San Joaquin River National Wildlife Refuge Draft Comprehensive Conservation Plan and Environmental Assessment

              U.S. Fish & Wildlife Service
San Joaquin River
National Wildlife Refuge
Draft Comprehensive Conservation Plan
and Environmental Assessment
Disclaimer
CCPs provide long term guidance for management decisions and set forth goals, objectives,
and strategies needed to accomplish refuge purposes and identify the Service’s best estimate
of future needs. These plans detail program planning levels that are sometimes substantially
above current budget allocations and, as such, are primarily for Service strategic planning
and program prioritization purposes. The plans do not constitute a commitment for staffing
increases, operational and maintenance increases, or funding for future land acquisition.
San Joaquin River
National Wildlife Refuge
Draft Comprehensive Conservation Plan
Prepared by:
U.S. Fish and Wildlife Service
California/Nevada Operations Office
San Luis National Wildlife Refuge Complex
947-C West Pacheco Blvd.
Los Banos, CA 93635
California/Nevada Refuge Planning Office
2800 Cottage Way, W-1832
Sacramento, CA 95825
Approved by:_________________________________________ Date______________________
California/Nevada Operations Manager
San Joaquin River NWR Comprehensive Conservation Plan
 
1 Introduction..................................................................................................1
Background..................................................................................................................................2
Purpose and Need for a Plan......................................................................................................3
Refuge Purpose and Authority..................................................................................................4
Refuge Vision Statement............................................................................................................4
Location and Size of the Refuge................................................................................................4
Ownership....................................................................................................................................5
Refuge Acquisition History........................................................................................................5
Fee Title Lands...........................................................................................................................9
Easement Lands..........................................................................................................................9
Refuge Management and Monitoring History.......................................................................11
2 The Comprehensive Conservation Planning Process.........................15
The Planning Process................................................................................................................15
The Planning Team....................................................................................................................16
Public Involvement in Planning...............................................................................................16
Overview of Public Scoping Comments and Discussions.....................................................16
Development of Alternatives....................................................................................................17
3 Refuge Setting............................................................................................19
Flyway Setting..........................................................................................................................19
Ecoregion...................................................................................................................................19
Historic Refuge Environment..................................................................................................20
Special Status Lands and Wilderness.....................................................................................21
Climate.......................................................................................................................................21
Soils and Geology.......................................................................................................................22
Topography and River Geomorphology..................................................................................22
Drainage.....................................................................................................................................23
Flood Management....................................................................................................................24
Water Quality.............................................................................................................................24
Vegetation...................................................................................................................................25
Wildlife........................................................................................................................................29
Historical and Cultural Resources..........................................................................................34
Refuge Facilities........................................................................................................................35
Current Management Activities..............................................................................................37
4 Opportunities and Problems....................................................................47
Water Quantity and Quality......................................................................................................47
Water Rights and Other Rights...............................................................................................48
Floodplain and Riparian Restoration......................................................................................49
Grassland Communities............................................................................................................49
Invasive Weeds & Other Exotic Species.................................................................................49
Threatened and Endangered Species.....................................................................................50
Fire..............................................................................................................................................52
Contents
ii San Joaquin River NWR Comprehensive Conservation Plan
Mosquito Abatement.................................................................................................................52
Public Use Programs.................................................................................................................52
Law Enforcement.....................................................................................................................53
Cultural Resources....................................................................................................................53
Refuge Farming Program.........................................................................................................53
Partnerships...............................................................................................................................54
5 Management Goals, Objectives, and Strategies.................................59
Introduction...............................................................................................................................59
Prior Management Activities at the Refuge...........................................................................59
Goals, Objectives and Strategies to Support the Proposed Management Action.............59
6 Management Plan Implementation........................................................83
Funding & Staffing.....................................................................................................................83
Step-Down Management Plans................................................................................................83
Compliance Requirements........................................................................................................86
Adaptive Management & Monitoring......................................................................................86
Plan Amendment and Revision................................................................................................87
Figures
1. Watershed Ecosystem Map........................................................................................................6
2. Location Map...............................................................................................................................7
3. Land Status..................................................................................................................................8
4. The Comprehensive Conservation Planning Process...........................................................16
5. Land Cover Map........................................................................................................................26
6. Refuge Roads and Facilities.....................................................................................................36
7. Wetland Units............................................................................................................................38
8. Management Units....................................................................................................................40
9. Proposed Habitat Management for San Joaquin River NWR............................................61
Tables
1. Existing Habitat Cover Types..................................................................................................27
2. Estimated Initial Capital Outlay to Implement the CCP.....................................................84
3. Estimated Annual Cost to Implement the CCP....................................................................85
Appendices.......................................................................................................89
A. Glossary of Terms .....................................................................................................................91
B. Environmental Assessment....................................................................................................109
C. Public Scoping and Involvement Process.............................................................................137
D. Compatibility Determinations................................................................................................145
E. Species List..............................................................................................................................185
F. Intra-Service Section 7 Consultation....................................................................................193
G. Step Down and Other Plans...................................................................................................195
H. Levee Breach Study................................................................................................................197
I. References and Literature Cited...........................................................................................199
J. Relevant Federal Laws and Mandates..................................................................................205
K. Mailing List..............................................................................................................................215
L. List of Preparers......................................................................................................................219
M. Wilderness Review...................................................................................................................221
N. Estimate of Refuge Water Needs..........................................................................................223
San Joaquin River NWR Comprehensive Conservation Plan
This Comprehensive Conservation Plan
(CCP) will guide the management of
the San Joaquin River National Wildlife
Refuge (NWR) for the next 15 years. The
San Joaquin River NWR is one of over
500 refuges that comprise the U.S. Fish
and Wildlife Service’s National Wildlife
Refuge System. The mission of the
National Wildlife Refuge System is to
conserve a network of lands and water for
the conservation and management of fish,
wildlife and plant resources of the United
States for the benefit of present and future
generations. As part of the system, the
San Joaquin River NWR provides a haven
for a unique assemblage of both wetland
and upland dependent wildlife species of
California’s Central Valley.




California’s Central Valley is ecologically
diverse and rich in wildlife. The Valley
averages forty miles wide by four hundred
miles long and consists of two lesser valleys
(Sacramento in the north and San Joaquin
in the south) and a delta where the two
drainages meet. San Joaquin River NWR is
located within the San Joaquin Valley, which
is bounded by the Sacramento/San Joaquin
Delta to the north, the Tehachapi Mountains
to the south, the Sierra Nevada to the east
and the Coast Range to the west. The San
Joaquin Valley is divided into two distinct
drainage basins; the San Joaquin basin in
the northern two-thirds, where the Refuge is
located, and the Tulare basin in the southern
one-third. The San Joaquin River and its
tributaries drain the San Joaquin Basin.
Historically, the Central Valley was a vast
grassland that graded up the sides of the
foothills of the surrounding mountains.
The grasslands were once dominated by
perennial bunchgrasses, which provided
rich forage for numerous grazers,
including pronghorn antelope (Antilocapra
1 Introduction
americana), elk (Cervus elaphus nannodes)
and mule deer (Odocoileus hemionus), and
a complex suite of small grazers and seed
predators (Barbour and Billings 1988).
They also supported an array of grassland-dependent
birds, including songbirds,
birds of prey and gamebirds. Woodlands
meandered across these grasslands in belts
that varied from half a mile to six miles
wide along rivers. Oak woodlands, which
had a park-like quality, became more dense
and mixed with cottonwoods (Populus
spp.), sycamores (Plantanus spp.), ash
(Fraxinus spp.) and willow (Salix spp.)
near the river edges and sloughs (Barbour
and Billings 1988). Acorns produced by
valley oaks (Quercus lobata) and other oaks
(Quercus spp.) provided abundant forage for
numerous wildlife species (Bonnicksen 2000,
McShea and Healy 2002). The riparian
tracts and woodlands served as forested
habitat for diverse breeding and migratory
songbirds, provided nesting sites for birds
of prey and colonial nesting waterbirds,
and acted as travel corridors for forest-dependent
wildlife. Extensive marshes were
a dominant feature along the water courses
of the valley, some large enough to be almost
impassable (Ornduff 1974). The marshes
were dominated by monocots particularly
tules (Scirpus spp.), cattails (Typha spp.)
and sedges (Carex spp. and Cyperus spp.).
These wetlands hosted one of the largest
concentrations of wintering waterfowl in the
world. In the mid-1800s, early explorers
reported vast numbers of waterfowl and
other marsh and shorebirds in the Central
Valley.
During the last 150 years, the natural
resources of the Central Valley have
been severely altered with the increase
in cultivation, ranching, urban centers
and industry. These changes significantly
altered or reduced a majority of the valley’s
San Joaquin River NWR Comprehensive Conservation Plan
native habitats and ecological processes.
The former native, perennial grasslands
that once dominated the valley are now
composed of “weedy,” non-native annual
grasses, such as Avena, Bromus, Lolium
and Erodium species, plus a large number
of non-native forbs (Barbour and Billings
1988). Large, herbivorous wildlife are no
longer dominant or, in some cases, present.
The once-stately valley oak woodlands,
which formerly supported the largest oaks
in North America, have been decimated with
the changing land use. Much of the riparian
forest along stream and river corridors has
also been eliminated (Bonnicksen 2000). Of
the eight oak woodland types of the Pacific
Coast, the valley oak woodland is now the
second rarest by total acreage (McShea
and Healy 2002). Suppression efforts and
changing land use have reduced fire as a
natural process within much of the Central
Valley; both water demands and flood control
activities for urban centers and agriculture
have drastically transformed the natural
hydrology. As a result, these changes have
destroyed or modified over 95 percent of the
historic wetlands in California (Heitmeyer et
al. 1989).
Although the Central Valley has been altered
since settlement, it still supports nationally
important and critical natural resources.
During the 1970s, an estimated ten to twelve
million ducks, geese and swans wintered in,
or migrated through, California (Heitmeyer
et al. 1989). California wetlands occur
primarily in the Central Valley, as do
most waterfowl. No other area in North
America is as important for wintering
waterfowl as California. California
supports greater than 60 percent of all
waterfowl (excluding sea ducks) wintering
in the Pacific Flyway and about 20 percent
in the entire United States. The Central
Valley plays the most significant role in
California’s importance to waterfowl. San
Joaquin River NWR supports significant
waterfowl and waterbird resources and
is capable of providing habitat for an
even greater abundance of these trust
resources. The Refuge has the potential
for protecting and restoring many of the
unique, native upland and wetland habitats
of the Central Valley and the wildlife
which they support.
Background
San Joaquin River NWR was established
in 1987 to primarily protect and manage
wintering habitat for Aleutian Canada
geese1 (Branta canadensis leucopareia), a
federally listed endangered species. Since
that time, the Refuge’s focus has expanded
to include other threatened and endangered
species, migratory birds, wildlife dependent
on wetlands and riparian floodplain habitat,
and restoration of habitat and ecological
processes. Nonetheless, providing wintering
habitat for and protecting Aleutian Canada
geese has remained a primary objective of
the Refuge since its beginning. This Refuge
and its management have been important
factors in the recovery of the Aleutian
Canada goose and its removal in 2001 from
the Threatened and Endangered Species
List.
The Aleutian Canada goose is a small
Canada goose subspecies; its size is between
the cackling Canada goose (smallest
subspecies) and Taverner’s Canada goose
(Johnson et al. 1979). The historic breeding
grounds for the Aleutian are believed to
have extended from near Kodiak Island,
Alaska, to the Kuril Islands in Asia. Their
wintering grounds included Japan, and
North America, from British Columbia
to northern Mexico (Delecour 1954). The
population declined during the early 1900s
due to the introduction of Arctic (Alopex
lagopus) and red (Vulpes vulpes) foxes to
their nesting islands. At the time of listing
(1975), the population was estimated at 800
individuals. The species was delisted in 2001
and the population now numbers over 40,000
individuals (Fitzmorris 2002). At present,
1 Subsequent to preparation of this plan, the American Ornithological Union made major revisions to the taxonomy
of Canada geese (Banks et al. 2003). Aleutian Canada geese are now classified as Aleutian cackling geese (Branta
hutchinsii leucopariea). For purposes of this document the old classification (Aleutian Canada goose) will be used
in the text.
San Joaquin River NWR Comprehensive Conservation Plan
San Joaquin River NWR and adjacent lands
are the primary wintering grounds for the
Aleutian Canada goose population.
The Refuge is part of the San Luis NWR
Complex, which includes three other units:
Merced NWR, San Luis NWR and the
Grassland Wildlife Management Area. All
four of the Refuge units, including the San
Joaquin River NWR, are managed by the
Complex.
Purpose and Need for a Plan
The U.S. Fish and Wildlife Service (Service)
is developing comprehensive conservation
plans (CCP) to guide the management
and resource use for each refuge of the
National Wildlife Refuge System (Refuge
System). The Refuge System includes
over 500 individual Refuges, forming the
largest network of public lands in the world
managed principally for fish and wildlife.
A CCP provides a description of the desired
future conditions and long-range guidance
necessary for meeting refuge purposes.
The CCP and associated environmental
assessment (EA) meet the mandates of the
National Wildlife Refuge Improvement Act
of 1977 (Improvement Act) and address
Service mandates, policies, goals and
appropriate National Environmental Policy
Act (NEPA) compliance. The Service’s
future management plan for the San Joaquin
River NWR is provided in this document.
The final plan is developed according to
revisions made during internal and public
review.
Refuge staff will use this CCP as a
management tool. The CCP will guide
management decisions for the next 15 years
and sets forth strategies for achieving
Refuge goals and objectives within that time
frame.
The Refuge does not currently have a
comprehensive management plan that
provides guidance for managing habitat,
wildlife and public use. The intent of
the CCP is to describe how the Refuge’s
founding purposes should be pursued over
the next 15 years. The plan sets Refuge
goals and objectives and provides strategies
for achieving them based on specific Refuge
purposes, Federal laws, National Wildlife
Refuge System goals and Service policies.
Management activities are selected based on
their efficacy in fulfilling Refuge goals and
objectives.
The CCP is comprehensive as it addresses
all activities that occur on the Refuge;
however, the noted management activities
or strategies are broadly stated. The
Refuge staff will prepare detailed step-down
plans that follow the CCP process
and describe how a management strategy,
such as developing an interpretive program,
will be applied. These plans are adjusted
based on monitoring results, available
funds, staff and current Service policy.
The effects of management actions are
monitored to provide information for needed
modifications of management practices or
activities. The CCP has flexibility and will
be reviewed periodically to ensure that its
goals, objectives, strategies and time frames
remain valid.
The Service is preparing this plan for the
Refuge to:
n Provide a basis for management that
is consistent with the Refuge System
mission and Refuge purposes and ensure
that the needs of wildlife come first,
before other uses.
n Provide a scientific foundation for Refuge
management.
n Provide a clear vision statement of
the desired future conditions when
Refuge purposes and goals have been
accomplished.
n Provide visitors with a clear
understanding of the reasons for
management actions on the Refuge.
n Ensure the compatibility of current and
future uses of the Refuge.
n Provide long-term continuity in Refuge
management.
n Provide a basis for operation,
maintenance and development budget
requests.
The CCP
will guide
management
decisions for
the next 15
years.
San Joaquin River NWR Comprehensive Conservation Plan
Refuge Purpose and Authority
The Refuge was established in 1987 to
provide winter forage and roosting habitat
for the threatened Aleutian Canada goose,
protect other species federally listed as
endangered/threatened, improve and
manage habitat for migratory birds and
conserve native fauna and flora. The Service
established the Refuge as a unit of the San
Luis NWR Complex under authority of the
Endangered Species Act of 1973, Migratory
Bird Conservation Act of 1929 and the Fish
and Wildlife Act of 1956.
The Refuge purposes as stated in the law
are:
“To conserve fish or wildlife which are listed
as endangered species or threatened species
or plants...” 16 U.S.C. § 1534 (Endangered
Species Act of 1973);
“...For use as an inviolate sanctuary, or
for any other management purpose,
for migratory birds.” 16 U.S.C. § 715d
(Migratory Bird Conservation Act); and
“...For the development, advancement,
management, conservation, and protection
of fish and wildlife resources.” 16 U.S.C. §
742f(a)(4) “...for the benefit of the United
States Fish and Wildlife Service, in
performing its activities and services. Such
acceptance may be subject to the terms
of any restrictive or affirmative covenant,
or condition and servitude.” 16 U.S.C. §
742f(b)(1) (Fish and Wildlife Act of 1956).
Refuge Vision Statement
San Joaquin River National Wildlife Refuge
will be managed to conserve, protect and
enhance native communities of the San
Joaquin Valley, with a focus on wildlife and
the ecological processes on which they
depend. A large segment of the native
valley habitats and their associated wildlife
communities have been reduced due to
intensive land use and development. This
Refuge will conserve and restore the area’s
native habitats, maintaining its role as an
important riparian corridor for natural
resources within the state’s Central Valley.
It will emphasize management of native
wildlife and the necessary actions that focus
on the recovery of Federal and State listed
endangered/threatened species and other
species of special concern, and protection
and/or enhancement of migratory bird
resources. Waterfowl and other waterbirds,
in particular the Aleutian Canada goose,
and neotropical migratory birds, are
management priorities. The San Joaquin
River NWR will be a key link—along with
other National Wildlife Refuges in the
Pacific Flyway—in providing high quality,
native habitat, particularly wetlands that
support an abundance and diversity of
waterbirds.
The Refuge will support a variety of native
habitats, ranging from valley oak gallery and
mixed riparian forests/woodlands to seasonal
and permanent wetlands, from native
grasslands to modified habitats, in order
to support and benefit select trust wildlife
species, particularly those of special concern.
These habitats will support a wide diversity
of native fish, wildlife and plants, such as
anadromous fish, neotropical migratory
birds, waterfowl and other waterbirds, as
well as resident wildlife.
The Refuge will provide an ideal
environment for environmental education
about native California habitats/wildlife
and their conservation/restoration. It will
provide the public with excellent wildlife
viewing and photographic opportunities, as
well as traditional area activities, including
waterfowl hunting and fishing.
Location and Size of the Refuge
The Refuge is nine miles west of the City of
Modesto, California, and straddles western
Stanislaus and San Joaquin counties. The
Refuge is located in the northern portion of
the San Joaquin Valley, which is enclosed by
the foothills of the Sierra Nevada Mountains
to the east and the Coast Range to the
west. The other units of San Luis NWR
Complex, San Luis and Merced NWRs are
located approximately thirty-five and forty
miles south, respectively, from San Joaquin
River NWR. The 12,887 acres within the
approved boundary of San Joaquin River
NWR are along the main stem of the
San Joaquin
River
National
Wildlife
Refuge will
be managed
to conserve,
protect and
enhance
native
communities
of the San
Joaquin
Valley.
San Joaquin River NWR Comprehensive Conservation Plan
 
San Joaquin River from just south of the
confluence with the Tuolumne River, then
north to the south bank of the Stanislaus
River. The Mohler Tract of the Refuge is a
noncontiguous parcel situated on the north
bank of the Stanislaus River three miles east
from the main portion of the Refuge. The
Refuge’s landscape represents a locally­—
as
well as regionally—significant remnant of
the once broad floodplain of these three
major rivers of California’s Central Valley
(Figure 1–Watershed/ Ecosystem Map
and Figure 2–Regional & Project Location
Map). Surrounding lands are largely used in
agricultural production.
Ownership
Lands within the Refuge boundary have
been acquired in both fee title (outright
purchases) and through easements (See
Figure 3–Land Status Map). All acquisitions
were on a willing-seller basis. Fee title
lands are owned by the Service and serve as
the core of Refuge lands. These lands are
managed for wildlife as the priority.
Easement lands are privately-owned lands,
where a willing owner has sold restricted
land-use rights to the Service to protect or
enhance wildlife habitats on these private
lands. Typically, Service easement lands
occur in proximity to fee title lands. The
Service perpetual conservation easements
were established to protect existing
resource habitat values while retaining
land in private ownership. In addition, the
U.S. Department of Agriculture National
Resource Conservation Service (NRCS)
holds both Wetland Reserve Program and
floodplain easements on some parcels of the
Service-owned lands. The NRCS Wetland
Reserve Program and floodplain easements
were a funding partnership to acquire fee
title land for the Service, whereby the
NRCS purchased easements on the land
and the Service paid the landowner the
remaining fee title value. The land is then
owned and managed in perpetuity by the
Service with an underlying NRCS easement.
Refuge Acquisition History
The Service became interested in the
present Refuge locale in 1976 when the
federally-listed Aleutian Canada goose
was discovered using the Faith Ranch and
Mapes Ranch as winter habitat. At that
time, the Faith Ranch was owned by the
Paul Davies family and the Mapes Ranch
by the Bill Lyons, Sr. family. Both ranches
were primarily beef cattle operations,
although the Mapes Ranch also had a small
amount of row crop agricultural production.
Although bounded by riparian habitat to the
north, west and south, the uplands of both
ranches were dominated by short-cropped
irrigated pasture, scattered wetlands and
stock ponds. This complex of habitats
formed optimum foraging and roosting
habitat for wintering Aleutian Canada geese.
Subsequent monitoring revealed that more
than 98 percent of the Aleutian Canada
goose population wintered on these lands.
The open terrain of the ranches provided
high quality habitat for other geese, lesser
and greater sandhill cranes, as well as
other wildlife. The Service established the
San Joaquin River NWR in 1987 for the
primary purpose of meeting the wintering
habitat objectives of the Aleutian Canada
Goose Recovery Plan. At that time, the
approved Refuge acquisition boundary (the
area within which the Service could acquire
and manage land) totaled 10,295 acres, and
included primarily the Faith Ranch and
Mapes Ranch east of the San Joaquin River,
and a portion of another property west of the
river. Initially, all Refuge land acquisition
was planned as fee title purchase.
The first land acquisition occurred in
1988 when the Service purchased the 777
acre Christman Island from the National
Audubon Society. Christman Island,
formerly part of the Mapes Ranch, had
been purchased by the Audubon Society
in 1986 through a donation from Joseph
M. Long and Don Lundberg, with the
intent of reselling it the Service. During
this time, the Service Realty Office was
meeting with the Davies family landowners
to pursue purchase of other lands within
the acquisition boundary. For a variety
San Joaquin River NWR Comprehensive Conservation Plan
Fresno
Sacramento
San Francisco
San Joaquin River
National Wildlife Refuge
Redding
Bakersfield
Modesto
101
101
99
5
80
580
99
5
O r e g o n
N e v a d a
C a l i f o r n i a
P a c i f i c O c e a n
SACRAMENTO
RIVER NWR
SAN LUIS
NWR
BITTER
CREEK
NWR
STONE
LAKES
NWR
KERN
NWR
SAN
PABLO
BAY
NWR
DON EDWARDS
SAN FRANCISCO
BAY NWR
SACRAMENTO
NWR
MODOC
NWR
PIXLEY
NWR
SUTTER
NWR
BLUE
RIDGE
NWR
MARIN
ISLANDS
NWR
ANTIOCH
DUNES
NWR
MERCED
NWR
GRASSLANDS
WMA
COLUSA
NWR
BUTTE SINK
WMA
DELEVAN
NWR
WILLOW CREEK -
LURLINE WMA
Figure 1. / Ecosystem Map
CA/NV Refuge Planning Office - April 2006 50 25 0 50
Miles
San Joaquin River Watershed Central Valley-San Francisco Bay Ecoregion
Pacific
Flyway
Area
Enlarged
Figure 1: Watershed / Ecosystem Map
San Joaquin River NWR Comprehensive Conservation Plan
 
San Joaquin River
National Wildlife Refuge
P a c i f i c O c e a n
San Jose
Stockton
Sacramento
San Francisco
Merced
Los Banos
Modesto
Fresno
101
5
80
50
101
101
5
152
33
580
99
99
Butte Sink WMA
Sutter
NWR
Stone
Lakes
NWR
San Pablo
Bay NWR
Marin
Islands
NWR
Don Edwards San
Francisco Bay NWR
Grasslands
WMA
Ellicott
Slough NWR
Salinas
River NWR
Antioch
Dunes NWR
San Luis
NWR
Merced
NWR
K i n g s
C o u n t y
M o n t e r e y
C o u n t y
S a n
B e n i t o
C o u n t y
S a n t a
C r u z
C o u n t y
S a n t a
C l a r a
C o u n t y
F r e s n o
C o u n t y
M e r c e d
C o u n t y
S a n
M a t e o
C o u n t y
M a d e r a
C o u n t y
M a r i p o s a C o u n t y
A l a m e d a C o u n t y
S t a n i s l a u s
C o u n t y
C o n t r a C o s t a C o u n t y
S a n
J o a q u i n
C o u n t y
M a r i n C o u n t y
C a l a v e r a s C o u n t y T u o l u m n e C o u n t y
S o l a n o
C o u n t y
A m a d o r
C o u n t y
S a c r a m e n t o
C o u n t y
N a p a
C o u n t y
S o n o m a
C o u n t y
A l p i n e
C o u n t y
Y o l o
C o u n t y
E l D o r a d o
C o u n t y
D o u g l a s
C o u n t y
C a r s o n
C i t y
P l a c e r
C o u n t y
S u t t e r
C o u n t y
C o l u s a
C o u n t y
N e v a d a
C o u n t y
L a k e
C o u n t y
Y u b a
C o u n t y
W a s h o e
C o u n t y
2. Location Map
CA/NV Refuge Planning Office - April 2006
CALIFORNIA
0 5 10 20 30 40 50
Miles
Area
Enlarged
Figure 2: Location Map
San Joaquin River NWR Comprehensive Conservation Plan
Beckwith Rd.
Gates Rd.
Shoemake Rd.
Dairy Rd.
Center Rd.
Orchard Rd.
River Rd.
Stanislaus Rd.
132 132
33
Miller Lake
Tuolumne River
San Joaquin
River
Stanislaus
River
San Joaquin County
Stanislaus County
Mohler Tract
Figure 3. Land Status
CA/NV Refuge Planning Office - April 2006 1 0.5 0 1
Miles
NRCS Wetland Reserve
Program Easements
Approved Refuge
Boundary
FWS Lands
FWS Conservation Easement
Private
Figure 3: Land Status
San Joaquin River NWR Comprehensive Conservation Plan
 
of reasons these negotiations were
unsuccessful.
In 1990, the Robert Gallo family purchased
the Faith Ranch. The new landowners were
not interested in selling the ranch to the
Service, but were willing to enroll the ranch
in a conservation easement in the future.
From 1990 to 1992, the Lyons family stopped
negotiations with the Service because the
Mapes Ranch was being considered as
one of several potential locations for the
site of a future University of California
campus. After the Mapes Ranch was
eliminated from consideration as a campus
site, the landowners reentered acquisition
negotiations with the Service; however, by
that time, funding that would have allowed
purchase of the entire Mapes Ranch in a
single acquisition action had been redirected
to other projects. Subsequent acquisition
proceeded on a parcel-by- parcel basis as
funds became available. Fee-title purchases
were made of 861 acres in 1993, 662 acres in
1996, and 577 acres in 1997 using Migratory
Bird Conservation Act funds. By 1997,
the Service owned 2,877 acres within the
Refuge.
In January 1997, a catastrophic flood
occurred on the lower San Joaquin River
system. Flood control levees failed and
most of the Refuge and Faith Ranch, and
much of the Mapes Ranch, were inundated
by floodwaters. Other private lands west
of the designated Refuge boundary also
received extensive flooding. In all, the
areas surrounding the Refuge suffered
more than $2 billion in property damages.
Subsequently, several landowners in
the floodplain west of the San Joaquin
River approached the Service with the
intent of selling their flood-prone land for
inclusion within the existing Refuge. This
coincided with a Congressional mandate
for the U.S. Army Corps of Engineers to
explore nonstructural alternatives for flood
protection; the same time period produced
statewide initiatives, such as the San
Joaquin River Management Plan, to restore
riparian habitat and hydrologic function and
provide alternate methods of flood control.
In support of these efforts, the Service
proposed a nonstructural flood protection
demonstration project in which it would
acquire those flood-prone properties, breach
or remove the existing flood control levee,
and allow periodic floodwaters to spread
over the Refuge-owned floodplain to reduce
downstream flooding. This proposal grew
into a multi agency effort, with the Service
partnering with NRCS, U.S. Army Corps
of Engineers, U.S. Bureau of Reclamation
and the California Department of Water
Resources. In 1997, the Service completed
an environmental assessment and Land
Protection Plan to expand the approved
Refuge boundary to 12,887 acres. Following
approval, in 1999 the Service acquired 2,037
acres of floodplain and riparian habitat
west of the San Joaquin River in fee title,
using a combination of Service (Emergency
Flood Appropriations) and NRCS (Wetland
Reserve Program) funds. In 2000, an
additional 210 acres of floodplain habitat
immediately south of and adjacent to the
Refuge were acquired with CALFED funds,
and 35 acres of riparian habitat along the
Stanislaus River north of the Refuge were
purchased by the Service Anadromous Fish
Restoration Program and turned over to
the Refuge for management. By 1998, the
owners of the Mapes Ranch had reversed
their original decision to sell their entire
ranch in fee title, and instead, were willing
to sell only a small portion of the remaining
ranch lands in fee title and enroll the rest
in perpetual conservation easements.
Accordingly, the Service purchased
Mapes Ranch lands both in fee title and
in easement, and purchased a perpetual
conservation easement on most of the Faith
Ranch.
Fee Title Lands
Purchase of fee title land began in 1988 and
is ongoing. The past five years have yielded
the greatest increase in land acquisition for
the Refuge. Figure 3 (Land Status Map)
illustrates the approved Refuge boundary
for acquisition, totaling close to 13,000 acres,
and the current land ownership status.
As of 2004, Fee title lands comprise 51
percent of the approved Refuge boundary.
Sources of acquisition funds have included
10 San Joaquin River NWR Comprehensive Conservation Plan
the Land and Water Conservation Fund,
Migratory Bird Conservation Act Fund,
CALFED Bay-Delta Program, emergency
flood control appropriations, Anadromous
Fish Restoration Program and the State of
California.
Easement Lands
Easements are legal agreements whereby
one party has binding authority regarding
some aspect(s) of a property owner’s land.
Easements will influence the management
activities and opportunities at the Refuge.
In some cases, the Service has easements
on adjacent private property; in other
instances, other agencies have easements on
Refuge lands.
Perpetual Conservation Easements
(USFWS)
The Service acquired perpetual conservation
easements on 1,834 acres of the 2,050 acre
Faith Ranch in 2001, and 1,112.9 acres of
the 4,000 acre Mapes Ranches in 2002.
Additional funding is currently being
sought to enroll much of the rest of the
Mapes Ranch into the easement program.
Both properties are within the Service’s
acquisition boundary for the Refuge. The
purpose of the easements is to protect
critical wintering habitat for Aleutian
Canada geese, State threatened greater
sandhill cranes, other threatened and
endangered species, and migratory birds.
The authority to acquire these easements
comes from the 1997 Environmental
Assessment for the expansion of the Refuge.
These easements are subject to all Federal
laws pertaining to those rights being
acquired through the easement. Locally,
the easements are administered by the San
Luis NWR Complex under the guidance of
the Easement Program Manager to ensure
the ecological integrity of the easements are
met.
The specific terms of the easements guide
the landowners and the Service in protecting
the integrity of the agricultural operations
(irrigated and native pasture and cereal
grains) while sustaining critical habitat for
migratory wildlife. In addition, the Service
acquired the right to continue providing
wildlife habitat on the property if the
landowner can no longer sustain a viable
agricultural operation.
The Service is considering an acquisition
boundary expansion concurrent with this
CCP that would extend along the San
Joaquin River floodplain from the southern
boundary of the Refuge southward to the
existing Grasslands Wildlife Management
Area in Merced County. Under this
proposal, most acquisitions would be
perpetual conservation easements developed
in conjunction with other agency easement
programs. The Service has prepared a
Study Report and drafted a Preliminary
Project Proposal, and is seeking the
authority to study land acquisition in this
area. The Study Report is currently being
reviewed within the Service.
Floodplain Warranty Easement
Program (NRCS)
This NRCS easement applies to San
Joaquin River NWR lands that the Service
purchased from J. P. Lara and the El Solyo
Ranch. This easement requires the Service
and any subsequent landowner, to protect
the floodplain and restore and manage for
native habitats and natural resource values.
The Lara and Vierra Units of the Refuge are
both enrolled in this program and comprise
515.69 and 632.65 acres, respectively. The
landowner (i.e., Refuge) is required to
provide for “the unimpeded reach and flow of
any waters in, over, or through the easement
area; to retard runoff and prevent soil
erosion through the restoration, protection,
or enhancement of the floodplain; to restore,
protect, manage, maintain, and enhance the
functional values of wetlands, riparian areas,
conservation buffer strips, and other lands;
to conserve natural values including fish and
wildlife habitat, water quality improvement,
flood water retention, groundwater
recharge, open space, aesthetic values, and
environmental education; and to safeguard
lives and property from floods, drought, and
the products of erosion” in perpetuity.
To ensure the enrolled easement lands
meet the program’s purposes and goals, the
management of these lands must conform
San Joaquin River NWR Comprehensive Conservation Plan 11
to the Planned Conservation Treatment
and Compatible Use Permit of NRCS. This
permit between the NRCS and landowner
addresses short-term management practices
that would be applied until fulfilling the
long-term goal of restoring riparian/wetland
habitat and natural floodplain hydrology
to maintain the ecological integrity of the
easement are. The permit applies to both
the Floodplain Warranty Easement and
Wetlands Reserve Program Easements.
Wetland Reserve Easement Program
(NRCS)
This NRCS-administered easement
applies to lands west of the San Joaquin
River that the Service purchased from
Mr. Ed Hagemann (Mehlhaff and Hay,
1999). It requires the owner to “restore,
protect, manage, maintain, and enhance
the functional values of wetlands and other
lands, and for the conserving of natural
values including fish and wildlife habitat,
water quality improvement, flood water
retention, groundwater recharge, open
space, aesthetic values, and environmental
education” for 30 years. The Hagemann
tract of the Refuge is part of this program
and comprises 2,017.8 acres. These
lands are also required to conform to the
Planned Conservation Treatment and
Compatible Use Permit of NRCS, which is
described above.
Refuge Management and Monitoring
History
The level and type of management activities
applied to the Refuge have evolved over
time. Beginning in 1976, prior to Refuge
establishment, graduate students or
contract researchers were present on-site
each winter during December to
March to monitor the geese as part of the
Aleutian Canada goose recovery program.
The Service’s Division of Research and
Development (now the Biological Research
Division of the U.S. Geological Survey)
oversaw these monitoring efforts. The
researchers collected goose population and
distribution data and maintained a daily
presence. They also monitored and reported
any trespassing or poaching to landowners
and Federal and State law enforcement
agents and conducted any necessary disease
control activities.
This monitoring effort continued after
the Refuge was established in 1987. The
Aleutian Canada goose researchers
provided daily on-site presence and
relayed information regarding the geese
and other Refuge issues to the San Luis
NWR Complex headquarters in Los Banos.
Following the acquisition of Christman
Island in 1988, an entry gate was installed,
access road improved and boundary signs
posted. The management focus remained
on Aleutian Canada geese even though
the Refuge did not own lands suitable as
goose habitat. The main issues at that time
were the limited roost pond habitat on the
Faith and Mapes Ranches due to prolonged
drought and the presence of Aleutian
Canada geese at the Modesto Sewage
Treatment Facility, south of the Refuge,
where they were exposed to recurring avian
cholera outbreaks and experienced losses to
that disease.
In 1991, the Service entered into cooperative
agreements with the owners of the Faith
and Mapes Ranches in which the Service
compensated the landowners to flood
wetlands on their properties to provide
roost ponds for the geese. An additional
agreement with the owners of the Faith
Ranch provided that they would grow and
mow down corn on their property as forage
for Aleutian Canada geese. From 1991 to
1993, Service funds were not available and
the landowners elected to provide those
services at their own expense. During this
same time, the Service contracted with U.S.
Department of Agriculture–Wildlife Services
to haze the geese at the sewage treatment
facility to move them away from the disease
outbreak sites. The combination of hazing
and the provision of roost ponds and cereal
grain forage were successful in getting the
geese to shift back to the Refuge area.
With the acquisition of irrigated pasture,
cropland and roost pond habitat in 1993,
the Service gained a limited ability to
manage for goose and sandhill crane
wintering habitat on Refuge lands. To
12 San Joaquin River NWR Comprehensive Conservation Plan
provide needed forage habitat, the Refuge
entered into a cooperative agreement with
the Lyons family. Under this agreement,
the Cooperator planted and grew corn on a
sharecrop basis and then harvested a share
as silage. The Refuge’s share of corn was
grown to maturity, and then mowed down by
the Cooperator on a schedule developed by
the Refuge to provide forage for the geese.
Cattle grazing was allowed on Refuge-owned
irrigated pasture and uplands to create the
short-grass foraging habitat preferred by
Aleutian Canada geese and other arctic
nesting geese, once they arrived in autumn/
winter. The Cooperator compensated the
Refuge for the value of grazing by planting
winter wheat on Refuge lands to provide
green forage for the geese (where the silage
corn was harvested), and providing water
to flood and maintain seasonal wetlands and
roost ponds on the Refuge.
The amount of habitat available for goose
and sandhill crane management increased
as new lands were acquired from the Mapes
Ranch. The existing Page Lake roost pond
was enhanced through a cooperative project
in 1996 by the Service, the Lyons family, and
Ducks Unlimited, and additional roosting
habitat (Goose Lake) was developed by
the Service in 1999. By 1999, 335 acres
of corn and winter wheat fields, 469 acres
of irrigated pasture, 371 acres of native
uplands, and 191 acres of roost ponds/
wetlands were actively managed for Aleutian
Canada geese, sandhill cranes, and other
migratory birds on the Refuge. Although
increasing numbers of geese made use of
Refuge lands, there continued to be goose
use at the Faith and Mapes Ranches.
In 1995, responsibility for monitoring
wintering Aleutian Canada geese for
the recovery program shifted to Region
1, Division of Refuges. Since that time,
seasonal biologists of the San Luis NWR
Complex have been based at the Refuge each
winter to monitor Aleutian Canada geese and
cackling Canada geese (Branta canadensis
minima). While Refuge staff maintained
the same level of goose monitoring as
did the previous researchers, they were
also available to perform other Refuge
management activities. The staff increased
disease control activities, took more control
of water management, and initiated biological
inventories, such as Refuge species lists,
heron/egret rookery counts, sandhill crane
counts, and vernal pool surveys.
Since 1996, a permanent Refuge staff
member has been assigned the oversight
and day-to-day management of the Refuge
as a primary duty. This, and assistance from
other San Luis NWR Complex staff, has
allowed for an expansion of management
activities at the Refuge. Management has
included removing debris and unneeded
facilities on new Refuge lands; demolishing
buildings, including asbestos removal in
Gardner’s Cove and the former El Solyo
Dairy site; repairing and upgrading lift
pumps, pipelines, water control structures,
and other water delivery facilities;
developing new wetlands on former
agricultural fields; initiating volunteer
projects; constructing a cooperatively-funded
observation tower for public use; preparing
habitat restoration plans; and submitting
major land acquisition and habitat
restoration grant funding requests.
San Joaquin River NWR Comprehensive Conservation Plan 13
San Joaquin River on the Refuge.
Photo: USFWS
14 San Joaquin River NWR Comprehensive Conservation Plan
San Joaquin River NWR Comprehensive Conservation Plan 15
The purpose of the Comprehensive
Conservation Plan (CCP) for the San
Joaquin River National Wildlife Refuge is
to guide the management of the Refuge.
The CCP provides managers with a 15-year
strategy for achieving Refuge purposes
and contributing toward the mission of the
National Wildlife Refuge System, consistent
with sound principles of fish and wildlife
conservation and legal mandates. A CCP is
required because the Refuge does not have
a current plan that provides direction for
managing wildlife, habitat and public uses.
This CCP for the Refuge is intended to
meet the compliance requirements of the
National Wildlife Refuge Improvement Act
of 1997 (Improvement Act) and the National
Environmental Policy Act (NEPA). Refuge
planning policy also directed the process and
development of the CPP, as outlined in Part
602, Chapters 1, 3 and 4 of the U.S. Fish and
Wildlife Service Manual (May 2000).
The Refuge initiated the comprehensive
conservation planning process in
February 1999. Initially, members of
the Complex staff and planning team
identified preliminary issues, concerns and
opportunities that were derived from wildlife
and habitat monitoring and field experience
associated with the past management of
the Refuge. This preliminary list of issues,
concerns and opportunities was further
refined and developed through the planning
process.
Service policy, the Improvement Act and
NEPA provide specific guidance for the
planning process, such as seeking public
involvement in the preparation of the
environmental assessment document.
2 The Comprehensive
Conservation Planning Process
This planning process included the
development and analysis of “reasonable”
management alternatives, including a “no
action” alternative that reflects current
conditions and management strategies. The
CCP highlights the Service’s preferred
management alternative for the Refuge;
other management alternatives were
developed and considered as part of this
planning process, and are found in Appendix
B: Environmental Assessment.
The Planning Process
Part of comprehensive conservation
planning includes preparation of a NEPA
document. Key steps in the CCP and the
parallel NEPA process are listed below:
1. Preplanning and team formation
2. Public scoping and involvement
3. Identifying issues, opportunities, and
concerns
4. Defining and revising vision statement
and Refuge goals
5. Developing and assessing alternatives
6. Identifying preferred alternative plan
7. Draft CCP and EA
8. Revising draft documents and releasing
final CCP
9. Implementing the CCP
10. Monitoring/feedback
Figure 4 shows the overall CCP steps and
process in a linear cycle, but the planning
process is actually a non-sequential
movement among the steps, with many
revisions occurring during the development
of the plan. The following sections provide
additional detail on individual steps in the
planning process.
16 San Joaquin River NWR Comprehensive Conservation Plan
CCP
Process
Final
CCP
Prepa re Draft
CCP
Develop
Alternative Objectives
And Strategies
Impleme nt
CCP
And Monitor
Review a nd
Revise th e
CCP
Public Scoping &
Identify Issues
Develop Vision
Statemen t &
Goals
Initiate Study
Preplan ning
Public
Input
Public
Input
Figure 4: The Comprehensive Conservation Planning Process
The Planning Team
Two planning teams were created and
used for this CCP. A core working team
was formed to develop the majority of
the documents and research background
information. An expanded team was also
formed comprising the core team, other
Service staff, California Department of Fish
and Game personnel and technical personnel
to provide overview and guidance through
the planning process. See Appendix M
for the list of team members. As with all
long-term projects, changes in the team
membership occurred throughout the
planning process.
Public Involvement in Planning
Public involvement is an important and
necessary component of the CCP and NEPA
process.
The Refuge held a public scoping workshop
in March 1999 to further develop and
ascertain planning issues for the Refuge.
The Refuge held quarterly Community
Forum Meetings to keep the public and
agencies informed regarding CCP progress
and determine, refine and clarify Refuge
issues. Several planning updates were
mailed during this process to interested
individuals, agencies, and organizations to
apprise them of the planning progress and
information generated. See Appendix C:
Public Scoping and Involvement Process.
Overview of Public Scoping Comments
and Discussions
The planning team identified issues,
concerns and opportunities internally and
through discussions with members of the
technical panel, other key contacts and
through the public scoping process. The
team received comments in writing via
regular mail and email.
The following key issues, concerns and
opportunities were identified during the
planning process and compiled by the
San Joaquin River NWR Comprehensive Conservation Plan 17
Service. Resource issues and opportunities
were also identified during this process:
n Wildlife Management and Restoration
n Recreation and Public Use
n Refuge Staffing and Resources
n Flood Management
n Wetland and Water Management
n Refuge Proximity to Private Lands
The comprehensive goals, objectives and
strategies of the CCP address all issues,
concerns and opportunities raised by the
public regarding management of the Refuge.
See Appendix C: Public Scoping and
Involvement Process and Chapter 5 for the
proposed management alternative.
The draft CCP and EA have been provided
to other agencies and the public for review
and comment. Comments will be addressed
and the document finalized for approval.
Once the CCP has been approved, the
Refuge can begin to implement the plan and
associated step-down plans. Please refer to
Chapters 5 and 6 of this document.
Development of Alternatives
The development of alternative management
regimes for the San Joaquin River National
Wildlife Refuge, assessment of their
environmental effects, and identification of
the preferred management alternative are
described in Appendix B: Environmental
Assessment (Figures 8–12). This CCP
highlights the preferred management
alternative for the Refuge.
18 San Joaquin River NWR Comprehensive Conservation Plan
San Joaquin River NWR Comprehensive Conservation Plan 19
Flyway Setting
The San Joaquin River NWR is situated
within the Pacific Flyway. The flyway
extends from the crest of the Rocky
Mountains west to the Pacific Ocean within
North America. It is used by millions of
waterfowl and shorebirds for migration to
and from wintering and breeding grounds.
California’s Central Valley is the largest
watered flatland in the flyway, providing
critical winter habitat for waterfowl, in
particular. Autumn/winter rains and melting
snow from the Sierra Nevada and Coast
ranges provide water for wetlands, and mild
winters make this area a major center for
wintering waterfowl. Approximately 60
percent of the flyway’s waterfowl winter
in the Central Valley, with wintering duck
populations ranging from two to five
million birds. Common valley waterfowl
species include the snow goose (Anser
caerulescens), Ross’ goose (Anser rossii),
white-fronted goose (Anser albifrons),
Aleutian Canada goose, green-winged teal
(Anas crecca), northern shoveler (Anas
clypeata), mallard (Anas platyrhynchos),
northern pintail (Anas acuta), cinnamon teal
(Anas cyanopters), gadwall (Anas strepera),
American widgeon (Anas americana),
canvasback (Aythya valisinieria), ring-necked
duck (Aythya collaris), bufflehead
(Bucephala albeola) and ruddy duck
(Oxyura jamaicensis) (Root 1988).
The Central Valley is also a key region
for many other waterbirds, including
the sandhill crane (Grus canadensis),
American coot (Fulica americana), moorhen
(Gallinula chloropus), sora rail (Porzana
carolina), Virginia rail (Rallus limicola),
killdeer (Charadrius vociferous), black-necked
stilt (Himantopus mexicanus),
American avocet (Recurvirostra
americana), greater yellowlegs (Tringa
3 Refuge Settings
melanoleuca), spotted sandpiper (Actitis
macularia), long-billed curlew (Numenius
americanus), western sandpiper (Calidris
mauri), least sandpiper (Calidris minutilla)
and long and short-billed dowitchers
(Limnodromus scolopaceus and L. griseus)
(Root 1988, Shuford et al. 1998).
Ecoregion
The San Joaquin River NWR is situated
in the Central Valley/San Francisco Bay
Ecoregion. The Central Valley is an
elongate depression that lies between
the Coast Ranges and the Sierra Nevada
Mountains. It is approximately 400 miles
long and 40 miles wide. Historically,
three principal habitats dominated this
ecoregion—valley grasslands, wetlands
and riparian woodlands/forests. Valley
grasslands consisted of perennial grasses
and dominated the landscape, comprising
81 percent of the area (Schoenherr 1992).
Wetlands were associated with rivers and
streams and widespread in low elevation
areas, comprising approximately 15
percent of the ecoregion (Schoenherr
1992). Wetlands, particularly seasonal
wetlands, were fed by winter rains and
runoff from the surrounding mountain
ranges. Riparian woodlands and forests,
frequently associated with rivers and
streams, encompassed four percent
of the ecoregion (Schoenherr 1992).
Wildlife of the ecoregion was diverse,
with grassland-dependent species,
including large grazers, which were a
dominant component of the community.
The ecoregion’s large wetland element
provided significant habitat for large
concentrations of waterfowl, shorebirds
and other waterbirds.
Following settlement and in the past
150 years major changes have occurred
20 San Joaquin River NWR Comprehensive Conservation Plan
in the ecoregion. Today, the ecoregion
has been converted into one of the most
productive agricultural areas in the world
(Schoenherr 1992). With this increase in
land devoted to agricultural use there was
an associated loss of wildlands. The valley
grasslands dominated by native perennial
grasses that once covered all well-drained
areas now only occur in a pristine
condition on just one percent of the
ecoregion (Schoenherr 1992). Likewise,
approximately 94 percent of the wetlands
and 89 percent of the riparian woodlands/
forests have also disappeared (Schoenherr
1992). Despite these losses, the remaining
wildlands in the ecoregion still provide
significant habitats for unique Central
Valley wildlife communities; they also offer
critical habitat for many wildlife species
both regionally and nationally, particularly
waterfowl and other waterbirds.
Historic Refuge Environment
Refuge lands were historically a mosaic
of riverine channels, broad riparian
floodplains, wetlands and grassland
savannas dominated by valley oaks. This
area was bisected by the main stem of
the San Joaquin River and was bounded
to the north by the Stanislaus River
and to the south by the Tuolumne River.
Historically, the San Joaquin River and its
tributaries would overtop natural levees
and inundate the floodplain following
winter rains and Sierra snow melt.
This system was dynamic, depositing
rich alluvium, creating and cutting
streambanks, creating and maintaining
riparian forests, creating oxbow lakes and
backwater sloughs by changing the rivers’
course, clearing and depositing debris,
scouring streambeds, and exposing and
depositing gravel and sand. The resulting
floodplain corridor was vegetated by trees,
such as button willow, black willow and
sandbar willow in the lower areas. The
upper areas were dominated by box-elder,
Fremont’s cottonwood, Oregon ash, arroyo
willow and valley oak. The most common
mid- and ground-story shrubs included
California rose, California blackberry,
elderberry and wild grape. Dominant
grasses and forbs included creeping
wild rye, basket sedge, mugwort and
goldenrod. The uplands adjacent to the
floodplain were less frequently inundated
by floods and were dotted with valley oaks
with an understory of perennial grasses
and forbs, such as creeping wild rye,
saltgrass, alkali sacaton, gum plant and
spikeweed. Wetlands and vernal pools
were abundant throughout the upland
savannahs. These habitats supported a
wide array of migratory birds, salmonids
and other fish, large herbivores and other
wetland and upland associated wildlife.
American Indians lived in permanent
villages on elevated locations above the
floodplain. These native people, the Yokuts,
made their homes along the San Joaquin
River and its tributaries in part, because of
the abundance of natural resources in the
area. When Lieutenant Gabriel Moraga led
the Spanish cavalry into the San Joaquin
Valley in 1805, the explorers were astonished
by the abundance of wildlife. The Spaniards
saw ducks, geese, cranes, herons, pelicans,
curlews, pronghorn antelope, tule elk and
grizzly bears, in large numbers.
Conditions began to rapidly change by the
1850s, following European settlement and
development. Pronghorn antelope were
extirpated, tule elk were nearly made extinct
and other wildlife were diminished by
commercial hunting that was driven by the
meat markets of San Francisco and mining
camps of the California Gold Rush. Valley
oaks and riparian forests were cut down
for lumber and firewood to fuel steamboat
traffic on the rivers. By the late 1800s and
early 1900s, wetlands were being drained,
creeks channelized and floodplains cleared of
trees to create farmland.
During the 1940s and 1950s, Friant Dam and
other water storage/flood control facilities
were built on the San Joaquin River and
its major tributaries, and water diversions
were made for agricultural, industrial and
metropolitan uses. Flood control levees
were constructed along the river’s course to
contain and greatly narrow the floodplain.
Nearly two centuries after Moraga’s
expedition, the San Joaquin Valley landscape
Refuge
lands were
historically
a mosaic
of riverine
channels,
broad
riparian
floodplains,
wetlands and
grassland
savannas
dominated
by valley
oaks.
San Joaquin River NWR Comprehensive Conservation Plan 21
is dominated by agriculture and is now one
of the most intensively farmed regions in
North America.
The Refuge area was drastically altered,
but to a lesser extent than most of the
lands along the San Joaquin River. Levees
were built on both sides of the river. To the
west, White Lake was drained, Ingram and
Hospital Creeks channelized and much of
the floodplain cleared for orchard and row
crop agricultural development in the early
1900s; however, the riparian forest and
associated sloughs on Christman Island and
along both sides of the river corridor were
retained. East of the river, much of the
floodplain and adjacent uplands was cleared
of trees and converted to grazing lands for
cattle. Stock ponds were developed and
natural slough channels were maintained to
provide water for cattle. Eventually, much
of the eastern land was leveled, canals and
pipelines were constructed for irrigation,
and native grass/forb plant communities
were replaced by domestic pasture grasses.
Habitat alteration has continued into
recent times. Valley oaks and other trees
in the river corridor were cut down in
the 1960s and 1970s, one-third of the
riparian forests on Christman Island
were cleared in the 1980s, and much of
the pasture land was converted to row
crop agriculture in the 1980s and 1990s.
Even with these recent developments, the
area provides critically important habitat
for a wide array of wildlife species. The
river channels and associated oxbows
serve as migration corridors and rearing
habitat for salmonids and other fish
species. The riparian forest and fallow
fields provide migration and nesting
habitat for neotropical birds and other
riparian associated species. The uplands
provide foraging and roosting habitat for
migratory birds, such as waterfowl, cranes
and shorebirds.
Special Status Lands and Wilderness
The Refuge is located on the northern
boundary of the Grasslands area, which
contains the largest remaining acreage of
freshwater wetlands in California. The
importance of this critical area for waterfowl
and other waterbirds has been recognized
by the Central Valley Joint Venture and the
North American Waterfowl Management
Plan. It is considered of international
importance for migratory waterfowl and
shorebirds of the Pacific Flyway. This
area also provides key habitats for several
priority species listed in the Service’s list
of Birds of Conservation Concern (USFWS
in preparation). Because of its value
to wildlife, the San Joaquin River NWR
functions as a northern extension of the
Grasslands area.
The San Joaquin River NWR is not
considered a federal wilderness study area
as it does not meet wilderness designation
criteria (Appendix N). The Refuge contains
no special status lands.
Climate
The San Joaquin Valley lies between the
Coastal Range and the Sierra Nevada
Range. Well-protected from the Pacific
Ocean, the area displays continental climate
characteristics of hot, dry summers, with
mild winters. Its location on the western
edge of the continent protects the region
from the weather extremes found farther
inland. The climate of the valley promotes
widespread grasslands. Precipitation occurs
during winter and spring months, but is
reduced because of the rain shadow effect
of the Coast Range. Patterson, a town near
the Refuge, has an average annual rainfall of
approximately 10 inches. The San Joaquin
Valley has a frost-free growing season of
270 to 300 days. The average temperature
ranges from a low of 38 degrees F to a high
of just over 100 degrees F; however, extreme
temperatures, as low as 20 degrees and
as high 115 degrees, have been recorded.
Cold-air drainage from the surrounding
mountains becomes trapped, forming a
persistent inversion layer in the valley.
During winter this is manifested in a dense,
ground-hugging fog known as tule fog.
Summer days are hot and hazy. Air quality
of the Central Valley is poor.
22 San Joaquin River NWR Comprehensive Conservation Plan
Soils and Geology
Schoenherr (1992) provides a broad
overview of the soils and geology of
California’s Central Valley:
“The Central Valley is a huge basin filled
with sediments. The deepest parts of the
gravels and sands are marine sediments
that have accumulated since the late
Jurassic—145 million years ago. The
sea retreated from the Central Valley at
about the same time that the southern
Coast Ranges were uplifted, and during
the long history of accumulation of marine
sediments in the valley, the basement
rock continued to subside. During most
of the Pleistocene the area was occupied
by shallow brackish and freshwater lakes.
During the last 5 million years, sediments
accumulated as alluvial deposits washed
out of the mountains. These deposits are
only a few thousand feet deep over most
of the valley floor.”




Physical conditions at the Refuge,
especially the geology of the watersheds,
are different on lands east or west of
the San Joaquin River. A soil survey for
eastern and western Stanislaus County
used the San Joaquin River to delineate
a boundary (McLauglin and Huntington
1968). Refuge lands on both sides of the
river consist primarily of recent alluvial
floodplains and basin lands. Soil types
are often mixed alluvium mapped as soil
associations. Basin soils are affected
by high water tables from river water
seepage, as well as saturation of the
land by deep penetration of rain and
irrigation water. Most soils exhibit very
poor drainage, with a high water table
at a depth of just three to six feet from
December through April (Arkley 1964).
If the land is irrigated, it provides prime
farmland, although it floods every few
years.
Topography and River Geomorphology
Elevations on the Refuge vary from 20 feet
along the edge of the San Joaquin River to
40 feet in several locations near the eastern
boundary. The Refuge is bisected by the San
Joaquin River, which has flood control levees
on both banks. Most of the Refuge lands
along the river have been laser-leveled and
intensively farmed in the past for row crops
and irrigated pasture. Small parcels that
retain the natural topography are present
on the East Unit (for Refuge management
purposes the area east of the San Joaquin
River is referred to as the East Unit and
lands west of the river as the West Unit).
The riparian corridors inside the levees
were not intensively developed and retain
their natural topography. Within the levees,
the sizes of the riparian areas range from
narrow corridors to large floodplains of 900
acres or more (i.e., Christman Island and
Gardner’s Cove areas). A remnant of what
used to be the main river channel is present
on the West Unit and forms the western
boundary of Christman Island.
Two major tributaries of the San Joaquin
River occur on the East Unit. The
Stanislaus River is located along part of
the Refuge’s north boundary where it flows
into the San Joaquin River. The Tuolumne
River forms the southern boundary of the
East Unit and flows into the San Joaquin
River near the Refuge’s southern end. Both
rivers contribute significant flows to the San
Joaquin River system and both have been
modified by levees, gravel mining and water
diversions, but to a lesser extent than the
San Joaquin River.
Eight smaller tributaries cross western
Stanislaus County, draining from the eastern
slopes of the Diablo Range to the San
Joaquin River. From north to south they
are: Hospital, Ingram, Kern, Del Puerto,
Salado, Crow, Orestimba and Garzas creeks.
These creeks have watersheds of similar
size and are spaced three to five miles apart.
Though rainfall is infrequent in these creek
watersheds, it is often heavy, making them
prone to erosion. None of the creeks flow
continuously. Two of these, Hospital and
Ingram creeks, cross the West Unit of the
Refuge. Both have been heavily channelized
on farmland located upslope from the Refuge
and essentially, act as agricultural drains.
Agricultural tailwater makes up the largest
contribution of flows entering the Refuge
from the watersheds of these two creeks.
San Joaquin River NWR Comprehensive Conservation Plan 23
Nearly all Refuge lands have been
separated from river flood water by
human-made levees. The course of the
San Joaquin River has been modified and
channelized to enhance water delivery
and flood control. Modification, levee
construction and water diversions to
enhance water deliveries and flood control
throughout the San Joaquin River system
have greatly altered the hydrology and
fluvial processes, such as river meandering
(Katibah 1984). Except for extreme flood
events that result in levee failure, water in
the river remains within the levee corridor
and does not spread across the floodplain.
These fluvial processes are reduced most
years, even in the riparian areas inside the
levee corridor, because the river flows are
reduced from historic levels.
Drainage
Due to the low elevation of Refuge lands
and the location of natural river channels,
numerous sources of surface water drain
onto the Refuge. Field drains, community
ditches and tributaries of the San Joaquin
River collect surface and subsurface
drainage from nearby agricultural fields.
Several irrigation districts that supply
irrigation water to upslope farmlands also
operate and maintain drainage channels that
flow into the Refuge as water proceeds to
the river.
In the East Unit, several lateral canals from
Modesto Irrigation District terminate on
or adjacent to the Refuge and contribute
intermittent flows to the Refuge or the San
Joaquin River. The Riley Slough portion of
the East Unit is saturated year round due
to the high water table and tail-water from
adjacent pasture lands.
On the West Unit, drainage rights and
maintenance costs have been recorded in
legal documents by previous landowners
for several locations on the Refuge. White
Lake Mutual Water Company pays 35
percent of drainage facility maintenance
and pumping costs for the drainage ditch
system over Refuge lands purchased from
Ed Hagermann. White Lake Mutual
Water Company has drainage rights over
those lands arising from a 1941 drainage
easement in the deed conveying the land
from Burkhard Investment Company to
the predecessor of Hagermann (i.e., Pietro
Rampone).
West Stanislaus Irrigation District obtained
a memorandum of agreement on May 8,
1928 with Burkhard Investment Company.
The agreement was amended in 1939. The
agreements address the right of access
and construction for the West Stanislaus
Irrigation District intake channel, as well
as the obligation to protect the Refuge
land from canal seepage. West Stanislaus
Irrigation District also has an obligation to
operate drainage pumps on Refuge property
purchased from J. P. Lara. The 1928
agreement refers to “maintain the water
level and seepage from the main canal at 22
U.S.E.D. and at least eight feet below the
natural, average ground level, the district to
install, maintain the necessary pumps and
operate the pumping of the seepage water.”
Access across the West Stanislaus Irrigation
District canal is required by installation
and maintenance of three pile bridges by
the District. The West Stanislaus Irrigation
District has expressed a desire to revise
the 1928 drainage agreement to eliminate
the pumping and bridge maintenance
requirements.
On February 12, 1947 West Stanislaus
Irrigation District obtained an agreement
for “use of a strip of land for ditch and road
purposes” 30 feet wide. This agreement
provides “free ingress, egress and regress”
for West Stanislaus Irrigation District along
a route generally parallel to Hospital Creek.
The agreement allows West Stanislaus
Irrigation District to construct “a ditch of
twenty (20) cubic feet per second capacity...”
and provides for West Stanislaus Irrigation
District to maintain the ditch, culvert pipes
and road right-of-way on Refuge lands.
The agricultural drainage water carries
suspended sediment that tends to drop
out of the water as flows slow down on the
flat basin land near the San Joaquin River.
Over time the deposition of sediment causes
water to back up in the creek channel.
24 San Joaquin River NWR Comprehensive Conservation Plan
Maintenance of drainage channels is a
concern to the West Stanislaus Irrigation
District, adjacent private landowners,
Turlock Mosquito Abatement District, as
well as the Refuge (Figure 6–Wetland Units
Map).




Flood Management
Most of the Refuge lands are within the
100-year floodplain of the San Joaquin
River. Historic records indicate the area is
subject to periodically significant rainfall and
flooding. Damaging floods occurred in 1937-
38, 1950-51, 1952, 1955-56, 1962-63, 1982-83,
1986, 1995, 1996-97 and 1998. Expanding
the Refuge west of the San Joaquin River
was motivated by a desire to expand the
floodplain and associated riparian habitat
beyond the existing levees.
All Refuge lands in the West Unit are
within the 100-year floodplain of the San
Joaquin River and subject to inundation
during floods. This entire unit (at the time
private land) was inundated due to levee
failure during the January 1997 flood.
Some lands in the West Unit were within
Reclamation Districts 2099, 2100 and 2102
prior to their acquisition by the Service.
When the Service acquired lands in the
West Unit, those Reclamation Districts
were disbanded. Lands in the East Unit
are within Reclamation District 2031, which
experienced extensive flooding during 1997.
The environmental assessment (EA) of
the effects of expanding the San Joaquin
River NWR was completed in 1997. Part
of the EA identified Refuge participation
in a partnership with the Natural Resource
Conservation Service (NRCS), U.S. Army
Corps of Engineers (Corps), California
Department of Water Resources and
California Reclamation Board regarding a
nonstructural flood control project for the
Refuge. This project involved acquiring
lands protected by Corps levees and
breeching the levees in up to seven locations
to allow future floods to inundate the new
Refuge lands which, in turn, would provide
flood protection to areas downstream by
offering temporary storage of peak flood
flows. The temporary flooding of the Refuge
lands would also return a more natural
flood regime to the San Joaquin River
floodplain and support the riparian habitat
that benefits from periodic inundation.
Another component of implementing the
nonstructural flood control alternative
is the Corps’ acquisition of flowage
easements from landowners adjacent to
the three reclamation districts (Appendix
H: Levee Breach Study). A Corps project
report selected this nonstructural flood
control project as the best flood control
proposal for the area in response to
damage caused by the January 1997 flood.
Water Quality
Water quality in the San Joaquin River
is degraded by irrigation drainwater
and urban runoff during summer and by
flushing of accumulated pollutants in urban
stormwater and other runoff in the winter.
The California State Water Resources
Control Board (SWRCB) designated 100
miles of the San Joaquin River, including the
reach in Stanislaus County, as an impaired
water body in 1990 (SWRCB 1990). In
addition, the lower San Joaquin River, from
Mendota Pool to Vernalis (130 mile stretch of
the River including the Refuge), is currently
listed as impaired in accordance with Section
303(d) of the Clean Water Act, for exceeding
salinity and boron water quality objectives.
Portions of the watershed upstream of the
Refuge are listed under the Clean Water Act
for organophosphorus pesticides, diazinon,
chlorpyrifos and selenium (Regional Water
Quality Board 2002). The greatest problems
occur on the River and its tributaries
upstream of its confluence with the Merced
River. At the Refuge and downstream,
relatively cleaner waters from Merced,
Tuolumne and Stanislaus rivers flow into the
San Joaquin River, which improves overall
water quality. Nevertheless, water quality
levels for some contaminants in the San
Joaquin River upstream of the Refuge are
still some of the highest in the nation (USGS
1998).
The Refuge is located in a reach of the San
Joaquin River that has also been identified
as the main contributor of nonpoint source
sediment in the San Joaquin River. Erosion
from agricultural irrigation is the main
San Joaquin River NWR Comprehensive Conservation Plan 25
contributor of the sediment, producing
1.2 million tons of sediment per year.
Organochlorine pesticides, such as DDT,
are adsorbed in the sediment carried by the
tailwater and transported to the San Joaquin
River.
Although there is substantial data on water
quality for the four rivers that flow into the
Refuge, little data has been collected from
the Refuge’s smaller waterways, including
the lateral canals that enter the Refuge from
agricultural and urban lands. Contaminants
monitoring data is not yet available for the
sloughs and managed wetlands. In July
1999 the Service’s Contaminants Branch
of the Sacramento Fish and Wildlife Office
conducted a one-time survey on the lands
west of the San Joaquin River. The report
concluded that further monitoring was
warranted, organochlorines should continue
to be a concern to the Refuge and the Vierra
Dairy should be closed (USFWS 1999).
Vegetation
The Central Valley contains three major
plant communities—riparian, wetland and
grassland—all of which occur at the San
Joaquin NWR (Schonenherr 1992) (Figure
5–Land Cover Map). Within each habitat
group, the Refuge identified communities
using Smith et al. (1995), Sawyer and
Keeler-Wolf (1995) and DFG (1999); they
include great valley oak riparian, black
willow riparian forest, permanent wetland,
semipermanent wetland, seasonal wetland,
vernal pool, tilled cropland, irrigated
pasture and native grassland (Figure
5–Land Cover Map and Table 1–Existing
Habitat Cover Types).
Riparian Habitats
Great Valley Oak Riparian
Oak woodland once covered much of the
landscape surrounding the San Joaquin
River NWR; however, only a remnant
of this habitat remains. Most of the oak
woodland was destroyed by logging,
ranching or conversion to agricultural fields.
Most of California’s oak woodlands were
relatively stable during the long period of
use by American Indians. Beginning with
European settlement approximately 150
years ago, oak densities and their dominance
declined in California due to the introduction
of livestock and land clearing for intensive
agriculture (McShea and Healy 2002).
Virtually all of the great valley oak riparian
community on the Refuge occurs within
the flood control levees. The overstory is
dominated by mature valley oaks, with
varying amounts of Fremont cottonwood
(Populus fremontii), box-elder (Acer
negundo) and willow (Salix spp.) present.
The understory is dominated by creeping
wild rye (Leymus triticoides), basket
sedge (Carex barbarae), California rose
(Rosa californica), California blackberry
(Rubus ursinus), and in more open areas,
mugwort (Artemisia douglasiana) and
western goldenrod (Euthamia occidentalis).
Although individual and scattered groves
of valley oaks are present on the floodplain
and adjacent uplands, most were previously
cleared for agricultural development.
The largest valley oaks and best examples
of this community type are present at the
Gardner’s Cove area, Christman Island,
Colwell Bottoms and the former Lara
property. Grazing and public use have
suppressed the regeneration of oaks and
other riparian species in the Gardner’s
Cove area; yet, during the past decade, the
cessation of those land uses and the presence
of soil scarification (i.e., clearing and soil
turning) due to flooding (1997 and 1998) have
Beaver crossing
waterway; good
water quality is a
critical issue for
many wildlife at the
Refuge.
Photo: Jerry Baldwin
26 San Joaquin River NWR Comprehensive Conservation Plan
Figure 5: Land Cover Map
Beckwith Rd.
Gates Rd.
Shoemake Rd.
Dairy Rd.
Center Rd.
Orchard Rd.
River Rd.
Stanislaus Rd.
132 132
33
Miller Lake
Tuolumne River
San Joaquin
River
Stanislaus
River
San Joaquin County
Stanislaus County
Buffington Field
Airport Field
Nelson Field
Figure 5. Land Cover Map
CA/NV Refuge Planning Office - April 2006 1 0.5 0 1
Miles
Cropland
Irrigated Pasture
Native Pasture
Permanent Wetland
Seasonal Wetland
Semipermanent Wetland
Riparian
Vernal Pool
Canals
Vernal Pool Complex
Refuge Boundary
Developed
San Joaquin River NWR Comprehensive Conservation Plan 27
allowed previously suppressed valley oak
seedlings/saplings to begin to grow. Valley
oak and other hardwood trees are naturally
regenerating, and a native understory of
mugwort, goldenrod, basket sedge, creeping
wild rye grass, wild rose and California
blackberry have become more common and,
in most places, have excluded nonnative
vegetation (Griggs 2000). Great valley
oak saplings are naturally regenerating
on Christman Island and a few other
locations on the Refuge; however, in other
locations, perennial pepperweed (Lepidium
latifolium), an invasive nonnative weed
species, has become established and is
expanding rapidly in the oak woodland
understory.
Black Willow Riparian Forest
The woody overstory of this vegetative
community, which typically grows along
water courses, is dominated by black willow
(Salix gooddingii) with varying amounts of
sandbar willow (Salix hindsiana), box-elder,
buttonbush (Cephalanthus occidentalis) and
Oregon ash (Fraxinus latifolia) (Ornduff
1974). Widely-spaced individual or small
groups of Fremont cottonwood (Populus
fremontii) are present and black walnut
(Juglans hindii) occurs in a few locations.
The black willow riparian forest community
at the San Joaquin River NWR occupies
much of the river corridor inside the
levees along the San Joaquin, Tuolumne,
and Stanislaus rivers, as well as Hospital
and Ingram creeks which drain into
the San Joaquin River. The quality of
riparian habitat that currently exists on
the Refuge is highly variable due to stand
age and successional stage. Black willow
riparian forest on the Refuge is classified
into early and late successional habitats.
Early successional habitat often occurs
in retired farmland that was inundated
by the floods of 1997 and 1998. Young
black willows and cottonwoods dominate
these areas. Scattered coyote bush has
become established as well. Forbs include
mugwort, goldenrod, and nettle (Urtica
dioica var. holosericea); however, invasive
weeds, such as poison hemlock (Conium
maculatum), perennial pepperweed, and
Johnson grass (Sorghum halepense),
now dominate the understory of some
areas. The late successional habitat is
characterized by a greater diversity of
trees and a more developed understory
consisting of California blackberry,
California rose, basket sedge and forbs.
Introduced invasive weeds are present in
varying degrees in much of these riparian
areas.
Wetlands
Permanent Wetlands
Permanent wetlands are those that remain
flooded all year and support hydrophytes
(water-loving plants)—either herbaceous
or woody species (Gritsch and Gosselink
2000). These wetlands at the San Joaquin
River NWR are ringed by a perimeter of
emergent vegetation, such as hardstem
bulrush (Scirpus acutus) and/or cattail
(Typha latifolia); oxbows are bordered
by riparian forest. Permanent wetlands
cover approximately 340 acres of the San
Joaquin River NWR. Wetlands that have
been present for decades include Miller
Lake, Quesma Field and Nelson Lake,
which are situated on the northern unit
of the Refuge. Oxbow lakes occur near
Gardner’s Cove and Christman Island. In
1999, changed drain pump management
in a former agricultural field allowed the
naturally high water table and irrigation
Habitat Cover Type Acreage
Cropland 744
Permanent Wetland 342
Riparian 1,919
Wet Meadow 0
Seasonal Wetland 218
Irrigated Pasture 506
Native Grassland 372
Semi-Permanent Wetland 132
Vernal Pool 4
Developed 56
Fallow 2,098
Irrigation / Drainage Canal 197
Total: 6,588
Table 1: Existing Habitat Cover Types
28 San Joaquin River NWR Comprehensive Conservation Plan
run-off from neighboring agricultural
lands to inundate the site and form White
Lake. A permanent wetland, which
fluctuates with the level of the San Joaquin
River, also exists on the west side of the
Refuge.
Semipermanent Wetlands
Semipermanent wetlands are flooded most
of the year but are dry during late summer
to early winter (Smith et al. 1995). There
are 132 acres of semipermanent wetlands
on the Refuge,
including the upper
benches of Riley
Slough, part of an
abandoned field on the
southwest corner of
the Refuge and oxbow
sloughs along the San
Joaquin River. Bulrush
and cattails thickly
vegetate these areas;
the oxbows are ringed
by riparian forest.
Seasonal Wetlands
Seasonal wetlands
are flooded during
autumn and maintained
throughout the winter
until drawdown occurs
in spring (Smith et
al. 1995). A total of
218 acres of managed
seasonal wetlands currently occur on the
Refuge. Depending on the water regime,
the dominant vegetation is swamp timothy
(Heleochloa schoenoides), watergrass
(Echinochloa crusgalli), smartweed
(Polygonum spp.), sprangletop (Leptochloa
fascicularis) and cockleburr (Xanthium
strumarium). Seasonal wetlands on the
East unit of the Refuge include Page Lake,
Watergrass Unit and Goose Lake, which
are maintained for roosting and feeding
ponds for Aleutian Canada geese and other
migratory birds. In addition, seasonal
wetlands develop on former agricultural
fields in the West Unit of the Refuge on an
irregular basis due to high flows in the San
Joaquin River, rainfall and upslope drainage
of irrigation water.
Vernal Pools
Vernal pools are a unique wetland that can
be found in the shallow basins of valley
grasslands where an impermeable soil
layer causes a perched water table to form
(Ferren and Pritchett 1988). They become
filled by winter rains and dry in the spring
by evaporation. Showy wild flowers, such as
downingia (Downingia spp.) and goldfields
(Lasthenia spp.), bloom as the pools dry,
but during the summer, the basins are bare
except for prostrate plants, such as annual
atriplexes (Atriplex spp.). The plants
and animals of vernal pools, including the
federally-listed endangered vernal pool fairy
shrimp (Branchinecta lynchi) and vernal
pool tadpole shrimp (Lepidurus packardi),
are highly restricted to specific locations and
are dependent on this shallow basin habitat
for their survival (Jain and Moyle 1981).
Based on examination of 1938 aerial
photography, vernal pools were once
common on lands within the Refuge
acquisition boundary east of the San Joaquin
River. Today only a remnant survives on the
few parcels of land where the topography
has not been altered. Four acres of vernal
pools in three locations occur on Refuge
lands (Figure 4–Land Cover Map). A vernal
pool complex of 14 pools, ranging in size
from 51 to 562 square yards, is present on
the Buffington Field unit. Some vernal pools
were eliminated or altered prior to Service
ownership. On the south and west sides
of the vernal pool complex, small channels
were installed to connect and deliver water
to several shallow pools, which are now filled
with vegetation typical of a seasonal wetland.
A raised dirt road in the center of the field
divides one vernal pool into halves.
A smaller complex of three vernal pools
is present in the Airport Field next to
Miller Lake. Invertebrates associated with
vernal pools have been found in one of the
pools. Pools are also present in the uplands
adjacent to Nelson Lake; although these are
characteristic of vernal pools, no vernal pool
invertebrates have been found in surveys.
Shorebirds are
dependent on
wetlands such as
this black necked
stilt.
Photo: Jerry Baldwin
San Joaquin River NWR Comprehensive Conservation Plan 29
Grasslands (Uplands)
Native Grasslands
Native grasslands on the Refuge consist of
lands with native undulating topography
modified by small channels and berms, but
not land-leveled. Central Valley grassland
habitats have been severely altered over
the past one hundred and fifty years.
Exotic annual grass species, principally of
Mediterranean origin, replaced the native
perennial grasses that likely once dominated
these grasslands. Many annual exotics,
including ripgut brome, soft chess, wild oats
and others, now prevail on the grasslands;
however, native grassland species, such as
alkali sacaton, saltgrass and spikeweed, are
still common in some areas. Restoration of
native habitats, including these grasslands,
is a critical element for Refuge management.
Noxious weedy species, such as yellow
starthistle and pepperweed, are also
beginning to invade some of these habitats.
Aggressive control of exotic species is
critical to maintain native habitat.
Tilled Cropland
Tilled croplands consist of lands that
have been converted from a more natural
condition by land-leveling and installation
of pipelines for irrigation, and are under
active management for agricultural crop
production. The Service acquired close
to 3,000 acres of tilled croplands. The
majority is presently in fallow condition and
will be restored to a combination of native
upland, riparian and wetland habitats. A
small portion of tilled cropland remains on
the Refuge to produce winter forage for
Aleutian Canada geese, sandhill cranes, and
other migratory birds. Most of the Refuge
tilled croplands are east of the San Joaquin
River and planted to corn (grain forage)
and winter wheat (green browse forage).
Privately owned tilled croplands within the
Refuge acquisition boundary are planted
to these and other cereal grains, alfalfa,
tomatoes, beans, and melons for commercial
production.
Fallow Field
Fallow fields are tilled croplands that
have been taken out of active agricultural
production. No irrigation water is applied
to these sites and the land develops a cover
of weedy, mostly nonnative, broadleaf
plants. The Service has purchased close to
3,000 acres of formerly tilled cropland that
has been allowed to lie fallow. Most of the
Refuge-owned fallow fields are on the west
side of the San Joaquin River. Fallow fields
will be restored as funds permit to a variety
of natural habitats, including riparian
forest, wetlands and grasslands. Very little
fallow field habitat is present on private
lands within the acquisition boundary of the
Refuge east of the San Joaquin River.
Irrigated Pasture
Irrigated pasture consists of lands that
have been converted from a more natural
condition by land-leveling, installing
pipelines to facilitate flood irrigation, and
planting a mixture of domestic grasses and
legumes. They are maintained by frequent
irrigation and are typically grazed by cattle
year round, following a rotational cycle that
averages about eight months of grazing
per year. The Service has purchased
approximately 500 acres of irrigated pasture
as part of the Refuge; irrigation has been
continued to provide shortgrass foraging
habitat for Aleutian Canada geese, sandhill
cranes and other migratory birds.
Wildlife
California’s diverse terrain and vegetative
communities provide conditions for a high
degree of wildlife diversity. San Joaquin
Valley NWR contains elements of the
Central Valley’s three major vegetative
types and has the potential to provide
habitat for over 325 species of wildlife.
Appendix E provides a species list of fish
and wildlife on the Refuge. A significant
portion of the Refuge consists of fallow
agricultural lands; their planned restoration
has the potential to increase the number of
wildlife species and their abundance over the
present distribution and abundance on the
Refuge.
Invertebrates
The Refuge provides habitat for both
aquatic and terrestrial invertebrate
species. Past invertebrate surveys have
been limited to the sampling of vernal
30 San Joaquin River NWR Comprehensive Conservation Plan
pools for the presence of tadpole and
fairy shrimp, but it is believed that the
aquatic and terrestrial invertebrate fauna
is representative for the Central Valley.
Non-systematic field observations have
detected the presence of representatives
from nine of the thirteen insect orders
with aquatic species (Merritt and
Cummins 1996), as well as two types of
native bees. Future work on invertebrates
is dependent on funding and may include
surveys for the endangered valley
elderberry longhorn beetle (Desmocerus
californicus dimorphus) and native bee
inventories.
Fish
Habitats for fish on the Refuge include
rivers, permanent wetlands, oxbows and
sloughs. Three major rivers (i.e., San
Joaquin, Tuolumne and Stanislaus) join
on the Refuge and provide an important
nexus for migratory fish. The stretch of the
San Joaquin River and tributaries on the
Refuge provide habitat and connectivity
to aquatic habitats for a wide range of
fish, including fall-run chinook salmon
(Oncorhynchus tshawytscha), steelhead
(Oncorhynchus mykiss) and Sacramento
splittail (Pogonichthys macrolepidotus)—all
species which are or proposed for federal
listing under the Endangered Species Act.
Appendix E provides the species list of fish
known to occur or have the potential to occur
at the Refuge.
Historically, California supported over 90
freshwater species of native fishes; the
Sacramento-San Joaquin Valley sustained
approximately 60 native species (Schoenherr
1992). Although there is still a diversity
of aquatic habitats in the Central Valley,
the natural assemblages of Central
Valley fish communities have been
degraded by altered flow regimes, levee
construction/maintenance and associated
loss of floodplain, reduction in riparian
habitats, the introduction of exotic fish
species and other factors. At San Joaquin
River NWR, many native fish species
have been extirpated or are severely
reduced in number, but several still
occur, including fall-run chinook salmon,
steelhead, Pacific lamprey (Lamptera
tridentata), river lamprey (Lamptera
ayresi), hitch (Lavinia exilicauda),
Sacramento splittail, Sacramento blackfish
(Orthodon microlepidotus), Sacramento
sucker (Catostomus occidentalis), tule
perch (Hysterocarpus traski), and prickly
sculpin (Cottus asper). Some of these
species are dependent on large river
systems while others use sloughs and
other backwater habitats. Introduced
species now dominate many of the aquatic
habitats of the Central Valley, including
those at San Joaquin River NWR.
Thirty-six introduced fish species are
present in the Central Valley (Schoenherr
1992). Refuge aquatic habitats are
now dominated by the following non-native
species: black bass (Micropterus
salmoides), carp (Cyprinus carpio),
bluegill (Lepomis macrochirus), threadfin
shad (Dorosoma petenese), red shiner
(Cyprinella lutrensis) and striped bass
(Morone saxatilis).
Although the Refuge was originally
established to benefit endangered and
other migratory birds, it has the potential
to benefit and enhance populations of
native fish. The restoration of floodplain
habitats on the Refuge, including riparian
forest, and a return to more natural water
regimes have the potential to benefit
many natives dependent on floodplains for
spawning and rearing purposes (Moyle
2002).
Amphibians and Reptiles
San Joaquin River NWR has the potential
for twenty-seven species of reptiles and
amphibians to occur (Appendix E). Semi-arid
regions such as the Central Valley
frequently possess diverse communities
of both lizards and snakes; by contrast,
whereas the turtle and amphibian
communities generally have a low species
diversity (Schoenherr 1992). The most
easily observable Refuge species include
the western pond turtle (Clemmys
marmorota), western fence lizard
(Sceloporus occidentalis), racer (Coluber
constrictor), Pacific gopher snake (Pituophis
melanoleuscus), common garter snake
San Joaquin River NWR Comprehensive Conservation Plan 31
(Thamnophis sirtalis) and introduced
bullfrog (Rana catesbeiana).
A preliminary survey of reptiles and
amphibians was conducted at the San
Joaquin River NWR in 1998; the survey
was not meant to be all encompassing, but
to focus on reptile/amphibian use of major
habitats. The survey indicated low overall
capture rates, but documented 13 of the
27 species of reptiles and amphibians with
the potential to occur on the Refuge. The
survey detected reptile and amphibians in
woodlands and native grasslands, but none
in fallow agricultural fields.
Birds
The San Joaquin River NWR was initially
established due to its importance to
migratory birds, particularly the Aleutian
Canada goose. The Refuge has the potential
to provide habitat for all the avian species
known to occur in the Central Valley, which
includes over 225 species of birds.
The most spectacular bird use at the Refuge
is by waterbirds, especially waterfowl.
Close to 30 species of ducks, geese and
swans make use of the Refuge and the
most common include the Aleutian Canada
goose, snow goose, white-fronted goose,
green-winged teal, northern shoveler,
mallard, northern pintail, cinnamon teal,
gadwall, widgeon and ruddy duck. Other
conspicuous Refuge waterbirds include the
pied-billed grebe (Podilymbus podiceps),
double-crested cormorant (Phalarcrocorax
auritus), white-faced ibis (Plegadis chihi),
white pelican (Pelecans erythrorhyncos),
sandhill crane, American coot, moorhen,
killdeer, black-necked stilt, American avocet,
greater yellowlegs, western sandpiper, least
sandpiper, as well as long and short-billed
dowitchers. Colonial nesting waterbirds
maintain colonies on the Refuge, such as
the great blue heron (Ardea herodias),
great egret (Ardea alba) and double-crested
cormorant.
Aside from waterbirds, the Refuge is an
important area to many other resident
and migratory bird species. Many
species of neotropical migrants have been
detected on the Refuge, including the
lazuli bunting (Passerina amoena), blue
grosbeak (Guiraca caerulea), ash-throated
flycatcher (Myiarchus cinerascens),
western wood-pewee (Contopus sordidulus),
black-headed grosbeak (Pheucticus
melanocephalus), Savannah sparrow
(Passerculus sandwichensis), horned lark
(Eremophila alpestris), yellow warbler
(Dendroica petechia), Nashville warbler
(Vermifora ruficappilla), orange-crowned
warbler (Vermivora celata), yellow-rumped
warbler (Dendroica coronata), Pacific-slope
flycatcher (Empidonax difficilis), and
ruby-crowned kinglet (Regulus calendula)
(Appendix E). A survey was conducted
for the yellow-billed cuckoo (Coccyzus
americanus), a rare species in the Central
Valley, but none was found, although
the Refuge does fall within its historic
range (Sawyer, et al. 1997, Gains and
Laymon 1984, Laymon 1998). Compared
to other habitats, oak woodlands and
riparian habitats, which support multiple
Drake northern
shoveler.
Photo: Jerry Baldwin
32 San Joaquin River NWR Comprehensive Conservation Plan
vegetation layers, have the highest
diversity of bird species on the Refuge.
Typically, natural habitats supported the
greatest diversity of bird species, whereas
crop fields and fallow agricultural lands
supported few birds (Hammond et al.
2002).
Mammals
California hosts an array of mammals
principally due to the state’s large size
and variety of habitats. Over 200 species
of mammals have been documented
in California, one of the largest state
species counts in the nation (Zeiner et al.
1990). Before European settlement, tule
elk (Cervus elaphus nannoides), grizzly
bear (Ursus arctos), pronghorn antelope
(Antilocapra americana), California
black-tailed deer (Odocoileus hemionus),
mountain lion (Felis concolor) and bobcat
(Felis catus) were conspicuous in the
Central Valley. The mammal composition
today is quite different, however, due to the
loss of suitable habitat, over-harvest and
introduction of nonnative plants and animals.
Most of the aforementioned large mammals
are no longer found in the area.
Rodent and rabbit species make up the
largest segment, approximately one third,
of the mammals found on San Joaquin
River NWR as in most areas (Eisenberg
1982). Three rabbit species occur on
the Complex, including the desert
cottontail (Sylvilagus audubonii),
black-tailed hare (Lepus californicus)
and endangered riparian brush rabbit
(Sylvilagus bachmanii riparius). Both
the hare and the desert cottontail are
conspicuous species at the Refuge. Large
rodents, which are also conspicuous on
the Refuge, include the aquatic muskrat
(Ondatra zibethicus) and beaver (Castor
canadensis) – both of which leave obvious
signs and play important roles in aquatic
systems. Dominant rodents at the
Refuge, which also act as keystone species
because of their grazing/seed predation
and/or tunneling, include the deer mouse
(Peromyscus maniculatus), California
vole (Microtus californicus) and
California ground squirrel (Spermophilus
beecheyi). The endangered San Joaquin
Valley woodrat (Neotoma fuscipes
riparia), as well as the introduced black
rat (Rattus rattus), also occur on the
Refuge
An inventory of the bat community has
not been conducted at the San Joaquin
River NWR, although by potential species
number they make up a sizable component
of the mammalian fauna. The most common
species probably include the big brown
bat (Eptesicus fuscus), western pipistrelle
(Pipistrellus hespornus), little brown bat
(Myotis lucifugus) and Brazilian free-tailed
bat (Tadarida brasiliensis).
Although the largest carnivore species of
the Central Valley were eliminated during
the settlement period, mid-size and small
carnivores are prevalent at the Refuge
and comprise approximately one fifth of
the potential mammalian community. The
most common carnivores/omnivores on the
Refuge include the coyote (Canis latrans),
raccoon (Procyon lotor), striped skunk
(Mephitis mephitis), northern river otter
(Lutra canadensis), longtailed weasel
(Mustela frenata) and Virginia opossum
(Didelphis virginiana) while the gray fox
(Urocyon cinereoargenteus) and mink
(Mustela vison) are present, but rarely
encountered.
Other mammals that occur on the Refuge
include the ornate shrew (Sorex ornatus)
Coyote, a
conspicuous
predator at the
Refuge.
Photo: Gary Powell
San Joaquin River NWR Comprehensive Conservation Plan 33
and mule deer (Odocoileus hemionus), and
several domestic mammals which either
trespass onto the Refuge or are used in the
Refuge’s grazing program. A permanent
mule deer population does not exist at the
San Joaquin River NWR, although transient
deer are periodically observed.
Threatened and Endangered Species
Several threatened and endangered
species occur or have the potential to occur
on the San Joaquin River NWR. The
Refuge was originally established for the
Aleutian Canada goose, which was listed as
endangered in 1967. Much of the population
had been ravaged by arctic foxes introduced
onto the Aleutian Islands in Alaska where
this subspecies breeds (USFWS 1991). The
population numbered 800 birds when the
Aleutian Canada Goose Recovery Program
was implemented in the 1970s. Since then,
breeding islands have been cleared of
foxes, captive-breeding programs started
and implemented and geese reestablished
on fox-free islands. By 1991, the Aleutian
Canada goose population had recovered to
more than 7,000 birds and, as a subspecies,
was down-listed to threatened status. By
1998 the population numbered more than
28,000 and the process of delisting Aleutian
Canada geese from threatened status began.
More than 95 percent of the world’s Aleutian
Canada goose population winters on the
Refuge. Most years, Page Lake is the main
roost pond. Aleutian Canada geese also
use Nelson Lake and the new Goose Lake.
Annual monitoring of these birds has been
conducted as part of the Aleutian Canada
Goose Recovery Program since 1976. Corn
and winter wheat are planted on the Refuge
annually to provide forage for the increasing
population. Aleutian Canada geese
populations have recovered dramatically and
have been delisted as a federally threatened
species. Managing and monitoring the
Aleutian Canada geese population continues
on the Refuge. Existing roost ponds have
been improved and expanded to potentially
reduce deaths from avian cholera by
physically spreading out the population.
These improvements and others would
further minimize avian cholera mortality
and local crop depredation, and discourage
poaching.
The federally listed endangered species
that occur or which could potentially occur
on the Refuge include the riparian brush
rabbit (Sylvilagus bachmani riparius), San
Joaquin Valley woodrat (Neotoma fuscipes
riparia), San Joaquin kit fox (Vulpes
macrotis mutica), bald eagle (Haliaeetus
leucocephalus), least Bell’s vireo (Vireo bellii
pusillus), giant garter snake (Thamnophis
couchi gigas), chinook salmon, Sacramento
splittail, steelhead trout, valley elderberry
longhorn beetle (Desmocerus californicus
dimorphus), vernal pool fairy shrimp, and
vernal pool tadpole shrimp.
The riparian brush rabbit is a subspecies of
the brush rabbit. Its original distribution
was the most limited of all the brush
rabbit subspecies, restricted to a small
stretch of the San Joaquin River and some
of its tributaries (Orr 1940). Presently,
the riparian brush rabbit only occurs in
three isolated populations, none of which
is considered secure for maintaining the
long-term status of the population. Plans
call for reestablishing a population on
the San Joaquin River NWR through a
captive breeding program (Williams et al.
2002). Existing riparian vegetation at the
Refuge, coupled with planned restoration
of riparian habitat on the Refuge, will
provide this subspecies the largest block
of contiguous habitat in its existing range.
The San Joaquin Valley woodrat uses similar
habitat as the riparian brush rabbit. Unlike
the rabbit, the woodrat has not disappeared
from the Refuge and small numbers of the
woodrat occur. The planned riparian habitat
restoration will benefit not only the rabbit
but the endangered woodrat, as well.
No records exist for the San Joaquin kit fox
on the Refuge, although there are records
within 20 miles. Bald eagles are routine
Refuge visitors, particularly during the
winter months, and are usually attracted
to the large concentrations of waterfowl.
Least Bell’s vireo nested in recently planted
riparian habitat at the Refuge in 2005.
Planned riparian restoration activities will
likely produce additional suitable habitat for
this endangered songbird. The giant garter
34 San Joaquin River NWR Comprehensive Conservation Plan
snake is listed as endangered and requires
permanent water as habitat. Although
suitable habitat appears to exist on the
Refuge, there have been no documented
records for the species. All three species of
listed or candidate fish species – Chinook
salmon, steelhead and Sacramento
splittail—occur on the Refuge. The valley
elderberry longhorn beetle is dependent on
elderberry (Sambucus mexicanus) for its
life cycle. Little elderberry habitat exists
on the Refuge but the small amount that
does occur may support populations of the
endangered beetle. Two vernal pool listed
shrimp have been documented at some of
the Refuge’s vernal pools; these habitats will
be maintained in perpetuity on the Refuge.
State of California listed endangered and
threatened species which occur on the
Refuge include the greater sandhill crane,
yellow-billed cuckoo, Swainson’s hawk,
willow flycatcher and bank swallow. The
greater sandhill crane annually winters on
and around the Refuge. Existing pastures,
agricultural lands, and wetlands are used for
foraging and roosting (Lewis 1979, Reinecke
and Drapu 1979, Iverson et al. 1982, Walker
and Schemnitz 1987). Unlike lesser
sandhill cranes, greater sandhill cranes
within the Pacific Flyway have shown
precipitous population declines because
of destruction of wetlands and riparian
habitat, lack of nesting habitat, and low
productivity (Pogson and Lindstedt 1991).
This area is one of eight geographic
regions in which greater sandhill cranes
winter in the Central Valley. The yellow-billed
cuckoo, which relies upon riparian
woodland, and the willow flycatcher,
which depends on wet, shrubby habitat,
have not recently been documented on
the Refuge, although planned habitat
restoration activities will likely create
additional habitat for these species. The
bank swallow require large cut banks
for its breeding colonies; although such
areas exist at the Refuge, there have
been no bank swallow colonies during
the last decade. The Swainson’s hawk is
conspicuous at the Refuge, which provides
habitat for several breeding pairs.
Historical and Cultural Resources
Cultural resources are physical remains,
sites, objects, records, oral testimony and
traditions that connect us to our nation’s
history and the land’s past. Cultural
resources include archaeological and
historical artifacts, sites, landscapes, plants,
animals, sacred locations and cultural
properties that play an important role
in the traditional and continuing life of a
community.
Little formal cultural resources survey
work has been conducted on the Refuge.
The known cultural resources in and within
one mile of the acquisition boundary of the
San Joaquin River NWR consist of eight
prehistoric sites and two historic sites.
Cultural resources, especially archaeological
sites, are fragile and nonrenewable. Most
consist of worked stone, fire-altered rocks
and organically enriched soil on or close
to the surface. When compared to the
surrounding landscape and contemporary
cultural features, such as roads, ditches and
structures, archaeological sites are small
and subtle.
Prehistory
The Refuge is in the homeland of several
Indian groups collectively known as the
Northern Valley Yokuts. Within the Refuge,
one group, the Tuolumnes aboriginal group,
has been identified. The Tuolumnes’ home
was east of the San Joaquin River, between
the Stanislaus and Tuolumne rivers (True
1981). The Refuge borders the territory
of, and at various times, was probably
occupied by, the Miwok tribe (Silverstein
1978). As neighbors, the Yokuts and Miwok
traded, intermarried and shared many
cultural practices. Acorns (valley oak) and
salmon were dietary staples, as were tule
elk, antelope and jackrabbit (Levy 1995).
Major Northern Valley Yokuts settlements
were located within a short distance of
the San Joaquin River banks and along
major tributaries. As the San Joaquin
and Tuolumne rivers have changed and
meandered considerably over the years,
these sites may appear most anywhere on
the Refuge. Villages were typically built on
ground higher than the surrounding area,
San Joaquin River NWR Comprehensive Conservation Plan 35
situated to best exploit the rich subsistence
resources without being consistently flooded.
Yokuts would mainly congregate in the
winter; during spring, summer and fall,
groups would disperse to gather different
resources (Jensen 1996). Villages were
typically a scatter of four or five to several
dozen structures. Each house served as a
home to one family. Large villages might
also have a great communal earth lodge for
ceremonial use.
History
Spanish colonization of California began
with the readily accessible coastal areas,
avoiding the interior valleys during the
18th century. Early in the 19th century,
military explorers and missionaries moved
away from the coast and to the inland
valleys. Early settlement by the Spanish
in California was accomplished through
the mission system, where livestock and
farming were mainstays. The arrival of the
Spanish into California shifted the use of the
land from hunting/gathering to an agrarian
use. By the 1820s many Native Americans
were assimilated into the mission system.
The Spanish also introduced both cattle and
sheep into California; at the height of the
mission period, there were 400,000 cattle and
300,000 sheep (Schoenherr 1992). During
the late 1840s, there was a decline in the
Spanish/Mexican influence in California,
particularly during the gold rush years;
however, livestock production continued as
a major agricultural activity. Due to a rapid
increase in miners and settlers during the
gold rush years, numbers of livestock were
vastly increased to meet this new demand;
by the 1860s, there were 3 million cattle
and 9 million sheep in the state. Damage to
California’s rangeland from overgrazing was
extensive by the 1870s and it has never fully
recovered (Schoenherr 1992). Agriculture
continued to be the primary land use of
the Central Valley into the 1900s. Dry
farming (i.e., farming without irrigation)
for wheat became popular in the late 1880s
but declining wheat prices brought an end
to this practice during the 1920s. Irrigated
agriculture in the Central Valley was
common in the 1850s but became widespread
during the 1900s, as it is today. The Central
Valley remains an agricultural center as
it was under the Spanish. The primary
agriculture products from the Central
Valley are dairy products, beef, grapes, rice,
orchard crops and cotton. Hay and alfalfa
production for livestock are also common
agricultural products.
Refuge Facilities
Most existing facilities at the San Joaquin
River NWR were on the land prior to
acquisition by the Service to establish and
develop the Refuge. Conditions of the
facilities vary greatly and range from very
good to hazardous. Some facilities and
structures are being used and maintained,
while others need to be removed.
Roads
There are numerous public roads within and
surrounding the approved Refuge boundary
(Figure 6–Refuge Roads & Facilities
Map). The Refuge is partially bounded by
Beckwith Road to the north, Gates Road to
the east, and Dairy and Pelican Roads to
the southwest. The Refuge is bisected by
Highway 132. Shoemake and Page Roads
(nonpublic) traverse the approved Refuge
boundary.
In addition to public roads, the Refuge
contains many interior roads, many of which
are unpaved. Most of these roads are shared
with other parties, such as the Faith and
Mapes ranches. Two paved roads that run
through the Refuge are the West Stanislaus
Road and an unnamed road that extends
south off Shoemake Road. There are no
existing walking trails on the Refuge.
Buildings
There are twenty-four buildings/structures
on the Refuge. These structures are
concentrated on the west side of the
Refuge, particularly the Vierra, Hagerman
and Lara Units. These structures range
from milk barns to pole sheds, livestock
run-in shelters, houses, and railroad cars.
All of these were acquired with the land
when purchased for the Refuge. Most of
the buildings and structures are in poor
condition and were not maintained for many
years. The three exceptions are houses
36 San Joaquin River NWR Comprehensive Conservation Plan
Figure 6: Refuge Roads and Facilities
Beckwith Rd.
Gates Rd.
Shoemake Rd.
Dairy Rd.
Center Rd.
Orchard Rd.
River Rd.
Stanislaus Rd.
132 132
33
San Joaquin County
Stanislaus County
Hanger
Two Houses
Lagoon/Pond
3 Barns
Small Barn
Large Barn
Green House
White House
Figure 6. Refuge Roads and Facilities
CA/NV Refuge Planning Office - April 2006 1 0.5 0 1
Miles
Barn
Hanger
House
Pond
Refuge Boundary
Private Roads
Public Roads
Refuge Roads
FWS Lands
San Joaquin River NWR Comprehensive Conservation Plan 37
in good condition, one of which is a life
estate, one a government quarters and the
remaining used as the office for the Refuge.
The majority of the buildings and structures
are a safety hazard and an attractive
nuisance and need to be removed.
Wetland Units and Water
Infrastructure
Most of the facilities now owned by
the Refuge are old and are in varying
conditions of usability. Many lift pumps
and pipelines on both the East and West
units were damaged during the January
1997 flood. In addition, the reliability, cost
and quality of water provided by these
facilities has a wide range of variability
(Figure 7–Wetland Units). To date, much
of the operational water delivery for
Refuge wetlands and uplands management
has been driven by the configuration and
condition of the agricultural wells, pumps,
pipelines and canals that were in place at
the time of purchase. In part of the East
Unit, water is provided by lift pumps and
wells, or conveyed by pipelines and canals,
owned by the Mapes Ranch as part of their
CLMA with the Refuge. Refuge-owned
water production facilities in the East Unit
include: a lift pump next to the MID Main
Drain and another along Riley Slough
(both rehabilitated after the 1997 flood);
a 70 h.p. agricultural well at the Dairy
Field (installed by the Refuge in 2000); a
domestic well at the Quesma Field wetlands
(condition uncertain); and a lift pump along
the Tuolumne River (damaged in 1997 flood
and needs to be rehabilitated and fitted with
a fish screen before operation). Water is
conveyed to Refuge wetlands and uplands
via a network of pipelines, concrete lined
ditches and earthen canals. Portions of the
MID Main Drain, MID Lateral 4, and MID
Lateral 7 water delivery canals run through
or adjacent to Refuge lands. Most of the
managed wetland units have inlet and outlet
structures that have been installed since
1993 and all have staff gauges to facilitate
water management.
A total of 12 lift pumps, six drain pumps,
nine domestic wells, and one agricultural
well were present on West Unit lands when
acquired by the Service. Many of these
facilities are currently inoperable due to
damage from the 1997 flood. Three lift
pumps (two 50 h.p. and one 34 h.p.) along the
West Stanislaus Irrigation District Intake
Canal were rehabilitated and fitted with
fish screens in the summer of 2001 to use
for habitat restoration and management.
The Refuge plans to rehabilitate and screen
additional lift pumps to meet restoration
and management needs, but others will be
abandoned. The drain pump at the White
Lake outlet was rehabilitated in 2000 and
is used to manage water levels of White
Lake wetlands and to meet Refuge drainage
obligations to the White Lake Mutual
Water Company. Five domestic wells were
filled and capped in 2001. The remaining
wells are operational and are being used
for restoration purposes, but water quality
concerns associated with these wells, as well
as test wells drilled in 2001, will limit the use
of ground water for long term management
of Refuge lands. An agricultural well on the
southern end of the unit (former Arambell
and Rose property) is currently being used
to irrigate alfalfa grown on the Refuge
through a CLMA. The water quality of that
well is unknown. The West Unit is overlaid
by a network of pipelines and canals that
were used to deliver and drain off irrigation
water to the former agricultural fields. Part
of these facilities will be maintained and
used for habitat restoration and subsequent
management. Canals and pipelines that are
not needed for management purposes will be
filled in or blocked (pipelines) as part of the
habitat restoration efforts.
Visitor Facilities
A wildlife viewing platform, information
kiosk and associated parking lot located off
of Beckwith Road are available to the public
for wildlife observations. These facilities
were constructed in 2002 and provide the
only public use facilities at the Refuge
Current Management Activities
Most of the past habitat management,
wildlife management, and biological
monitoring and research at the Refuge were
focused on supporting the recovery goals
for Aleutian Canada geese. As the Refuge’s
38 San Joaquin River NWR Comprehensive Conservation Plan
Figure 7: Wetland Units
Lower
White
Lake
River
Bend
Oxbow
Field
Food
Plot
Chrisman
Island
Riley
Slough
Goose Lake
Nelson
Lake
Mid Lateral 4
Ingram Creek
Mid Lateral 3
Mid Main Drain
Mid Lateral 7
Ringneck
Wetland Beckwith Rd.
Gates Rd.
Shoemake Rd.
Dairy Rd.
Center Rd.
Orchard Rd.
River Rd.
Stanislaus Rd.
132 132
33
Creekside
Pond
Upper
White
Lake
Miller Lake
Tuolumne River
San Joaquin
River
Stanislaus
River
San Joaquin County
Stanislaus County
Figure 7. Wetland Units
CA/NV Refuge Planning Office - April 2006 1 0.5 0 1
Miles
Agricultural Well
Domestic Well
Drain Pump
Lift Pump
Aquaduct
Canals
Pipelines
Refuge Boundary
San Joaquin River NWR Comprehensive Conservation Plan 39
land base increased and additional staff
support became available, these activities
were expanded to include additional species
and other resource concerns. Management
changed after acquisition of the large
floodplain area west of the San Joaquin
River. Currently, the Refuge is actively
managing upland and wetland habitats, as
well as restoring the riparian floodplain,
for the benefit of endangered species and
migratory birds. Refuge management units
are identified on Figure 8.
Habitat Management
Wetland Management
Water management is required for most of
the wetlands on the San Joaquin River NWR
due to alteration of the original or natural
hydrology of the area for agricultural
and urban purposes and needs. Water
for managed Refuge wetlands is supplied
through various lift pumps on the San
Joaquin, Stanislaus and Tuolumne rivers,
deep wells, Modesto Irrigation District
supplies, operational spill, and tailwater
from adjacent farming operations. It is
conveyed via irrigation district, privately-owned,
or Refuge-owned canals and other
infrastructure (Figure 6. Wetland Units).
Most of the wetland units have staff gauges
in place to monitor water levels. Current
wa