burro
Estuary:
pH=
8.2
drain,
7.9
creek,
8.0
lagoon,
and
8.2
surf
zone;
dissolved
oxygen=
8.4
surf
zone,
13.4
lagoon,
8.8
drain,
and
7.8
creek
(Sercu
at
al
2008).
Rush
Ranch
however
has
no
signs
of
human
disturbance
or
water
pollution
that
occurs
in
the
estuary.
17.
17
Physical
Structure
Attribute
Structural
Patch
Richness:
Rush
Ranch
Estuary
resulted
in
a
“
3/12”
while
Arroyo
Burro
received
a
“9/12”
(Table
1).
Rush
Ranch
Estuary
resulted
in
a
lower
score
compared
to
Arroyo
Burro
Estuary
this
indicates
only
two
or
less
structural
patch
richness
features
that
occurred
in
this
study
site.
However,
the
score
I
received
was
“6/12”
for
Rush
Ranch
Estuary
indicating
four
out
of
sixteen
structural
patch
richness
features,
and
we
found
organic
debris
in
the
channel,
bank
slumps,
depressions
in
channels,
and
secondary
channels
(Table
1
and
figure
2).
These
scores
could
result
from
the
choosing
of
the
Assessment
Area
and
Buffer
locations
because
the
wetland
composition
could
vary
through
out
the
study
site.
Attribute
Topographic
Complexity:
Rush
Ranch
resulted
a
“9/12”
while
Arroyo
Burro
Estuary
scored
a
“6/12”
(Table
1).
There
was
no
difference
between
the
two
study
sites.
Arroyo
Burro
Estuary
resulting
in
a
low
score
signifies
lack
of
a
tidal
channels
and
soil
cracks
furthermore
this
particular
estuary
had
the
tidal
channel
restored
because
of
drainage
and
sediment
filling
issues.
Arroyo
Burro
Estuary
has
a
large
reservoir
that
builds
up
sediment
along
with
regulating
water
releases
this
could
impact
fecal
coliform
loadings.
However,
tidal
flushing
and
storm-‐water
could
raise
the
fecal
coliform
contamination
levels
(Steets
et
al
2003).
Biotic
Structure
Attribute
Plant
Number
of
Plant
Layers:
Rush
Ranch
Estuary
received
a
“12/12”
while
Arroyo
Burro
Estuary
scored
a
“9/12”
(Table
1).
This
attribute
did
not
show
enough
variation
between
the
two
study
sites.
18.
18
Attribute
Number
of
Co-‐Dominant
Species:
Rush
Ranch
Estuary
scored
a
“12/12”
while
Arroyo
Burro
Estuary
scored
a
“9/12”
(Table
1).
These
results
did
not
show
much
difference
between
the
two
freshwater
estuarine
wetlands.
Attribute
Percent
Invasion:
Rush
Ranch
Estuary
scored
a
“12/12”
while
Arroyo
Burro
Estuary
did
not
have
a
documented
percent
invasion
CRAM
score
in
the
Eco-‐Atlas
or
show
signs
of
invasive
plant
species
in
the
Year
One
Annual
Monitoring
Report
(Kisner
2007).
Rush
Ranch
Estuary
has
been
comparatively
analyzed
by
topographic
data
that
correlated
estuarine
plant
species
and
their
distributions.
The
topographic
data
concludes,
the
habitat
of
Rush
Ranch
is
considerable,
but
will
have
continuous
exotic
plant
species
invading
the
ecosystem
(Andrew
et
al.
2009).
Attribute
Horizontal
Interspersion:
Rush
Ranch
scored
a
“12/12”
while
Arroyo
Burro
Estuary
received
a
“3/12”
(Table
1).
The
results
show
a
difference
between
the
two
study
sites
(Table1
and
graph
1).
A
vegetation
study
was
conducted
on
Rush
Ranch
Estuary
with
species
richness
by
calculating
their
relative
abundance:
subplot=
5.2±0.2,
plot=12.4±0.6,
plot_all=
15.9±0.7,
site=39,
and
site_all=
44
(table
5)
(Vasey
et
al
2013).
The
results
showed
no
obvious
signs
of
human
disturbance,
no
shifts
in
wetland
composition,
rich
plant
biodiversity,
no
invasive
plant
species,
and
rich
vegetation
patterns.
Rush
Ranch
Estuary
is
a
very
rich
ecosystem
with
rich
biodiversity
in
plant
species,
such
as
Cirsium
hydrophillum,
Schoenoplectus
acutus,
Typha
latifolia,
Typha
domingensis,
Typha
angustifolia,
Schoenoplectus
californicus
(Vasey
et
al
2012).
The
low
score
for
Arroyo
Burro
Estuary
indicates
the
Assessment
Area
supporting
less
than
5%,
no
plant
layers,
or
19.
19
signs
of
concrete,
rip
rap,
or
newly
restored
vegetation.
The
One
Year
Annual
Report
for
the
Arroyo
Burro
Estuary
Restoration
Project
consisted
of
57%
of
California
native
plant
cover
and
11%
non-‐native
plant
cover
(Table
4
and
5),
(Kisner
2007).
Furthermore,
Arroyo
Burro
Estuary
also
consists
of
rip
rap
that
was
installed
along
the
newly
constructed
tidal
channel
(URS
2013).
Attribute
Vertical
Biotic
Structure:
Rush
Ranch
Estuary
scored
a
“12/12”
while
Arroyo
Burro
Estuary
scored
a
“3/12”
because
the
Assessment
Area
is
deficient
in
living
vegetative
canopy.
The
results
showed
a
difference
between
the
two
study
sites
indicating
lack
of
dense
canopy
and
shelter
for
wildlife
in
Arroyo
Burro
Estuaries
habitat
(Table
1
and
graph
1).
Recent
studies
have
shown
with
quantitative
data
on
Arroyo
Burro
Estuary,
31
non-‐native
plant
species
and
84
California
native
plant
species
that
occurred
along
the
line
transects
(Table
5),
(Kisner
2007).
This
study
concludes
the
relative
abundance:
an
average
of
57%
of
average
plant
cover,
36%
of
average
bare
ground
cover,
80%
survival
rate
for
the
first
year
of
newly
restored
plants
(Kisner
2007).
Table
1.
CRAM
Scoring
Sheet:
Perennial
Estuarine
Wetlands
Attributes
Rush
Ranch
(I
conducted
these
scores)
Rush
Ranch
(Documented
scores)
Arroyo
Burro
(Documented
scores)
Aquatic
Area
Abundance
6
12
9
Percent
of
AA*
with
Buffer
12
12
12
Average
Buffer
Width
12
12
9
Buffer
Condition
9
12
9
Water
Source
12
12
6
20.
20
Hydro-‐period
12
12
12
Hydrologic
Connectivity
9
12
6
Structural
Patch
Richness
6
3
9
Topographic
Complexity
9
9
6
Horizontal
Interspersion
12
12
3
Vertical
Biotic
Structure
12
12
3
Number
of
Plant
Layers
12
12
9
Number
of
Co-‐
dominant
Species
12
12
9
Percent
of
Invasive
species
12
9
IN.
*Assessment
Area
Table
2.
The
total
attribute
scores
and
total
CRAM
score
for
each
estuary.
Attributes
Rush
Ranch
(I
conducted
these
scores)
Rush
Ranch
(Documented
scores)
Arroyo
Burro
(Documented
scores)
Buffer
and
Landscape
68%
100%
79%
Hydrology
92%
100%
67%
Physical
Structure
63%
50%
63%
Biotic
Structure
100%
92%
44%
Total
CRAM*
score
81%
86%
63%
*
California
Rapid
Assessment
Methods
for
Wetlands
Table
3.
Biodiversity
at
Rush
Ranch
Species
Common
Name
Species
Latin
Name
Salt
Marsh
Harvest
Mouse
Reithrodontomys
raviventris
Suisun
Ornate
Sorex
ornatus
sinuosus
Delta
Smelt
Hypomesus
transpacificus
21.
21
Sacramento
Splittail
Pogonichthys
macrolepidotus
Giant
Garter
Snake
Thamnophis
gigas
California
Clapper
Rail
Rallus
longirostris
obsoletus
California
Black
Rail
Laterallus
jamaicensis
Suisun
Song
Sparrow
Melospiza
melodia
maxillaris
American
White
Pelican
Pelecanus
erythrorhynchos
Waterfowl
(Vasey
et
al
2012)
Table
4.
Transplanted
California
native
plant
species
in
Arroyo
Burro
Estuary.
Species
common
name
Species
Latin
name
California
Boxelder
Acer
negundo
var
californicum
White
alder
Alnus
rhombifolia
rhombifolia
Yerba
mansa
Anemopsis
Californica
Mugwort
Artemisia
douglasiana
Marsh
baccharis
Baccharis
douglasii
Plummer’s
Baccharis
Baccharis
plummerae
Mule
fat
Baccharis
salicifolia
Creek
dogweed
Cormus
sericea
Saltgrass
Distichlis
spicata
Common
spikerush
Eleocharis
macrostachya
Seacliff
buckwheat
Eriogonum
parviflorum
Western
goldenrod
Euthamia
occidentalis
Everlasting
Gnaphalium
canesceus
Toyon
Heteromeles
arbutifolia
Coast
goldenbush
Isocoma
menziesii
Basket
rush
Juncus
textilis
Giant
rye
grass
Leymus
condensatus
Coascliff
aster
Malacothrix
saxatilis
Western
sycamore
Platanus
reacemosa
Black
cottonwood
Populus
balsamifera
subsp
trichocarpa
Hollyleaf
Cherry
Pruns
ilicifolia
Coast
Live
Oak
Quercus
agrifolia
Lemonade
sumac
Rhus
integrifolia
Fuchsia
flowered
gooseberry
Ribes
speciosum
California
Blackberry
Rubus
ursinus
Arroyo
Willow
Salix
lasiolepis
Purple
sage
Salvia
leucophylla
22.
22
Black
sage
Salvia
Mellifera
Alkali
bulrush
Scirpus
maritimus
(Kisner
2007)
Table
5.
Quantitative
Data
for
Rush
Ranch
Estuary.
Site
CC
PM
CI
RR
BI
SMS
Subplot
2.5±0.1
2.8±0.1
2.3±0.1
5.2±0.2
4.7±0.2
5.4±0.2
Plot
5.2±0.5
5.8±0.5
4.8±0.6
12.4±0.6
10.4±0.6
10.8±0.8
Plot_All
6.2±0.4
7.1±0.7
6.2±0.7
15.9±0.7
13.2±0.8
13.4±1.1
Site
10
14
21
39
48
44
Site_All
10
17
23
44
55
56
(Vasey
et
al
2012)
CC=China
Camp
PM=
Petaluma
Marsh
CI=Coon
Island
RR=Rush
Ranch
BI=
Browns
Island
SMS=
Sand
Mound
Slough
Table
6.
Non-‐native
plant
species
on
line
transects
at
Arroyo
Burro
Estuary.
Scientific
Name
Common
Name
A
B
C
D
E
F
G
H
I
J
K
L
Agrostis
virdis
Water
bent
grass
*
Anagallis
arvensis
Scarlet
pimpernel
*
Brassica
nigra
Black
mustard
*
Chamaesyce
maculata
Spotted
Spurge
*
*
24.
24
Graph
1.
The
bar
graph
for
the
4
attribute
scores
on
each
estuary.
0
20
40
60
80
100
120
Buffer
&
Landscape
Hydrology
Physcial
Structure
Biotic
Structure
Numeric
Scores
4
Attribute
Scores
The
2
non-‐saline
estuaries
Rush
Ranch
(documented)
Rush
Ranch
(I
conducted)
Arroyo
Burro
(document)
25.
25
Graph
2.
Percent
CRAM
Score
of
all
non-‐saline
estuaries
throughout
California.
Table
7.
Total
CRAM
scores
for
CA
non-‐saline
estuaries.
Location
Name
of
Estuary
Total
CRAM
Score
San
Francisco
Suisun
City
Rush
Ranch
86%
San
Francisco
Browns
Island
85%
San
Francisco
Napa
Pond
2
84%
San
Francisco
Montezuma
Bridge
80%
San
Francisco
Pacific
Atlantic
Terminal
76%
San
Francisco
Mackavoy
Marsh
74%
San
Francisco
Suisun
City
72%
San
Francisco
Browns
Island
Oversample
71%
San
Francisco
Port
Chicago
Pier
2
72%
San
Francisco
Pond
2A
Over
Sample
71%
San
Francisco
Grey
Goose
70%
San
Francisco
Coyote
Creek
Lagoon
70%
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
Total
CRAM
Score
(%)
Individual
Non-‐saline
Estuaries
Total
CRAM
Scores
CA
Non-‐saline
Estuaries
Rush
Ranch
Arroyo
Burro
26.
26
San
Francisco
Coyote
Creek
69%
Central
CA
Tembladero
Lower
Marsh
66%
Southern
CA
Arroyo
Burro
Estuary
63%
Figure
2.
Rush
Ranch
Estuary
27.
27
Figure
3.
The
line
transects
in
Rush
Ranch
Estuary.
28.
28
Map
3.
Arroyo
Burro
Estuary
29.
29
Figure
1.
Arroyo
Burro
Estuary
and
Mesa
Creek,
before
restoration
(USFWS
Photos)
Figure
2.
Arroyo
Burro
Estuary
and
Mesa
Creek,
after
restoration.
(USFWS
Photos)
30.
30
Conclusion
Discussion
I
am
accepting
my
hypothesis
for
this
senior
thesis
because
I
have
supportive
evidence
to
distinguish
the
difference
between
disturbed
and
undisturbed
non-‐
saline
estuaries
in
California.
I
established
discernible
differences
between
Rush
Ranch
Estuary
(undisturbed
wetland)
and
Arroyo
Burro
Estuary
(disturbed
wetland),
by
using
the
Level
II
California
Rapid
Assessment
Methods
for
Estuaries
to
comparatively
analyze
the
CRAM
scores.
Furthermore,
undisturbed
versus
disturbed
wetlands
are
comparatively
analyzed
by
their
ecological
processes,
system
components,
topographic
complexity
features,
and
their
intended
purpose.
The
results
show
Rush
Ranch
Estuary
having
the
highest
score
86%
and
being
well
above
average
75%,
versus
Arroyo
Burro
Estuary
having
the
lowest
score
63%
(Graph
1
and
table
7).
This
graphical
approach
visually
demonstrates
variation
between
the
two
study
sites
among
other
California
non-‐saline
estuaries,
and
their
differences
include
hydrology
and
biotic
structure.
There
was
no
difference
between
the
buffer
and
landscape
context,
and
physical
structure.
However
in
this
case
disturbed
compared
to
undisturbed
wetlands
are
different
in
the
landscape
context.
Rush
Ranch
Estuary
functions
as
a
high
quality,
undisturbed
non-‐saline
estuary
while
Arroyo
Burro
Estuary
functions
as
a
low
quality,
highly
disturbed
non-‐
saline
estuary
this
type
of
low
quality
function
is
known
as
wetland
treatment
system
(Kadlec
1996).
Disturbed
and
undisturbed
wetlands
are
very
different
in
the
landscape
context
because
Arroyo
Burro
Estuary
has
no
room
for
marsh
migration.
31.
31
Since
there
is
lack
of
undisturbed
areas
and
the
affect
by
human
fecal
pollutants
contaminating
the
storm
drains
(Sercu
et
al
2008).
While
undisturbed
areas
dominate
Rush
Ranch
Estuary
and
are
used
for
marsh
migration.
An
undisturbed
wetland
such
as
Rush
Ranch
Estuary
provides
a
high
quality
wildlife
habitat
for
the
Salt
Marsh
Harvest
Mouse
Reithrodontomys
raviventris,
Suisun
Song
Sparrow
Melospiza
melodia
maxillaries,
and
Waterfowl
(Table
3).
In
addition,
Rush
Ranch
Marsh
is
also
the
ecological
niche
for
endemic
species
of
San
Francisco,
such
as
Lathyrus
jepsonii
and
Cirsium
hydrophilum
var.,
200
organisms,
47
plant
species,
15
mammals,
and
230
birds
(Parker
et
al
2011),
(Andrew
et
al.
2009).
Rush
Ranch
is
the
largest
remaining
tidal
wetland
located
in
the
Suisun
Bay
with
rare
and
valuable
ecological
features,
such
as
up-‐land
transition
habitats
making
this
estuarine
wetland
a
National
Research
Reserve
under
the
San
Francisco
Bay
National
Estuarine
Research
Reserve
(Vasey
et
al
2012).
Rush
Ranch
is
a
great
example
of
an
undisturbed
freshwater
marsh
since
it
is
anticipated
for
conserving
and
protecting
threatened
or
endangered
tidal
marsh
species
(Table
3),
(Whitcraft
et
al
2011).
Species
listed
under
the
State
or
Federal
Endangered
Species
Act
fall
under
the
legal
jurisdiction
of
the
ESA,
and
any
damage
to
critical
habitat
or
species
is
prohibited.
The
notion
of
the
rapid
assessment
tactics
discusses
the
environmental
impacts,
such
as
degradation,
bank
erosion,
and
poor
water
quality.
These
environmental
impacts
are
results
from
human
caused
alterations
toward
wetlands.
Therefore,
Arroyo
Burro
Estuary
functions
as
a
treatment
wetland
to
improve
the
water
quality
from
bacteria
loading
and
subsequent
beach
closures
that
increase
32.
32
pollution
levels
caused
by
urbanization
(Aguinaga
et
al
2004).
Arroyo
Burro
Estuary
is
under
the
“Water
Quality
Limited
segments
in
the
Clean
Water
Act
Section
303-‐(d)
List”,
for
example
the
California’s
single
sample
standard
for
fecal
coliform
in
a
recreational
waters
should
not
exceed
4E6
MPN/m3
and
in
February
1999
the
Arroyo
Lagoon
resulted
in
a
4E6
and
8E6
MPN/m3
(Sercu
et
al
2008),
(Steets
et
al
2003).
The
stressors
that
were
found
to
affect
the
Arroyo
Burro
Estuary
was
the
urbanization
runoff,
urban
residential,
industrial
and
commercial,
active
recreation,
excessive
human
visitation,
discharges
of
urban
runoff,
contaminated
storm
drain,
rip
rap,
engineered
channel,
nutrient
impaired,
bacteria
and
pathogens
impaired
(CRAM
field
book
2013).
These
two
different
non-‐saline
estuaries
differ
in
a
few
ways
that
include
function,
wetland
composition,
and
wetland
condition.
An
assumption
of
the
California
Rapid
Assessment
Method
for
Wetlands
indicates
any
sign
of
human
disturbance
is
as
a
negative
environmental
impact
on
the
estuary
and
will
lower
the
CRAM
score.
High
CRAM
scores
indicate
that
the
wetland
is
in
excellent
condition
compared
to
other
wetlands
in
that
class,
and
they
may
provide
a
reference
for
wetland
restoration
or
conservation.
The
California
Rapid
Assessment
Methods
for
Wetlands
is
not
accurate
for
determining
the
performance
standards,
health
status
for
individual
wetlands,
or
should
be
used
for
a
statistical
approach.
Since
the
Assessment
Area
and
Buffer
could
both
be
mapped
in
a
biased
location
within
the
study
site
of
Arroyo
Burro
Estuary.
Arroyo
Burro
Estuary
received
a
higher
CRAM
scores
even
though
it
lacks
in
water
quality,
hydrologic
connectivity,
aquatic
abundance,
buffer
width,
buffer
33.
33
condition,
buffer
percent.
CRAM
is
a
way
to
rapidly
compare
and
contrast
the
wetland
condition,
stressors,
and
condition
of
the
wetland.
34.
34
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