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 grasslanddependent 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 forestdependent 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 stepdown 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—a

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

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i

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f

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c

e

a

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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. Watershed / 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 T u o l u m n e C o u n t y C a l a v e r a s 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

Figure 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

O

.

rchard 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 Pla

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 

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 onsite 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 Pla

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 

San Joaquin River on the Refuge. 

Photo: USFWS
14 San Joaquin River NWR Comprehensive Conservation Pla
San Joaquin River NWR Comprehensive Conservation Plan  

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 Pl

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  

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 Pla
San Joaquin River NWR Comprehensive Conservation Plan  

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), ringnecked 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), blacknecked 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 welldrained 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 2

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 th

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 2

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 Pla

Figure 5: Land Cover Map

Beckwith Rd.

Gates Rd. Shoemake Rd.

Dairy Rd.

Center Rd

O

.

rchard Rd.

River Rd.

Stanislaus Rd.

132 132

33

Miller Lake

Tuolumne River

San

Joaquin

River

S at nislaus

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 Pla

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 o

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 nonnative 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). Semiarid 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 

(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), Pacificslope 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)  Compare

to other habitats, oak woodlands and 

riparian habitats, which support multiple 

Drake northern 

shoveler. 

Photo: Jerry Baldwin
32 San Joaquin River NWR Comprehensive Conservation Pla

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 

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)  Th

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 Pla

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, Walke

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 yellowbilled 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 territor

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  

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 wer

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 Pl

Figure 6: Refuge Roads and Facilities

Beckwith Rd.

Gates Rd. Shoemake Rd.

Dairy Rd.

Center Rd

O

.

rchard 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  

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 Pla

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

O

.

rchard Rd.

River Rd.

Stanislaus Rd.

132 132

33

Creekside

Pond

Upper

White

Lake

Miller Lake

Tuolumne River

San Joaquin

Rive r

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  

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, privatelyowned, 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 

water management practices have developed 

over time based on land acquisitions, 

partnerships, location in the Modesto 

Irrigation District service area, legal 

drainage obligations to upslope landowners, 

pumping constraints due to anadromous fish 

and the availability of operating funds to pay 

power costs. Refuge wetlands are managed 

as single units or complexes, as described 

below (Figure 7. Wetland Units Map).

Page Lake Complex

The Page Lake complex consists of Page 

Lake, Goose Lake, Watergrass Unit and 

Upper Miller Lake. Water is supplied from 

the Stanislaus River via a lift pump owned 

and operated by the Lyons family, a deep 

well owned by the Refuge, and operational 

spill from the end of the Modesto Irrigation 

District system. The management objective 

of Page and Goose lakes is to serve as 

winter roost habitat for Aleutian Canada 

geese and other migratory birds. Both 

lakes are drawn down in mid-April and not 

irrigated during the summer. The pond 

bottoms become vegetated with swamp 

timothy. In autumn, the lakes’ islands, 

shorelines and any tall vegetation, such as 

cocklebur, are mowed prior to floodup to 

provide loafing habitat and to maintain the 

open character necessary for goose roost 

ponds. Page and Goose lakes are flooded 

in early October prior to the arrival of 

Aleutian Canada geese and water levels 

are maintained through the winter. The 

Watergrass Unit, immediately west of and 

an extension of Page Lake, is managed to 

provide foraging habitat for ducks in the 

winter and shorebirds in spring. Irrigation 

tailwater from Refuge cornfields (grown as 

goose forage) immediately north of the unit 

is allowed to drain into the unit to promote 

a thick stand of watergrass. It is flooded in 

October with the arrival of waterfowl, and 

then drawn down slowly in April (as are 

Page and Goose lakes) to provide mudflat 

foraging habitat for migrating shorebirds. 

Miller Lake, immediately south of Page 

Lake and the Watergrass Unit, is managed 

as a permanent wetland. It is ringed by 

cattail and roundstem bulrush and provides 

habitat for grebes, marsh nesting birds and 

other wetland dependent wildlife.

Nelson Lake Complex

East and West Nelson lakes are managed 

as a complex of seasonal and permanent 

wetlands. These units are situated within 

the Modesto Irrigation District service 

area. Water is supplied by the irrigation 

district from spring through fall, and 

by a well owned and operated by the 

Lyons family during the winter. East 

Nelson Lake is the deepest (three to six 

feet deep) and is the only permanent 

pond in the unit. West Nelson Lake 

is a seasonal extension of East Nelson 

Lake and averages approximately 12 

inches deep when filled. It is drawn 

down in mid-April. It is irrigated by 

tailwater and subirrigation from adjacent 

irrigated pasture, and grows a mixed 

stand of swamp timothy, watergrass and 

smartweed. The unit is flooded up in 

late September or early October and the 
40 San Joaquin River NWR Comprehensive Conservation Plan

Figure 8: Refuge Management Units

Beckwith Rd.

Gates Rd. Shoemake Rd.

Dairy Rd.

Center Rd

O

.

rchard Rd.

River Rd.

Stanislaus Rd.

132 132

33

Miller Lake

Tuolumne River

San

Joaquin

River

Stanislaus

River

San Joaquin County

Stanislaus County

Mohler Tract

J

F

P

L

G

N H

C

E

K

I

O

A

B

D

M

Figure 8. Refuge Management Units

CA/NV Refuge Planning Office - April 2006 1 0.5 0 1

Miles

Maze Bottom

Page Field

So. Johnson Pasture

Vierra

M

N

O

P

Gardner's Cove

Hagerman

Johnson Corral

Lara

I

J

K

L

Buffington

Christman Island

Christman and Colwell Fields

Dairy Field

E

F

G

H

90 Acre Field

Airport Field

Arambel

Beet Field

A

B

C

D
San Joaquin River NWR Comprehensive Conservation Plan 4

water level maintained through the winter. 

The cattail-lined East Nelson Lake is 

used throughout the year by waterfowl, 

marsh nesting birds and other wetland 

dependent wildlife. West Nelson Lake is 

primarily used as a roost site by Aleutian 

Canada geese during autumn, but is 

heavily used from fall through spring 

by white-fronted geese (Anser albifrons 

frontalis), ducks, sandhill cranes, wading 

birds and shorebirds. 

Ringneck Pond

This wetland unit consists of a permanent 

cattail-dominated wetland adjacent to a 

Modesto Irrigation District canal and a 

meandering seasonal channel extending 

from the wetland across native uplands. 

The Modesto Irrigation District Canal 

supplies water to the unit. Management 

capabilities are extremely limited due to 

the poor condition of the water control 

structure and limited operating season of the 

Modesto Irrigation District canal system. 

Within that limitation, the management 

regime is to flood-up the seasonal channel 

in November and maintain levels until May. 

The area is heavily used by sandhill cranes, 

ducks, wading birds and shorebirds, and is 

minimally used by geese. 

White Lakes

Upper and Lower White lakes are the 

remnants of a larger White Lake complex 

that was drained and converted to 

agricultural fields in the early 1900s. Upper 

White Lake is supported by a high water 

table which is supplemented by upslope 

drainage from off-refuge lands. It is 

maintained as a permanent wetland and its 

management flexibility is limited. Prior to 

Service acquisition, Lower White Lake was 

recently agricultural cropland bisected by a 

series of ditches that conveyed drainwater 

from upslope agricultural fields to the San 

Joaquin River. The Service is required by 

law to allow surface tailwater to continue 

draining across the Refuge. In spring 2000, 

Refuge staff allowed these drain flows to 

recreate part of Lower White Lake by 

restricting flows at the drainage outlet and 

letting water back into lower portions of the 

former fields. Within one growing season, 

scattered clumps of cattail and roundstem 

bulrush vegetated the area, which was being 

used by waterfowl, pelicans, cormorants, 

wading birds, marsh-nesting birds and 

other wetland- dependent wildlife. White 

Lake is currently managed as a permanent 

wetland, but Refuge staff has the ability to 

alter wetland regimes by controlling flows 

from the outlet structure. Monitoring was, 

and continues to be, conducted to ensure 

that water levels remain lower that the 

upslope field drains and do not impact 

drainage of adjacent private lands. There is 

an opportunity to expand the size of Lower 

White Lake by recontouring the former 

wetland basins and installing additional 

water control structures. 

San Joaquin River Oxbows, Creeks and 

Sloughs

The Refuge staff has little-to-no control 

over water levels in the sloughs, creeks and 

oxbows that are present on the Refuge. 

Riley Slough meanders across the Mapes 

Ranch, Refuge lands and the Faith Ranch, 

and ultimately drains into the San Joaquin 

River. It is maintained by groundwater and 

surface tailwater from adjacent irrigated 

pastures and fields and has highly variable 

water levels. The Refuge portion of the 

slough is heavily vegetated by cattails and 

roundstem bulrush. It is used by ducks, 

grebes, marsh nesting birds, beaver, western 

pond turtles (Clemmys marmorota) and 

other wetland-dependent wildlife. The 

channelized Hospital Creek, on the west 

side of the Refuge, conveys agricultural 

drainwater from upslope sources to the 

San Joaquin River. The Service is required 

by law to allow continued drainage of 

this surface tailwater flow across Refuge 

lands. Water levels in Hospital Creek are 

variable. A narrow oxbow (former main 

channel of the San Joaquin River) extends 

from the San Joaquin River and forms the 

west side of Christman Island. The north 

end of the oxbow is connected to the river, 

while the south end is connected only during 

high water. It is maintained by river flows, 

groundwater and drainage from Hospital 

Creek. The oxbow and associated plant 

community supports ducks, cormorants, 

herons, egrets, riparian associated 
42 San Joaquin River NWR Comprehensive Conservation Plan

songbirds, western pond turtles and other 

wetland dependent wildlife. 

Vernal Pools

Vernal pools are managed by strictly 

protecting the sites and avoiding any 

earthmoving activities or other development 

on native uplands. Seasonal cattle grazing 

is used to manage for short grass and native 

forb communities associated with vernal 

pools.

Upland Management

Current management of upland habitats 

includes cattle and sheep grazing by 

cooperators, sharecropping and custom 

farming, invasive weed control, prescribed 

burning and floodplain riparian restoration 

by staff, cooperators and contractors (Figure 

5. Refuge Management Unit Map). 

Irrigated Pasture and Native Grasslands

Refuge pastures and native grasslands are 

grazed by cattle through a long-standing 

CLMA with the Lyons family to provide 

short grass foraging habitat for Aleutian 

Canada geese, other geese, sandhill cranes, 

long-billed curlew (Numenius americanus), 

white-faced ibis (Plegadis chihi) and 

mountain plover (Charadrius montanus). 

In consultation with the grazing cooperator, 

the Refuge develops annual grazing plans 

to produce the desired habitat conditions 

and maintain the long-term viability of 

pastures and native grassland communities. 

The irrigated pastures are under a year 

round grazing regime where cattle are 

rotated so individual pastures are grazed 

eight out of 12 months. Native grasslands 

are grazed seasonally from December 1 

through May 15. Due to the size of these 

grasslands, cattle are moved off and on 

individual units to avoid overgrazing. In 

wet springs, grazing may be extended to 

June 15 to control nonnative invasive weeds. 

Under terms of the CLMA, grazing fees 

owed to the Service by the Cooperator 

are exchanged for an equivalent value in 

pumping costs to provide water for wetlands, 

and the production of winter wheat for goose 

and crane forage on Refuge lands. 

Croplands

Corn, winter wheat and alfalfa are grown 

on Refuge lands to provide winter forage 

supplies for geese, sandhill cranes and other 

migratory birds. On the east side of the San 

Joaquin River (East Unit), approximately 

335 acres of corn (Page and Dairy Fields) 

are grown on a sharecrop basis. The 

cooperator (Lyons family) harvests his share 

as silage in September and continues to 

grow the Refuge share to full maturity as 

grain corn. The Refuge share of the corn is 

later mowed by Refuge staff in December 

or January to provide forage for geese and 

sandhill cranes. The acreage on which the 

cooperator’s share of corn was grown is 

disked down and planted to winter wheat 

in October for the Refuge. Irrigation dates 

for the wheat are timed to provide a suitable 

forage height (three to six inches) for geese 

arriving in October and November.

Forage crops are grown on the west side 

of the San Joaquin River (West Unit) to 

promote goose and sandhill crane use on the 

more recently acquired lands. A 130-acre 

alfalfa field, which was present prior to the 

Service acquiring the land in 2000, is being 

maintained by a cooperator via a CLMA. 

The management objective for this unit is 

not only to provide goose and crane habitat 

in the winter, but also year round foraging 

habitat for white-faced ibis and long-billed 

curlew. CLMA revenues owed to the Service 

are used to pay for Refuge infrastructure 

repair, water pumping costs and producing 

winter wheat. Approximately 100 acres 

of winter wheat are planted each fall as 

foraging habitat for geese and cranes. 

Fallow Agricultural Fields

Guided by this CCP, Refuge staff will restore 

the fallow agricultural fields to a mosaic of 

forested riparian and wetland habitats in 

much of the Refuge land in the floodplain 

west of the San Joaquin River. Interim 

management objectives for these lands are 

to limit the spread of introduced noxious 

weeds and provide short vegetation winter 

foraging areas for geese, sandhill cranes and 

other migratory birds. This is accomplished 

through mowing and prescribed burning 

by Refuge staff, and sheep grazing by a 

cooperator via a CLMA. 
San Joaquin River NWR Comprehensive Conservation Plan 4

Riparian Forest Management

Little or no active habitat manipulation 

occurs within the Refuge’s riparian 

habitats. Cattle are excluded from riparian 

corridors to allow understory and mid-story 

vegetation to be grown in areas that were 

grazed prior to acquisition. 

Invasive Weed Control

The Refuge uses an integrated approach 

using herbicide application, mowing, 

prescribed burning, and grazing to control 

invasive weeds. The amount of weed control 

to date has been limited due to staffing 

constraints. Past efforts have focused on 

herbicide application and mowing to control 

yellow star thistle on native grasslands on 

the East Unit and roadside corridors on the 

West Unit. Removing and foliar spraying 

of giant reed in the riparian corridor of the 

West Unit started in summer 2000 and is 

ongoing. 

Habitat Restoration

Recent land acquisition at the Refuge 

particularly in the western portion consists 

of fallow agricultural lands. A key element 

for Refuge management during the next 15 

years will be the restoration of these lands.

Wetland Restoration

The Refuge has been funded, through 

the CALFED program, to restore 300 

acres of wetland habitat in the West Unit. 

A restoration plan has been approved. 

Engineering design and construction will be 

initiated in the next few years.

Riparian Restoration

Much of the riparian restoration to date 

has been passive. Cottonwood, willow, 

valley oak and other species have become 

established on portions of the floodplain 

in recent years after floods and other high 

water events. Refuge staff and volunteers 

have also planted cottonwood, valley oak, 

California rose, box elder and other riparian 

plant species at Gardner’s Cove and the 

Christman Island area in 1997 and 1999. 

The Refuge has been funded, through the 

CALFED program, to restore 800 acres 

of riparian floodplain in the West Unit. A 

reforestation plan has been developed and 

a nursery was established on the Refuge 

in spring 2000 to supply cuttings for that 

reforestation effort. Planting and growing 

native trees, shrubs, forbs and grasses 

began in the winter/spring 2002 through a 

contract with Sacramento River Partners.

Wildlife Management and Monitoring

Wildlife management and biological 

monitoring activities to date have been 

conducted through the Aleutian Canada 

Goose Recovery Program, special projects 

funding and grants. Operational biological 

monitoring has been limited due to staff 

constraints, and focused on endangered 

species, flyway and state-wide surveys and 

avian disease management. 

Baseline information on migratory birds, 

mammals, fish, amphibians, reptiles and 

vernal pool invertebrates on the Refuge 

has been expanded through a biological 

inventory conducted as part of a CALFED 

habitat acquisition and restoration grant 

(Phase 1). Biological monitoring will be 

expanded through funding provided in a 

current CALFED grant (Phase 2). Data 

collected would be used to compare longterm wildlife population and habitat use 

trends as Refuge lands are restored and 

subsequently managed.

Avian Disease Control

The Refuge staff monitors roost ponds 

regularly during the winter for bird 

carcasses or birds displaying disease 

symptoms. Disease management activities 

follow the protocols established in the San 

Luis Complex/Grasslands Management 

Area Disease Contingency Plan (FWS 1991) 

and the Aleutian Canada Goose Disease 

and Contaminant Hazard Contingency Plan 

(FWS 1987). Mortality and morbidity from 

avian diseases is common in the Central 

Valley of California.

Low-level chronic die offs are ordinary, while 

large avian epidemics are rare. Generally, 

disease outbreaks occur seasonally in 

relation to high densities of waterbirds and 

extreme hot or cold weather conditions. 

In recent years, avian cholera has been 

the primary concern for refuge disease 
44 San Joaquin River NWR Comprehensive Conservation Plan

managers; however, other important 

diseases include avian botulism, fungal 

infections, lead poisoning and chemical toxin 

poisoning. 

Most disease control activities at the Refuge 

involve avian cholera and are concentrated 

around goose roost ponds. Avian cholera is 

a highly contagious bacterial disease that 

causes the greatest amount of mortality 

and morbidity in mid to late-winter when 

waterfowl are concentrated and daily 

temperatures remain below 10 degrees 

Celsius. Annual Refuge die-offs range 

from <50 to >1,200 per year. Beginning in 

November, the Refuge staff makes regular 

visits to roost ponds searching for carcasses 

or birds displaying disease symptoms. All 

recovered birds are removed from the site 

and either buried or shipped to the National 

Wildlife Health Research Center to confirm 

cause of death. Once an outbreak occurs, 

daily bird pick-up and disposal is initiated to 

limit the spread of pathogens to uninfected 

birds. Under severe epidemics, hazing of 

waterfowl is initiated to disperse populations 

and reduce the likelihood of disease 

transmission. Avian botulism, another 

disease more common in the southern end 

of the Central Valley, is uncommon in the 

northern San Joaquin Valley and has never 

been recorded at the Refuge. Control 

activities and documented losses are 

summarized in annual disease management 

reports. 

Aleutian Canada Goose Monitoring

Refuge staff monitor abundance and 

habitat use of Aleutian Canada geese to 

assess response to habitat management 

actions, document deaths and address crop 

depredation complaints. In joint operation 

with the CDFG personnel, refuge staff 

and volunteers conduct rocket-netting 

each December to band and neck-collar 

geese. As funding allows, intensive neck 

collar observations are made during 

winter to determine annual population 

levels and survival rates as outlined in the 

Pacific Flyway Aleutian Canada Goose 

Management Plan and meet Service 

Endangered Species Act obligations for post 

delisting monitoring.

 

Riparian Brush Rabbit Reintroduction

The Refuge staff participates with other 

Federal, State and university personnel in 

an interagency working group to plan and 

implement recovery actions for the federally 

listed endangered riparian brush rabbit. A 

reintroduction of riparian brush rabbits onto 

Refuge lands was initiated in the summer of 

2002. An elevated mound, to be used as an 

island refugium by the endangered rabbits 

during floods, was built and planted to 

vegetation in the summer of 2001. 

Other Migratory Bird Monitoring

Waterfowl

The Refuge staff participates in flyway and 

state-wide surveys by conducting ground 

counts to determine species and subspecies 

flock composition in the November dark 

goose surveys, periodic white goose 

surveys, annual midwinter waterfowl 

surveys and other special surveys. Refuge 

specific surveys are generally limited to 

nonsystematic observations to document 

use of restored and managed habitat. 

To promote nesting by wood ducks and 

other cavity nesting birds, nest boxes are 

maintained by Refuge staff and volunteers. 

Nest production data is forwarded to the 

California Waterfowl Association’s Wood 

Duck Program for inclusion in a state-wide 

database. 

Sandhill Cranes

The Refuge staff participates in flyway-wide 

greater sandhill crane surveys in October. 

Refuge-specific counts are conducted 

periodically to document sandhill crane use 

and abundance on restored and managed 

habitats. 

Shorebirds

Refuge specific surveys are generally limited 

to nonsystematic observations to document 

species occurrence and abundance on 

restored and managed habitat. 

Neotropical Migratory Land Birds

The Refuge, jointly with the Point Reyes 

Bird Observatory, has completed a 

three year study (2000 to 2002) of avian 

distribution, abundance, and productivity 

on Refuge riparian and floodplain habitats. 
San Joaquin River NWR Comprehensive Conservation Plan 45

A permanent MAPS (Monitoring Avian 

Productivity and Survival) station has 

been established on the Refuge. 

Heron and Egret Rookeries

Counts are conducted each spring to 

determine the status and abundance of 

great blue herons and great egrets nesting 

at traditional rookery sites on Christman 

Island. 

Vernal Pool Fauna Monitoring

Fauna associated with vernal pools are 

periodically surveyed. Sampling is done on 

a presence/absence basis rather than more 

intensive quantitative methods, to avoid 

impacting populations of federally-listed 

vernal pool fairy shrimp species and vernal 

pool tadpole shrimp. 

CALFED Restoration Monitoring

A multiyear biological monitoring 

program was initiated in the autumn of 

2001 by Refuge staff and contractors as 

part of the current CALFED habitat 

restoration grant (Phase 2). Elements of 

the monitoring program include migratory 

bird use of riparian, floodplain and wetland 

habitats; success of riparian brush rabbit 

reintroduction efforts; survival of native tree 

and shrub plantings; development of shaded 

riverine aquatic habitat; effectiveness 

of natural versus cultivated riparian 

restoration; and floodplain habitat changes 

that result from levee breeching. Depending 

on a request to amend the CALFED 

proposal, the monitoring would be expanded 

to inventory anadromous fish populations; 

monitor hydrological/fluvial processes 

following floodplain restoration; determine 

the status of the endangered species 

(giant garter snake) and valley elderberry 

longhorn beetle; and inventory primary 

pollinator (native bee) populations. 

Fire Management

One large wildfire (>500 acres) on Refuge 

lands occurs on average once every five 

years and several firestarts usually caused 

by trespassers occur each year. The borders 

of interior roads are usually mowed during 

early summer to reduce the occurrence 

and spread of any wildfire. The Refuge 

lands west of the San Joaquin River, due 

to their relative isolation and fuel type, 

pose the greatest risk for wildfire. Wildfire 

suppression capability is primarily provided 

through the San Luis NWR Complex fire 

crews and other fire-trained Refuge staff as 

detailed in the Complex-wide Wildlands Fire 

Management Plan. The Service also has a 

signed Memorandum of Understanding with 

the West Stanislaus County Fire Protection 

District to provide mutual firefighting 

support. If necessary, additional firefighting 

support from other Federal, State, and 

county agencies can be deployed through 

the State of California Master Mutual Aid 

Agreement. 

Prescribed fire has been used by the Refuge 

in an effort to control weeds and prepare 

lands for restoration work. Plans call for 

the continued use of fire for site preparation/

habitat maintenance, where it is determined 

to be the most beneficial and/or cost efficient 

way to produce desired results. Since 1999, 

prescribed burning has been used on 300 to 

500 acres annually at the Refuge.

Public Use Program

The Refuge has been closed to all public 

uses since its establishment. This CCP 

will provide guidance for the future visitor 

services of the Refuge. Limited public 

access has been made available for an 

observation platform, special events and 

tours led by Refuge staff. Occasional tours 

are also provided by the Modesto Rotary 

Club on the Faith Ranch. 

Law Enforcement and Public Safety

Law enforcement patrol and surveillance 

is conducted primarily by the San Luis 

Complex law enforcement officer and/or 

collateral-duty officers. Most problems 

encountered on the Refuge involve trespass 

into closed areas, illegal fishing, littering, 

marijuana cultivation, other drug-related 

activities, campfires and violation of 

Migratory Bird Treaty and Endangered 

Species Act regulations. Additional support 

is provided as necessary by Service Special 

Agents, CDFG wardens and other law 

enforcement agencies. 
46 San Joaquin River NWR Comprehensive Conservation Pla
San Joaquin River NWR Comprehensive Conservation Plan 47

All National Wildlife Refuges possess 

inherent distinctive characteristics and 

infrastructure which influence and impact 

management of the Refuge’s resources. 

These refuge-specific attributes at times can 

be challenges, needs and/or opportunities 

and can augment, enhance, diminish or 

facilitate the management of natural 

resources at a National Wildlife Refuge. 

In order to meet management goals and 

planning requirements, these challenges, 

opportunities, restrictions and needs of the 

Refuge must be identified and addressed. 

The following list contains attributes and 

characteristics of the San Joaquin River 

NWR which present either opportunities, 

needs and/or challenges to the management 

of the Refuge and which need to be 

considered for this planning process.

Water Quantity and Quality 

Supplies

Lack of a reliable water supply is a critical 

problem for this Refuge. Water is needed 

for management of wetland habitats, as well 

as for management of some upland habitats 

and riparian woodland restoration activities. 

Unlike most Central Valley National 

Wildlife Refuges, the San Joaquin River 

NWR does not receive a water allocation 

from the Bureau of Reclamation under 

the authority of the Central Valley Project 

Improvement Act. Only a small portion of 

the San Joaquin River NWR is within the 

Modesto Irrigation District and use of that 

water is restricted to their service area. 

Water used for Refuge management east of 

the San Joaquin River has been provided by 

the privately-owned Mapes Ranch as value 

due to the Service through their CLMA, as 

tailwater from adjacent grazing/farming 

operations or as water in excess of their 

needs. This CLMA does not generate 

4 Opportunities and Problems

enough fees to cover the cost of providing 

water. Supply of free tailwater and excess 

water will likely be limited in the future 

due to water conservation measures and 

potential water marketing. The availability 

of water from existing lift pumps on Refuge 

lands recently acquired by the Service is 

restricted due to limited resources, funding 

and other constraints. Service-owned 

wells, which could meet some water supply 

needs, are present on the Refuge but funds 

for their operation are lacking. The water 

supply available to the Refuge will impact 

the management of both upland and wetland 

habitats.

Infrastructure

Water production and associated delivery 

systems on Refuge lands are either in 

poor or in flood-damaged condition. Of 

the six lift pumps along the San Joaquin 

(five) and the Tuolumne (one) rivers, five 

need to be rehabilitated to make them 

operational and upgraded to meet OSHA 

safety standards, and all need fish screens 

installed to preclude impacts to threatened 

and endangered fish. The Service-owned 

canals and other water conveyance systems 

need to be repaired and in some cases, 

realigned to more efficiently deliver water 

to Refuge habitats. In addition, water used 

to manage lands east of the San Joaquin 

River must be transported across lands and 

through delivery systems owned by private 

owners. An alternate delivery system or 

formal conveyance agreements need to be 

developed and completed to ensure the longterm ability to provide water to the Refuge’s 

habitats.

 

Contaminants

The San Joaquin River is designated 

as an impaired waterway by the U.S. 

Environmental Protection Agency. Although 
48 San Joaquin River NWR Comprehensive Conservation Plan

water quality is generally acceptable, there 

are times of the year when this water should 

not be applied to Refuge wetlands due to 

potential long-term impacts to wildlife and 

habitat. Regional mandates associated with 

managing salt, boron, dissolved oxygen and 

selenium levels/loads may in future years 

restrict the ability of the Service to use its 

water rights to manage Refuge lands.

Surface drainage and tailwater are also 

used from upslope agricultural operations to 

manage part of the Refuge’s wetlands. The 

Refuge needs to ascertain if the quality of 

this water is acceptable for use in managing 

wetlands or whether it should be conveyed 

directly through the Refuge only to meet the 

legal drainage requirements for adjacent 

lands.

Water Rights and Other Rights 

Water is a critical element for management 

of the majority of lands in the Central Valley, 

including the management of wildlife on 

wildlands. Because of the high cost of water 

in the Central Valley, wetland management 

for wildlife on a per acre basis in the Central 

Valley is probably the highest in the nation 

(Heitmeyer et al. 1989). Access to water, as 

well as its quantity and quality, will impact 

land management activities. Water rights 

and agreements associated with land will 

influence and constrain natural resource 

management planning and decisions at the 

San Joaquin River NWR. The following 

sections detail these rights for Refuge lands.

Water Rights 

The availability and cost of water will impact 

the planned wildlife management programs 

which could occur at the San Joaquin 

River NWR. The State Water Resources 

Control Board conducted a review to 

determine the water rights associated with 

the San Joaquin River NWR. The State of 

California recognizes both appropriative 

and riparian water rights. The use of 

water for a beneficial purpose establishes 

an appropriative water right that must be 

accompanied by a water use permit issued 

by the State. A riparian water right is 

established by ownership of land abutting a 

natural water course. The review indicated 

that there are two appropriative and one 

riparian water right. These three water 

rights supplied water to a portion of the 

lands purchased from the El Solyo Dairy, 

Ed Hagemann and J. P. Lara (Rausch 1999).

There are also one appropriative and three 

riparian water rights on lands within the 

approved Refuge boundary that are not 

owned by the Service. This inquiry did not 

detail water rights with points of diversion 

outside the area considered (for example, 

the Modesto Irrigation District water right 

which serves the western portions of the 

Refuge, but the point of diversion is outside 

the vicinity of the Refuge). 

Drainage (White Lake Mutual Water 

Company) 

This agreement maintains that the 

West Stanislaus Irrigation District has 

drainage rights over land purchased from 

Hagemann (Mehlhaff and Hay, 1999), now

Service-owned land, which arise from a 

drainage reservation easement in the 1941 

deed conveying the land from Burkhard 

Investment Company to Hagemann’s 

predecessor (Mr. Pietro Rampion). The 

agreement protects those lands against 

seepage from the District’s canal, except 

those lands outside of the District. West 

Stanislaus Irrigation District obtained a 

Memorandum of Agreement on May 8, 1928 

with Burkhard Investment Company, which 

was later amended in 1939. The 

agreement addresses the right of access 

and construction for the White Lake Mutual 

Water Company intake channel, as well as 

the obligation to protect the Refuge land 

from canal seepage. 

In addition, the White Lake Mutual Water 

Company pays 35 percent of drainage 

facility maintenance and pumping costs 

for the drainage ditch system over land 

purchased from Hagemann (Mehlhaff 

and Hay 1999). White Lake Mutual

Water Company also has an obligation 

to operate drainage pumps on Refuge 

property purchased from J. P. Lara. The 

1928 agreement requires the landowner 

(now the Service) to “maintain the water 

level and seepage from the main canal at 22 

U.S.E.D. and at least eight feet below the 
San Joaquin River NWR Comprehensive Conservation Plan 49

natural, average ground level, the district to 

install, maintain the necessary pumps and 

operate the pumping of the seepage water.” 

Access across the White Lake Mutual Water 

Company canal was previously provided by 

three pile bridges, which are now unusable.

Rights-of Way

White Lake Mutual Water Company Right 

of Way

This agreement grants “free ingress, egress 

and regress” to White Lake Mutual Water 

Company and the “use of a strip of land 

thirty feet wide along the natural channel of 

Hospital Creek” extending from the existing 

creek crossing along the main river levee to 

the confluence with the San Joaquin River 

for “drainage ditch and road purposes.” The 

White Lake Mutual Water Company shall, 

at its own cost, maintain 20 cubic feet per 

second (cfs) capacity and replace the culvert 

when necessary.

Hetch Hetchy Aqueduct Right of Way

The January 2, 1924 agreement between 

the Central-California Orchard Company 

(Grantor) and the City and County of San 

Francisco, a municipal corporation, to 

“grant, bargain and sell” parcel 1 and 2 (as 

described in the indenture) to the “Grantee 

and to its successors (Service) assigns 

forever” upon which the center line of the 

two parcels is a part of the center line of the 

Hetch Hetchy Aqueduct right of way. The 

City and County of San Francisco own “all 

the lands of Grantor included within a strip 

of land 110 feet in width” along the aqueduct 

corridor (certain reservations and conditions 

are outlined in the official document). 

Easements also exist on Parcel 1 and 2 for 

three canals. Parcel 1 includes an easement 

for road purposes and Parcel 2 includes an 

easement for single pole transmission lines, 

conveyed to the Pacific Gas and Electric 

Company. 

Floodplain and Riparian Restoration

The majority of Refuge lands west of 

the San Joaquin River are abandoned 

agricultural fields that currently provide 

little benefit to riparian and wetland 

dependent wildlife species. A major 

Refuge initiative and need is to restore 

natural habitats for wildlife. A project to 

restore wetland and riparian habitats on 

approximately one-third of these lands has 

been funded and planning has been initiated. 

Additional habitat restoration funding is 

needed to restore the remaining floodplain 

to maximize benefits to riparian and wetland 

dependent species.

Grassland Communities

Central Valley grassland habitats have 

been severely altered over the past 150 

years. Exotic annual grasses, principally of 

Mediterranean origin, replaced the valley’s 

native perennial grasses, which probably 

dominated these grasslands. Restoration of 

native habitats is a critical element of Refuge 

management. Typically, techniques for 

restoring native Central Valley grasslands 

have not been successful on a large scale, 

or have been too costly. To reestablish 

native grasslands at the Refuge, successful 

methods based on reasonable costs will need 

to be adopted and/or developed.

Invasive Weeds & Other Exotic Species

Invasive weeds are non-native plants which 

have the capacity to invade and dominate 

a plant community. These invasive weeds 

frequently reduce the quality of the habitat 

to wildlife, are extremely costly to eradicate, 

resist control efforts and are a major source 

of concern for many natural resource 

managers in many regions. 

Non-native plants dominate major portions 

of the Central Valley landscape. Serious 

pest plants occurring in the Refuge’s 

uplands include yellow star thistle, perennial 

pepperweed, poison hemlock, Russian 

thistle, milk thistle, bull thistle and prickly 

lettuce. Infestations are greatest in fallow 

agricultural fields, roadsides, canal banks, 

and undergrazed pastures, as well as other 

disturbed sites. Efforts to control thistles 

need to be addressed within managed 

pastures, especially those undergoing 

rehabilitation. Control of these invasive 

weeds will improve the quality of upland 

wildlife habitat at the Refuge. 

A major effort is also required to control 

invasive weeds in areas being restored 

to natural riparian and wetland habitats. 
50 San Joaquin River NWR Comprehensive Conservation Plan

Perennial pepperweed is established 

throughout the Refuge’s riparian areas 

and stands of arundo are scattered along 

the banks of the San Joaquin River. These 

invasive plants, if left untreated, will crowd 

native plants and eventually dominate the 

riparian corridor, reducing the quality of 

the habitat for wildlife. Efforts need to 

be greatly expanded to control perennial 

pepperweed and ensure the eradication of 

arundo. At certain times of the year, the San 

Joaquin River can be heavily infested with 

water hyacinth. These floating plants have 

a rapid growth rate and high reproductive 

capabilities, which lead to clogged water 

delivery canals and impenetrable surfaces 

covering oxbows and other wetlands. 

Physical barriers and other control 

measures need to be established to ensure 

that hyacinth is not transported to Refuge 

wetland habitats.

The black rat is another invasive species that 

may be impacting the Refuge. Originally 

restricted to Europe and Asia, this species 

has colonized portions of North America. 

In California, the black rat is found in 

the Central Valley and coastal areas. Its 

preferred habitat is urban areas and stream 

courses (i.e., riparian habitat). The black rat 

is considered to have a negative impact on 

the endangered San Joaquin Valley woodrat. 

Although the black rat is known to occur at 

the Refuge, its abundance and impact on 

native fauna and flora is not known. Control 

programs regarding the black rat may 

become necessary if research indicates the 

woodrat or other indigenous species are 

severely impacted by this species. 

Threatened and Endangered Species

Threatened and endangered species are 

wildlife and plants designated by the 

Service as species whose population or local 

population is in danger of extirpation. The 

management of threatened and endangered 

species is a priority for the Service’s 

National Wildlife Refuge System. The San 

Joaquin River NWR supports and has the 

potential to benefit a number of these rare 

species. Programs conducted at the Refuge 

for threatened and endangered species 

can also set limits on other activities at the 

Refuge.

Riparian Brush Rabbit

This endangered rabbit remains in only four 

known locales -- one of which is the San 

Joaquin River NWR. The riparian brush 

rabbit’s decline is largely attributed to the 

loss of riparian forest in the Central Valley. 

The Refuge has the potential to significantly 

increase the population of this endangered 

species due to its present riparian forested 

habitats and plans for the restoration of 

additional riparian forest. Management for 

the riparian brush rabbit will require that 

the Refuge protect, manage and restore 

riparian habitats. 

San Joaquin Valley Woodrat

The presence of the San Joaquin Valley 

woodrat requires that it become a 

management priority. Similar to the riparian 

brush rabbit, the endangered San Joaquin 

Valley woodrat requires riparian forest as 

habitat, and in particular, an overstory of 

oak with a dense woody understory. The 

loss of riparian forest within the San Joaquin 

Valley has led a decline in this species. This 

endangered woodrat has been documented 

at the San Joaquin River NWR; however, 

no systematic surveys have been conducted. 

Initially, the Refuge needs to determine this 

species’ current distribution and abundance; 

future plans will depend on the outcome of 

this survey work.

San Joaquin Kit Fox

The endangered San Joaquin Kit Fox is the 

smallest canid in North America. Its habitat 

includes arid grasslands in the southern 

half of the Central Valley. No sightings of 

kit fox have been documented at the San 

Joaquin River NWR and the fox’s preferred 

habitat is scarce at the Refuge. The kit fox 

is known to occur directly to the west of 

the Refuge. The Complex will monitor the 

Refuge for kit fox use and, depending on its 

presence, modify its management programs, 

as needed, for the species. 

Bald Eagle

The threatened bald eagle is a sporadic 

winter visitor to the San Joaquin River 

NWR. It tends to be attracted to waterfowl 

concentrations on the Refuge. Eagles are 

largely absent from the Refuge during 
San Joaquin River NWR Comprehensive Conservation Plan 5

the breeding season. Wetland restoration 

efforts will likely benefit this species.

Aleutian Canada Geese

Although the Aleutian Canada goose was 

delisted as a Federal Threatened Species 

in March 2001, it remains a Service Species 

of Special Concern. The Endangered 

Species Act mandates that populations 

of recovered species be monitored for 

five years post-delisting to ensure that 

recovery goals continue to be met. The 

long-standing monitoring program at the 

Refuge needs to continue to comply with 

the law and document whether Aleutian 

Canada goose numbers remain stable, 

increase or decrease. This is part of a 

larger monitoring program and cannot 

be sustained with existing Refuge funds. 

Specific project funds are needed to 

implement this monitoring. In addition, onrefuge monitoring is necessary to evaluate 

use of Refuge habitat and address localized 

crop depredation complaints from nearby 

landowners. 

Least Bell’s Vireo

This federally-designated endangered 

songbird was documented as breeding for 

the first time at the Refuge in 2005. It used 

as breeding habitat, a unit with restored 

riparian habitat. Although once a common 

breeder in the Central Valley, least Bell’s 

vireo during the last few decades has been 

confined to southern California. Plans to 

restore significant tracts of riparian habitat 

at the Refuge will likely provide additional 

habitat for this species and the Refuge 

will need to monitor for the presence and 

abundance of this species during the next 

fifteen years.

Giant Garter Snake

The status of the federally-designated 

endangered giant garter snake at the 

San Joaquin River NWR is unknown. No 

systematic surveys have been conducted for 

this species, although the Refuge appears to 

contain suitable habitat. The Refuge needs 

to conduct surveys to determine if the giant 

garter snake is present and, if so, at what 

locations and habitats so that appropriate 

protective measures can be taken.

Anadromous and Other Listed Fish 

Species

Chinook salmon, Sacramento splittail, and 

potentially, steelhead trout can be impacted 

by Refuge management. Fish screens need 

to be installed on the Refuge lift pumps 

along the San Joaquin and Tuolumne 

rivers to ensure that juvenile fish are not 

negatively affected by pump operation. The 

design for levee breeching and floodplain 

restoration at the Refuge needs to be closely 

coordinated with fisheries biologists to 

avoid creating conditions that promote fish 

entrapment (Appendix H: Levee Breach). 

Because salmon and splittail fry would 

probably use the floodplain wetlands 

during high-water or flood years, wetland 

management must limit populations of 

predatory non-native fish. Through design 

and management, the floodplain wetlands 

have the potential to benefit Chinook salmon 

and Sacramento splittail populations by 

providing high quality rearing habitat. 

Valley Elderberry Longhorn Beetle

To date, there has been little effort to 

document the presence of the valley 

elderberry longhorn beetle at the Refuge 

or to inventory elderberry locations, 

the only habitat it uses. It is necessary 

to increase knowledge of the actual and 

potential distribution of this species on the 

Refuge to ensure that ongoing and future 

restoration incorporates its habitat needs 

and subsequent management contributes to 

species recovery.

Vernal Pool Invertebrate Species

Two federally-listed vernal pool 

invertebrates (i.e., vernal pool fairy shrimp 

and vernal pool tadpole shrimp) occur at 

the San Joaquin River NWR. Protection 

of vernal pool habitats at the Refuge needs 

to be established and rigorously enforced. 

Protocols for monitoring these invertebrates 

and their habitats also need to be developed 

and implemented.

State-Listed Species

The State of California has also developed 

its own list of threatened and endangered 

species. The species addressed in the 
52 San Joaquin River NWR Comprehensive Conservation Plan

preceding descriptions are federally 

designated threatened/endangered species, 

although many of these are also listed 

by the State. State-listed species known 

to occur or with the potential to occur at 

the San Joaquin River NWR include the 

greater sandhill crane, yellow-billed cuckoo, 

Swainson’s hawk, willow flycatcher and bank 

swallow. As a first step, the Refuge needs to 

determine the distribution and abundance 

of these species on the San Joaquin River 

NWR; then, the Refuge should develop 

and implement management plans for each 

species that is present. 

Fire

Wildfire is a natural process in most 

terrestrial systems. Wildfires are a major 

ecological process impacting vegetative 

succession and structure in many regions. 

Many species of plants and wildlife are 

adapted to fire disturbance. Climate, 

terrain, vegetation and drainage all 

influence the role and timing of wildfire 

occurrence and impacts. Some areas 

have short interval wildfire regimes, while 

others have extremely long interval wildfire 

regimes (greater than 500 years). Typically, 

grassland-dominated areas have short 

interval fire regimes and many species of 

grass are well adapted and suited to wildfire 

disturbance.

However, grassland habitats in California’s 

Central Valley, including the Refuge, 

have been severely altered over the past 

150 years. Exotic annual grass species 

principally of Mediterranean origin 

replaced native perennial grasses that likely 

dominated these grasslands.. Although 

there is some thought that the original fire 

regime in the Central Valley was a shorttime interval, there is little information 

available to land managers regarding 

suitable time intervals and seasonal timing 

for the use of fire in maintaining or restoring 

native grasslands, as well as other Central 

Valley native habitats. The Refuge will 

face challenges in determining suitable 

fire regime intervals and seasonal timing 

for the application of fire in terrestrial 

habitats, restoring native grasslands from 

exotic annual-dominated grasslands, and 

implementing a prescribed fire program to 

mimic a natural ecological process in an area 

with air quality problems.

Mosquito Abatement

Issues concerning mosquitoes and their 

associated problems (i.e., nuisance biting 

and vector-born diseases) are frequently 

encountered with aquatic habitats, 

particularly when they are in proximity 

to human habitations (Pratt and Moore 

1993)  Aquatic habitats and wetlands, a

well as irrigated pasture, provide conditions 

for breeding mosquitoes on the Refuge. 

The San Joaquin River NWR is situated 

within two local mosquito control agencies 

(Turlock and Eastside Mosquito Abatement 

Districts). Both are active districts and 

conduct mosquito monitoring programs 

(both larvae and adults), as well as disease 

monitoring programs (i.e., encephalitis, 

malaria and West Nile Fever) on the Refuge. 

Both districts also conduct larvaciding 

programs on the Refuge with the approval 

of the Refuge Manager and when conditions 

warrant. Control programs for adult 

mosquitoes are not permitted on the Refuge 

unless there is a declared public health 

emergency. In the past 15 years, only one 

public health emergency has been declared 

concerning a mosquito-born disease at the 

San Joaquin River NWR or its vicinity. 

Mosquito abatement on Refuge lands will 

require that the USFWS ensures that 

mosquito programs do not negatively impact 

natural resources and addresses legitimate 

mosquito nuisance and disease issues in 

neighboring communities. 

Public Use Programs

Public use programs can be extremely 

beneficial in promoting wildlife and 

National Wildlife Refuges, establishing 

community involvement with the Refuge, 

creating cooperative partnerships to benefit 

wildlife, offering environmental educational 

opportunities and providing wildlifedependent recreational opportunities for 

the public. The San Joaquin River NWR has 

never been opened to public use, with the 

exception of a recently-established roadside 

wildlife observation platform. 
San Joaquin River NWR Comprehensive Conservation Plan 5

Opening the Refuge to the public offers a 

major opportunity and challenge. This will 

require developing and implementing a stepdown public use plan for the Refuge that will 

outline which activities will occur, where they 

will occur, and what precautions are needed 

to assure that the public use program does 

not negatively impact the wildlife resource. 

National Wildlife Refuges have public use 

programs to allow for the enjoyment of our 

nation’s fish and wildlife resources. The 

Improvement Act for the National Wildlife 

Refuge System identified wildlife as the 

principal management goal of all Refuges. 

If the Refuge can accommodate a public use 

program, the Act indicates it should focus on 

six wildlife-dependent public uses—wildlife 

viewing, photography, hunting, fishing, 

environmental education and nature 

interpretation.

Law Enforcement

During its first 15 years, there has been no 

staff permanently stationed at the Refuge. 

As a result, a strong Service presence has 

been lacking and trespass has routinely 

occurred, as well as other illegal activities, 

such as all terrain vehicle use, dumping, 

marijuana cultivation and vandalism. To 

rectify this situation, over the past two years 

USFWS personnel have been permanently 

stationed at the San Joaquin River NWR. 

Additional measures are still required to 

protect Refuge natural resources and assure 

public safety, including increased public 

contact, patrols, interagency cooperation and 

coordination, boundary posting and signage. 

Cultural Resources

The Central Valley has a rich Native 

American cultural history. The cultural 

resources on the San Joaquin River NWR 

have not been determined or mapped, even 

though most of the present Refuge lands 

were previously disturbed (principally 

for agricultural activities) by former 

landowners. Any activity identified in this 

plan, including land development, grazing, 

and changes in public use, has the potential 

to impact cultural resources; however, 

Federal legislation (National Historic 

Preservation Act of 1966) protects cultural 

resources and requires agencies, such as 

the Service, to consider, and if necessary, 

mitigate the impacts of its projects on 

cultural resources before implementation. 

The Service will comply by consulting with 

the USFWS Region 1 Cultural Resources 

Team regarding management activities and 

programs at the San Joaquin River NWR. 

The Service is not proposing any project, 

activity or program that would result 

in changes in the character of, or would 

potentially adversely affect, any historic 

cultural resource or archaeological site. 

Refuge Farming Program

Irrigated pastures, which are part of the 

Refuge’s CLMA program, provide critical 

foraging habitat for Aleutian Canada geese, 

sandhill cranes, white-faced ibis and other 

migratory birds. Several of these pastures, 

especially those north of Highway 132, 

have not been rehabilitated or rotated for 

decades. Although the fields are maintained 

in a short-cropped condition by grazing, the 

grasses and forbs are decreasing in forage 

quality for wildlife. Ultimately, wildlife use 

of the pastures will decline. These pastures 

need to be rehabilitated by discing under 

the existing vegetation, reseeding with 

a mix of grass and forbs and controlling 

invasive weeds as pastures are established. 

Refuge funding is currently unavailable 

to accomplish this work, and the current 

CLMAs do not generate enough value 

to allow cooperators to rehabilitate the 

pastures in exchange for grazing fees owed 

to the Service. Pasture rehabilitation needs 

to be pursued through the USFWS Refuge 

Operating Needs (RONS) process and/or 

other funding initiatives.

The current practices of sharecrop 

production of corn and farming of winter 

wheat on the Refuge provide winter foraging 

habitat for geese, sandhill cranes, and other 

migratory birds; however, these practices do 

not provide any benefits for ground nesting 

birds during the breeding season. Normally, 

the wheat field is disced to prepare it for 

planting corn in the spring. Producing corn 

by a means other than sharecropping would 

free the cooperator’s share (80 percent) 

of this acreage, which could be left as a 

fallow wheat field in the spring and summer. 
54 San Joaquin River NWR Comprehensive Conservation Plan

Such a practice would provide high quality 

habitat for ground nesting birds such 

as waterfowl, northern harriers (Circus 

cyaneus), savannah sparrows (Passerculus 

sandwichensis), and other grasslanddependent songbirds. The value of the 

CLMA grazing at the Refuge is insufficient 

to pay for the production of corn on a custom 

farming basis. The farming program will 

provide limited benefits to ground nesting 

birds until another mechanism is found 

to pay for the production of corn, where 

the Refuge owns all of the crop for use as 

wildlife forage—thus reducing the acreage 

needed for planting.

Partnerships Partnerships are key to the management 

of National Wildlife Refuges. These 

partnerships can be with other agencies, 

private groups and/or individuals and 

have a focus on accomplishing some 

aspect of the Refuge’s mission. Although 

the San Joaquin River NWR’s direction 

to date has principally focused on land 

acquisition, the Refuge has formed 

significant partnerships for a variety of 

natural resource management issues and 

activities. Partnerships are beneficial to the 

Refuge, not only in accomplishing projects 

which would not have been possible with 

limited Refuge staff and funds, but also by 

expanding public outreach for the Refuge, 

bringing community input and support into 

the management process and providing 

for natural resource management on a 

landscape scale. 

Refuge partnerships have resulted in 

land acquisition, enhanced programs for 

endangered/threatened species, natural 

resource monitoring, and habitat restoration 

activities, among other projects. Partners 

involved with the Refuge include local 

landowners and representatives from the 

NRCS, California Department of Fish 

and Game (CDFG), CALFED Bay-Delta 

Program (CALFED), U.S. Army Corps of 

Engineers (Corps), Endangered Species 

Recovery Program, Central Valley Habitat 

Joint Venture, Tuolumne River Technical 

Advisory Committee, U.S. Fish and Wildlife 

Service’s Anadromous Fish Restoration 

Program (AFRP), Bureau of Reclamation 

(BOR) and Ducks Unlimited, Inc. These 

existing and potential partnerships for the 

San Joaquin River NWR will influence 

planning and management efforts.

Point Reyes Bird Observatory

The Point Reyes Bird Observatory and the 

San Luis NWR Complex initiated a project 

in 2000 to monitor songbird use of Refuge 

lands along the San Joaquin River between 

the Stanislaus and Tuolumne rivers. A 

large-scale riparian restoration project 

planned by the Refuge is in the planning 

stage and involves 3,300 acres of former 

agricultural lands within the floodplain. The 

objective of this partnership is to establish 

a long-term songbird monitoring program 

to determine the baseline condition of the 

bird community, assess bird population 

responses to the riparian habitat expansion 

and monitor songbird recolonization and 

use of restored areas. Prerestoration data 

on songbird abundance, distribution and 

reproductive success were collected in 

existing riparian habitat and in the fallow 

agricultural fields slated for restoration. 

Preliminary results from the first year’s 

data indicate the Refuge’s potential as an 

important area for songbirds.

San Joaquin River Resource 

Management Coalition

The purpose of this organization is “to create 

a clearly defined, landowner-led organization 

that partners with nongovernmental 

organizations and Federal, State and local 

agencies with diverse interest, mandates 

and fiscal responsibilities in the San Joaquin 

River to collaboratively and proactively 

address resource management challenges 

and can communicate more effectively across 

jurisdictional boundaries” (San Joaquin 

River Resource Management Coalition 

Workplan). The coalition would work 

together to increase political understanding, 

increase awareness of the importance of a 

balanced healthy river ecosystem, provide 

a forum to address resource management 

issues and address current and proposed 

legislation that affects the San Joaquin River.

Partnerships 

are key to the 

management 

of National 

Wildlife 

Refuges. 
San Joaquin River NWR Comprehensive Conservation Plan 55

Tuolumne River Technical Advisory 

Committee

The Tuolumne River Technical Advisory 

Committee (TRTAC) was formed as result 

of the 1995 Federal Energy Regulatory 

Commission (FERC) Settlement Agreement 

for relicensing the new Don Pedro Dam. 

The group is composed of representatives 

from Federal, State, and local agencies, nongovernmental organizations and interested 

private parties, and has been directed to 

coordinate and administer restoration and 

management activities on the Tuolumne 

River. The Service participates in the 

committee and provides funding for 

projects. The Refuge boundary includes the 

confluence of the San Joaquin and Tuolumne 

rivers, and approximately 1.5 shoreline 

miles of the Tuolumne River. Restoration 

and management of Refuge riparian habitat 

contributes to the objectives of the TRTAC, 

and in turn, upstream actions of TRTAC 

will improve the ecological health of Refuge 

lands and assist in attaining -large-scale 

ecosystem restoration goals of the Service. 

CALFED Bay-Delta Program

The CALFED Bay-Delta Program 

(CALFED) is a collaborative effort among 

23 state and federal agencies to improve 

water supplies in California and the health 

of the San Francisco Bay-SacramentoSan Joaquin River Delta watershed. It 

is cooperatively implemented by those 

signatory agencies through their respective 

program authorities and pertinent funding 

mechanisms. Restoration and subsequent 

management of Refuge lands directly 

contribute to the goals of CALFED’s 

Ecosystem Restoration Program. CALFED 

has become a funding partner with the 

Refuge through issuance of major habitat 

protection/restoration grants. Since 1997, 

the Refuge has obtained CALFED grants 

for land acquisition, habitat restoration and 

biological inventories/monitoring. 

Nonstructural Flood Control 

Alternative—Corps

The U.S. Army Corps of Engineers, 

Sacramento Office, has been working 

to develop a nonstructural flood control 

alternative on the west side of the Stanislaus 

River to address flooding problems at and 

adjacent to the San Joaquin River NWR. 

The purpose of this project is to replace 

existing flood control measures via levees 

with a more natural, resources-friendly 

alternative. The Corps’ proposal is a joint 

project with the Service to acquire lands 

for the Refuge protected by the levee; 

obtain and/or offer easements for areas that 

were not within the project boundary but 

received flood protection provided by the 

freeboard of the project levee; construct ring 

levees to protect structures and buildings 

on the Refuge; and work cooperatively to 

deauthorize the levees and create breeches 

in the levees to establish a more natural 

floodplain hydrology on Refuge lands. A 

joint-agency agreement for this project is in 

place. The Corps’ environmental assessment 

for this project has also been approved. The 

Service has already acquired the properties 

previously protected by the Corps’ project 

levee in accordance with the agreement and 

the Corps has obtained/offered easements 

to private landowners whose property is not 

within the project levee boundary but which 

received some level of flood protection. 

The ring levees to protect buildings on the 

Refuge are scheduled to be constructed the 

summer of 2004. 

Sacramento-San Joaquin River 

Comprehensive Study—Corps

In response to the January 1997 floods along 

the Sacramento and San Joaquin rivers, 

the U.S. Army Corps of Engineers and the 

California Reclamation Board are preparing 

the Sacramento and San Joaquin River 

Basins Comprehensive Study. The study 

will include a comprehensive master plan 

for flood damage reduction and ecosystem 

restoration within the Sacramento River 

and San Joaquin River basins. Due to 

the physical, socioeconomic and political 

complexities, and resource issues within the 

study area, the master plan will consist of 

different components and corresponding 

evaluation of the components. The study will 

develop broad scale systematic components 

and the resulting report will present a 

system-wide analysis of the physical and/or 

operation changes to the exiting flood control 

system. Other programmatic components 

Refuge 

partnerships 

have resulted 

in land 

acquisition, 

enhanced 

programs for 

endangered/

threatened 

species, 

natural 

resource 

monitoring, 

and habitat 

restoration 

activities.
56 San Joaquin River NWR Comprehensive Conservation Pla

could identify new or modified land use 

management and flood damage reduction 

programs. 

The study first looked at the flood control 

and environmental problems in the system. 

Topographic and bathymetric data of the 

Sacramento and San Joaquin River basins 

were collected, describing the contour of 

the existing land surface and river channels 

to be used in the analysis of hydraulic and 

environmental effects of potential measures. 

Using this data, hydrologic and hydraulic 

models of the Sacramento and San Joaquin 

Rivers systems were developed. These 

basin-wide models incorporated historic 

rainfall-runoff, reservoir operations and 

flood routing, including unsteady flow along 

the major river systems. A conceptual 

plan for an Ecosystems Function Model 

was developed. In combination with the 

hydrologic modeling, the Ecosystems 

Function Model will focus on physical 

processes that drive biological responses 

in river systems and floodplains and will be 

used to evaluate the effects of hydrologic and 

hydraulic changes on existing and potential 

aquatic, wetland and riparian habitats. 

The comprehensive study is scheduled 

for completion in the next few years. 

Complex staff have been interacting with 

personnel working on the Comprehensive 

Study to integrate issues involving the 

San Joaquin River NWR into the process. 

It is anticipated that the plan would be 

implemented in stages.

Highway 132 Realignment—Caltrans

The California Department of 

Transportation (Caltrans) began 

investigating the possibility of the expansion 

and/or realignment of Highway 132 

before the San Joaquin River NWR was 

established. Highway 132 is the east-west 

highway that roughly bisects the Refuge. 

Although the project has remained inactive 

for years, recent increases in traffic volume 

have made these improvements a higher 

priority. Currently, Caltrans anticipates that 

an expressway would be constructed within 

the 15- year planning cycle of this CCP. 

During the establishment of the Refuge in 

1987, the Service issued a formal letter to 

Caltrans stating that the Service would not 

oppose expanding Highway 132, but would 

work with the State agency and others to 

address and minimize impacts to the Refuge 

and meet environmental regulations. 

Anadromous Fish Restoration 

Program

The Anadromous Fish Restoration Program 

was established by the Secretary of 

Interior through the Central Valley Project 

Improvement Act, with the mandate to 

double the natural production of anadromous 

fish in Central Valley streams. The program 

is administered by the Service and BOR 

in cooperation with State agencies, such as 

CDFG and other partners. The three rivers 

present on the San Joaquin River NWR 

make it a key area for this joint program.

Local Landowners

The Refuge has greatly benefited from a 

long-term partnership with the Bill Lyons 

Sr. family, owners of the Mapes Ranch; 

and the Robert Gallo family, owners of the 

Faith Ranch. The owners of those two 

ranches have worked with the Service to 

provide high quality wildlife habitat. While 

conducting their regular ranching and 

farming operations, the Gallo and Lyons 

families have limited disturbance to wildlife 

on their properties, maintained waterfowl 

roost ponds and tolerated increasing 

levels of goose foraging on their pastures 

and fields. In previous years, the Service 

contracted with both ranches to grow crops 

exclusively for waterfowl. Currently, the 

Service has a cooperative land management 

agreement (CLMA) and sharecropping 

agreement with the Lyons family on Refuge 

lands. The Gallo family, in conjunction with 

a local Rotary Club and the Service, has 

implemented a regular tour program on the 

Faith Ranch and Refuge lands for school 

groups from Stanislaus County.

Cooperative Land Management 

Agreement (CLMA)

Since its inception, the San Joaquin 

River NWR has entered into a number of 

cooperative land management agreements 

with members of the community. These 
San Joaquin River NWR Comprehensive Conservation Plan 57

agreements allow a limited agricultural 

program (i.e., grazing, small grains, etc.) 

to occur which benefit both specific wildlife 

resources, as well as the cooperator. The 

CLMA process is a tool of the Refuge that 

allows an expanded management program 

for wildlife, while not depleting limited 

Refuge staff and funds. 

Other Restoration and Management 

Partners 

The San Joaquin River NWR has benefited 

from the research of many agency and 

non-agency personnel who have conducted 

annual Aleutian Canada goose monitoring 

on site as part of the Aleutian Canada Goose 

Recovery Program since 1975. Complex 

and CDFG staffs have jointly banded and 

neck-collared Aleutian Canada geese at 

the Refuge annually since 1995. Staff and 

students of CSU-Stanislaus and Modesto 

Junior College have assisted Refuge staff 

in goose banding and other management 

activities. The Complex staff is working 

jointly with the Service’s Endangered 

Species Office, BOR, the California State 

University—Stanislaus Endangered Species 

Recovery Program and CDFG to reintroduce the riparian brush rabbit onto the 

Refuge as part of its Recovery Program. 
58 San Joaquin River NWR Comprehensive Conservation Plan
San Joaquin River NWR Comprehensive Conservation Plan 59

Introduction

This chapter focuses on the goals, objectives 

and strategies selected for the management 

of San Joaquin River NWR. During 

the preparation of this Comprehensive 

Conservation Plan, the Service examined 

and analyzed various management 

alternatives for the San Joaquin River 

NWR to best achieve the mission of the 

National Wildlife Refuge System, Refuge 

purposes, vision statement and goals; it also 

considered the existing infrastructure of 

the Refuge as outlined in Chapters 1 and 

3 and the Refuge’s resource challenges 

and needs, listed in Chapter 4. Agencies, 

non-governmental organizations and the 

public provided input used to develop the 

management alternatives. The alternatives 

were examined for both natural resource 

management and public use activities at the 

Refuge. These alternatives were considered 

and their impacts were reviewed in an 

environmental assessment (EA) as part of 

this plan’s compliance with the National 

Environmental Policy Act (Appendix B). 

Prior Management Activities at the 

Refuge

The San Joaquin River NWR was 

established in 1987 and its original purpose 

was to provide winter habitat for the 

then endangered Aleutian Canada goose. 

Original fee title lands comprising the 

Refuge included the East Unit parcels 

and Christman Island. Since Service 

acquisition, the East Unit lands have been 

actively managed as winter habitat for 

the Aleutian Canada goose. In 1996, the 

Refuge developed a set of interim informal 

goals to guide Refuge management until 

a management plan could be developed. 

These interim goals include the following: 

n	Provide feeding and resting habitat for 

wintering waterfowl;

5 Management Goals, 

Objectives, and Strategies

n	Provide habitat and manage for 

endangered, threatened and/or sensitive 

species of concern;

n	Protect and provide habitat for 

neotropical migratory landbirds;

n	Preserve a natural diversity and 

abundance of plants and animals;

n	Provide an area for compatible, wildlifeoriented research; and

n	Provide public use activities such as 

wildlife observation, photography, 

environmental education, fishing, and 

hunting.

Although activities were conducted to meet 

these interim goals on the Refuge, the 

dominant management activities remained 

managing winter habitat for the Aleutian 

Canada goose. Expansion of the existing 

program was largely precluded due to a 

shortage of staff and funding, although 

groundwork was laid for future development 

of the Refuge’s programs. The principle 

public use activities at the Refuge were 

wildlife viewing and photography from an 

observation platform. The only prepared 

and approved plan for the San Joaquin River 

Refuge was the Wildland Fire Management 

Plan, completed by San Luis National 

Wildlife Refuge Complex in 2001, and a Spill 

Response Plan, completed in 2003. 

Goals, Objectives and Strategies to 

Support the Proposed Management 

Action

This section presents long-term guidance for 

the Refuge in the form of goals, objectives 

and strategies. Goals guide the future 

direction of the Refuge. Goals support 

the Refuge purpose and System mission 

by providing guidance regarding how the 

Refuge should operate and what the Refuge 

should be. Goals represent end results 

and provide management direction for the 
60 San Joaquin River NWR Comprehensive Conservation Pla

Refuge purposes. Each goal is supported 

by measurable, achievable objectives, where 

appropriate; these are the efforts or action 

items required to achieve the goals. The 

intent is to accomplish objectives during 

the duration of this plan; however, actual 

implementation may vary due to funding and 

staffing. Objectives, in most cases, provide 

quantitative benchmarks that indicate 

progress toward achieving goals. Strategies 

are specific actions or projects that would 

lead to the accomplishment of management 

objectives.

Five broad goals were developed for San 

Joaquin River NWR. They are consistent 

with the Refuge purposes, ecoregion goals, 

National Wildlife Refuge System goals, 

Refuge Improvement Act, Service policy 

and international treaties. These goals, 

objectives and strategies are detailed 

below. Figure 9 shows the proposed habitat 

management plan for the Refuge.

Goal 1 (Biological Diversity)

 

Conserve and protect the natural diversity 

of migratory birds, resident wildlife, 

fish and plants through restoration and 

management of riparian, upland and 

wetland habitats on Refuge lands.

Narrative: Healthy, high quality habitats 

are a key to functioning, self-sustaining 

fish and wildlife communities. Natural 

conditions that existed during the mid-1800s 

provide a reference point for comparisons 

with existing conditions. An assumption 

is that at this point in time, ecological 

processes were functioning at a natural 

frequency and intensity and were not as 

influenced, as they are today, by human 

activities (land clearing, water diversions, 

etc.). 

Native assemblages of fish and wildlife are 

best restored and maintained by providing 

a diversity of natural habitats typical of the 

ecoregion prior to European settlement. 

Restoring natural diversity is a desired 

direction for management of the San 

Joaquin River NWR. Some restoration at 

the Refuge can be accomplished passively 

by allowing natural processes to resume. 

However, because of regional changes in 

river hydrology, presence of flood control 

levees, the proliferation of invasive species, 

as well as other factors, many restoration 

activities will require direct action, such as 

planting trees and shrubs, breaching levees, 

recontouring leveled land, reintroducing 

wildlife, building water control structures, 

managing invasive species, rehabilitating 

derelict building sites, restoring fire 

regimes, etc. Once restored, various levels 

of management will be required to replicate 

natural processes and maintain those habitat 

conditions in the highly altered San Joaquin 

Valley ecosystem. This management will 

range from allowing periodic flood events 

to inundate and maintain natural river 

functions in the West Unit floodplain to 

actively managing wetland units, grazing 

uplands, mimicking natural fire regimes and 

controlling invasive weed species.

 

Objective 1. Restore and enhance 2,500 

acres of wetlands, riparian forest and 

upland habitats on Refuge lands within 

six years of this plan’s approval and 

restore and enhance an additional 1,000 

or more acres by the end of this 15 year 

planning cycle to provide the diversity 

of habitats necessary to support native 

assemblages of fish, wildlife and plants.

Foraging whitefaced ibis. 

Photo: Gary Powell
San Joaquin River NWR Comprehensive Conservation Plan 

Figure 9: Proposed Habitat Management for San Joaquin River NWR

Beckwith Rd.

Gates Rd. Shoemake Rd.

Dairy Rd.

Center Rd

O

.

rchard Rd.

River Rd.

Stanislaus Rd.

132 132

33

Miller Lake

Tuolumne River

San

Joaquin

River

Stanislaus

River

San Joaquin County

Stanislaus County

Figure 9. Proposed Habitat Management for San Joaquin River NWR

CA/NV Refuge Planning Office - April 2006 1 0.5 0 1

Miles

Fallow

Riparian

Permanant Wetland

Semipermanent Wetland

Seasonal Wetland

Irrigated Pasture

Wet Meadow

Vernal Pool

Native Pasture

Cropland / food plot

Developed

Canal

Approved Refuge Boundary
62 San Joaquin River NWR Comprehensive Conservation Pla

Narrative: Most of the existing Refuge 

lands have been highly altered through 

drainage, farming, wildfire suppression 

and flood control activities. Large scale 

restoration projects and active management 

will be required to recreate the natural 

diversity of habitats found on the floodplain 

and adjacent uplands of the San Joaquin 

River.

Strategies:

1.1.1 Complete the wetlands and riparian 

forest restoration and the uplands 

enhancement on the West Unit of the San 

Joaquin River NWR, as identified in the 

CALFED ERP-01-N08 habitat restoration 

grant by June 2004.

1.1.2 Coordinate with the staff of the FWS 

Anadromous Fisheries Recovery Program 

and other fisheries professionals to ensure 

that restored wetlands and riparian habitats 

support and enhance rearing, migration and 

spawning habitat for native fish species.

1.1.3 Work cooperatively with the U.S. 

Army Corps of Engineers to breach the 

flood control levees on Refuge lands west 

of the San Joaquin River as part of a nonstructural flood alternative program and 

facilitate natural flood events and restore 

natural floodplain function.

1.1.4 Finalize and implement the 

restoration plan to create riparian habitat 

and restore natural floodplain function on 

the Mohler Tract.

1.1.5 Develop and implement plans to 

restore and enhance wetland and riparian 

habitats in the East Unit focusing on the 

Page/Goose Lake complex, Quesma Field 

wetlands, Buffington Fields, Riley Slough, 

Nelson Lake and the Colwell/Christman 

fields and bottoms.

1.1.6 Develop and implement projects to 

protect and enhance riparian habitat at 

Christman Island and the Gardner’s Cove 

area, and restore eroded river stream 

banks to minimize erosion and subsequent 

sedimentation.

1.1.7 Develop and implement restoration 

projects for the remaining fallow 

agricultural lands outlined in the PreRestoration Plan for the West Units of the 

San Joaquin River NWR, as prepared by 

River Partners in 2000. 

1.1.8 Develop and implement projects 

to restore the West Unit’s current alfalfa 

field (former Arambel property) to riparian 

forest.

1.1.9 Prioritize proposed riparian 

restoration projects with areas and give 

the highest priority to those that provide 

corridors from lowland to upland habitats, 

are within the 100-year floodplain and are 

adjacent to existing riparian habitat.

1.1.10 Clean up and remove abandoned 

buildings, farming operation equipment 

and debris, concrete pads, trash dumps and 

unneeded fences. Restore these sites to 

natural habitats. 

1.1.11 Prepare a North American Wetlands 

Conservation Act project proposal for 

wetlands and riparian habitat restoration/

enhancement on the East Unit and parts of 

the former Vierra property for submittal in 

2003 and implement, if funded.

1.1.12 Prepare CALFED habitat 

restoration proposals (phases 3 and 4 of a 4-

phase project) as a follow-up to ERP-01-N08 

to continue habitat restoration of the West 

Unit; implement if funded.

1.1.13 Prepare restoration project funding 

requests through Service funding programs, 

the North American Wetlands Conservation 

Act and other sources. 

Objective 2. Manage approximately 

700 acres of seasonal wetlands 

and approximately 750 acres of 

semipermanent/permanent wetlands 

to meet the habitat needs of migratory 

waterfowl, shorebirds, sandhill cranes and 

other wetland-dependent wildlife.
San Joaquin River NWR Comprehensive Conservation Plan 

Narrative: The altered hydrology and loss 

of historic wetlands in the Central Valley of 

California requires that natural resource 

managers actively manage wetland habitats 

by manipulating water through its delivery 

and retention and by controlling vegetation 

and maintaining water control structures in 

order to provide a diversity of habitats for 

wetland dependent wildlife species. 

Strategies:

1.2.1 Develop a water management 

facilities inventory and wetland management 

plan for the San Joaquin River NWR and 

incorporate both into the San Luis NWR 

Complex Wetland Management Plan.

1.2.2 Prepare and implement annual drawdown and flood-up plans for seasonal and 

semipermanent wetlands at the Refuge. 

1.2.3 Maintain stable water levels in 

permanent wetlands such a Miller Lake, 

Nelson Lake and Lower White Lake to 

provide summer water and habitat for 

wildlife and limit encroachment by emergent 

vegetation.

1.2.4 Maintain a regular schedule of staff 

gauge water level readings to monitor water 

management and regulate water control 

structures and water deliveries to maintain 

prescribed water levels and provide 

maintenance flows. 

1.2.5 Control excessive robust vegetation 

(i.e., cockleburr, cattail, roundstem bulrush, 

etc.) in goose roost ponds and other wetlands 

through water management practices, preflood-up mowing, prescribed burning and 

herbicide application.

1.2.6 Conduct annual evaluations to see 

if management objectives are being met, 

units need to be rehabilitated and water 

control structures/delivery systems need to 

be replaced. Schedule and implement unit 

rehabilitation activities and water control 

structure/delivery system replacement, as 

needed.

1.2.7 Record unit prescriptions, 

management activities, staff gauge readings 

and other records and incorporate into a 

long-term database.

Objective 3. Manage 3,500 to 3,700 acres 

of riparian forest and floodplain habitat 

to meet the needs of neotropical migratory 

birds, colonial nesting waterbirds and 

other riparian forest associated wildlife. 

Narrative: Active management of riparian 

forest and floodplain habitats will be 

much less intensive than that required for 

wetlands. Once restored and established, 

natural processes will dominate in these 

habitats. Over time, floodwaters coming 

through the levee breaches will carve out 

channels and oxbows and recontour the 

floodplain on the West Unit. In addition, the 

disturbance effects of periodic flood flows 

will increase diversity by creating different 

age and species structures within the 

riparian forest communities. Nonetheless, 

certain management practices will be 

required to offset the impacts of altered 

hydrology, and to protect riparian habitat 

from the effects of adjacent land uses and 

Refuge operations. 

Strategies:

1.3.1 Promote the establishment of native 

riparian trees, shrubs and herbaceous plants 

after restoration projects are complete 

through periodic replanting, irrigation and 

weed control.

1.3.2 Breech levees to allow floodwaters to 

inundate the West Unit floodplain to benefit 

riparian habitat systems. 

1.3.3 Limit the amount of roads, grazing, 

food plots and unnecessary disturbance 

adjacent to riparian habitats to reduce 

negative edge effects, such as brown-headed 

cowbird nest parasitism.

1.3.4 Install fences around riparian habitats 

adjacent to pastures to preclude grazing 

damage.

1.3.5 Incorporate riparian forest habitat 

needs into the Refuge fire management 

plan and annual invasive weed management 

plans.
64 San Joaquin River NWR Comprehensive Conservation Pla

1.3.6 Repair eroded stream banks where 

appropriate to reduce sedimentation and 

stabilize trees.

Objective 4. Manage 1,250 acres of 

agricultural lands (irrigated pasture, 

alfalfa, small cereal grains and corn) and 

350 acres of native grasslands and oak 

savannah uplands to meet the habitat 

needs of sandhill cranes, arctic-nesting 

geese, other migratory birds and other 

grassland associated wildlife. 

Narrative: Since the early 1900s many 

species of migratory birds have become 

highly dependent on agricultural lands 

during part of their annual life cycle. There 

is a long history of geese, sandhill cranes and 

other migratory birds using the croplands 

and pastures of the Faith and Mapes 

Ranches, and that use is a major reason the 

San Joaquin River NWR was established. 

In addition, other unique wildlife, such as 

white-faced ibis and long-billed curlew, 

heavily use the grasslands and pastures for 

foraging. A portion of the lands that were 

farmed or grazed at time of acquisition, 

especially those on the East Unit, need 

to remain in that type of management to 

maintain the resource values that first 

attracted birds into the area. 

Few stands of native grasslands or oak 

savannah uplands remain in this part of the 

San Joaquin Valley. It is important that 

these plant communities on the Refuge be 

maintained and enhanced for the benefit 

of ground nesting birds and other wildlife 

associated with these habitats. Without 

grazing or other management, these habitats 

would become infested with invasive weeds, 

such as yellow starthistle, milk thistle and 

poison hemlock, thus reducing the habitat 

quality for wildlife.

Management of the agricultural lands 

and native grasslands for the benefit 

of migratory birds and other uplandassociated wildlife will be an integral part 

of the farming and grazing management 

program (see Goal 3, Objective 6 and Goal 4, 

Objectives 1 and 2). 

Strategies:

1.4.1 Continue livestock grazing through 

a CLMA on irrigated pasture and native 

grasslands to maintain short-cropped winter 

foraging habitat in accordance with annual 

grazing plans.

1.4.2 Limit grazing on native grasslands 

from December through May-June to 

accommodate invasive weed control 

objectives and allow vegetative growth for 

ground nesting birds. 

1.4.3 Continue growing corn and 

winter wheat for winter forage through 

sharecropping agreements and CLMAs. 

1.4.4 Begin growing alfalfa by 2004 through 

a CLMA to provide winter forage for geese 

and cranes. Work with the CLMA operators 

on ways to reduce pesticide use and 

minimize impacts of hay harvest on groundnesting birds. 

1.4.5 Protect existing young valley oak 

trees in areas being grazed and, where 

appropriate, plant additional oaks to 

increase the amount of oak savannah habitat. 

1.4.6 Incorporate upland habitat 

management needs into the Refuge fire 

management plan and the annual weed 

management plan.

Objective 5. Within two years, develop 

and implement an invasive weed 

management plan to reduce the area 

coverage of non-native invasive plants 

that adversely impact native plant and 

wildlife communities and meet Refuge 

habitat management objectives.

Narrative: Non-native invasive plants are 

present at varying degrees throughout 

the Refuge. They have the potential to 

dominate sites; in some locations, they have 

already proliferated, altering the vegetative 

community, lowering overall diversity and 

creating marginal or unsuitable habitat 

conditions for native plants and wildlife. 

The spread of invasive plants threatens 

successful restoration of riparian plant 

communities of the San Joaquin River 
San Joaquin River NWR Comprehensive Conservation Plan  

floodplain, maintenance of current plant 

communities in existing riparian forest and 

native grassland habitats, and successful 

production of wildlife forage in managed 

wetlands and cropfields. Species of greatest 

management concern on the Refuge include, 

but are not limited to, yellow starthistle, 

perennial pepperweed, arundo, poison 

hemlock, milk thistle, tobacco tree and salt 

cedar. 

Strategies:

1.5.1 Inventory the occurrence and map the 

distribution of non-native invasive weeds 

on the Refuge and incorporate into the GIS 

database to allow monitoring through time.

1.5.2 Develop and implement an integrated 

invasive pest management plan for the 

San Joaquin River NWR. Within the plan 

include weed management strategies for 

individual pasture units, cropland fields 

and native upland units. Incorporate 

specific needs and constraints associated 

with invasive management of wetlands, 

riparian and upland habitats into the plan. 

Incorporate integrated pest management 

principles, such as grazing, mowing, 

burning and herbicide application, into the 

management plan.

1.5.3 Conduct weed control and monitoring 

activities on the West Unit as outlined in the 

CALFED ERP-01-N08 restoration grant. 

1.5.4 Use grazing, planting of cover crops 

and other techniques to control the spread 

of invasive weeds in the fallow fields of the 

West Unit until they are planted to native 

trees and shrubs as part of the ongoing 

riparian restoration projects.

1.5.5 Assume responsibility for weed control 

of restored riparian areas in the West 

Unit after River Partners have met their 

restoration contract obligations.

1.5.6 Place a high priority on eradicating 

non-native invasive weed species, such as 

Russian knapweed and Himalaya berry, 

that are currently present in low levels but 

have the potential to become widespread 

throughout the Refuge.

1.5.7 Conduct regular monitoring to assess 

results of control activities and to detect the 

presence of any new infestations of current 

or newly established species. 

1.5.8 Continue to participate as a member 

of the multi-agency Northern San Joaquin 

Valley Weed Management organization.

1.5.9 Seek opportunities for funding pest 

management activities through local, State 

and Federal initiatives. 

Objective 6. Within 10 years develop a 

dependable water supply and delivery 

system, and ensure that at least 20,000 

acre/feet of water is available for Refuge 

use annually to manage habitats for 

native assemblages of fish and wildlife. 

Narrative: Adequate water supplies and 

the ability to efficiently move water is a 

critical component in the management of 

Refuges in the Central Valley of California. 

Water will be used on the Refuge to manage 

wetlands and agricultural habitats and for 

the restoration of riparian forests. 

Strategies:

1.6.1 Document annual water needs, status 

of existing water delivery infrastructure, 

existing water rights, water allotment from 

Modesto Irrigation District, existing well 

capacity, and potential water sources, and 

incorporate into a water management plan. 

Prescribed burn 

by Refuge staff to 

control invasive 

plants.

Photo: Perry Grissom
66 San Joaquin River NWR Comprehensive Conservation Pl

1.6.2 Continue to work with CLMA 

operators to provide water for management 

of the Refuge agricultural and wetland 

habitats.

1.6.3 Use groundwater supplies by 

upgrading existing wells if feasible and, 

where necessary, develop new wells to meet 

the water needs of the Refuge. 

1.6.4 Repair and fit with fish screens 

existing lift pumps on the San Joaquin and 

Tuolumne rivers so existing riparian rights 

can be employed for Refuge water needs.

1.6.5 Initiate negotiations with Modesto 

Irrigation District for additional water 

supplies to the Refuge. Consider using 

accretion supplies and well supplies.

1.6.6 Upgrade existing, and where 

necessary, construct new canals, ditches, 

pipelines and other water delivery 

infrastructure facilities necessary to manage 

existing and proposed Refuge habitats. 

 

Objective 7. Within 10 years ensure that 

Refuge water supplies meet Regional 

Water Quality Control Board (RWQCB) 

standards for use on wetlands and Refuge 

discharges from managed wetlands do not 

exceed total daily maximum load limits 

established by that Board.

Narrative: Water quality is an important 

aspect of Refuge operations and is critical 

to maintaining the health and productivity 

of fish and wildlife communities. Water 

discharges from the Refuge should not 

contribute to the degradation of the San 

Joaquin River. This is complicated by the 

fact the San Joaquin River, which is the 

predominant source of water for the West 

Unit, has been designated as an impaired 

waterway and the Refuge is forced to 

accept agricultural surface drainwater from 

upslope lands.

 

Strategies:

1.7.1 Collect published reports and 

documents on the water quality of existing 

and potential water supplies within five 

years to determine potential water quality 

problems.

1.7.2 Develop a monitoring program to 

determine the baseline water quality for 

Refuge lands and monitor Refuge water 

supply quality on a quarterly basis.

1.7.3 Work with local water districts to 

conduct voluntary assessments of quality of 

water delivered to the Refuge.

1.7.4 Ensure that water applied to Refuge 

wetlands does not exceed 2 parts per 

billion (ppb) selenium (minimum RWQCB 

standards). 

1.7.5 Clean up the dairy waste lagoon at the 

former Vierra dairy operation to preclude 

impacts to the Refuge’s water quality.

1.7.6 Work with the FWS Sacramento 

Ecological Services office to fund and 

implement water quality and contaminants 

assessments on the Refuge.

1.7.7 Work with NRCS and upstream 

landowners to reduce sediment loads of 

drainwaters coming onto the Refuge by 

implementing recommendations outlined 

in the U.S. Dept. of Agriculture Sediment 

Reduction Plan (USDA 1992) and,

where possible, implement those same 

recommendations on the Refuge to further 

reduce sediment flow into the San Joaquin 

River.

1.7.8 Participate in the Regional Water 

Quality Control Board process to establish 

total maximum load limits of salts, boron and 

other constituents in the San Joaquin River. 

Objective 8: Within two years, develop 

and implement a Refuge inventory and 

monitoring program that incorporates 

existing and new surveys/censuses of 

plants, fish and wildlife, as well as their 

responses to restoration/management 

activities that can be employed to guide 

the management of the Refuge. 

Narrative: Knowledge of the distribution 

and abundance of species, species’ needs and 

status is critical for the management of the 

Refuge. Biological monitoring is necessary 

to assess the status of fish and wildlife 

populations, as well as how they respond 
San Joaquin River NWR Comprehensive Conservation Plan  

to management actions. Management 

effectiveness can be evaluated and corrected, 

if needed, based on a monitoring program. 

Monitoring will consist of both long and 

short-term projects and be conducted by 

Complex staff, partners, contractors and 

other researchers. Some monitoring efforts 

will be conducted to meet Refuge data 

needs, while others will contribute to or be 

a part of larger-scale ecoregion, Flyway or 

National monitoring initiatives. 

Strategies:

1.8.1 Develop and implement a monitoring 

plan to determine the abundance, 

distribution and productivity of neotropical 

migratory landbirds, wetland dependent 

birds, mammals, reptiles, amphibians and 

fish using Refuge lands.

1.8.2 Work with both public and private 

partners to monitor threatened and 

endangered species found at the Refuge to 

facilitate their recovery (see Goal 3). 

1.8.3 Update inventories of fish, amphibian, 

reptile, bird and mammal species present 

in the established and restored waterways, 

wetlands, riparian areas and uplands of the 

Refuge. 

1.8.4 Develop and implement a habitat 

monitoring plan to measure habitat changes 

and results/impacts of restoration efforts.

1.8.5 Expand and update the Refuge GIS 

database to document habitats, land use 

practices and restoration project results. 

1.8.6 Integrate wildlife population data 

(i.e., abundance and distribution) with GIS 

habitat layers to facilitate management 

actions.

1.8.7 Work with USGS/BRD, universities, 

organizations and individuals to develop 

research projects regarding natural resource 

issues to guide management at the Refuge.

Objective 9. Restore natural processes 

where possible to ensure ecosystem 

function.

Narrative:

Ecosystem health 

depends not only 

on ecosystem 

components but 

also, the natural 

processes that drive 

ecosystem functions. 

Many natural 

processes that are 

vital to ecosystems, 

such as river events 

and wildfire, have 

been eliminated or 

suppressed by flood 

control structures 

and fire suppression 

programs 

respectively. Many 

of these natural 

processes maintain 

ecosystem diversity 

by their actions. 

Impediments 

preventing natural processes to function 

will be minimized or eliminated, if deemed 

appropriate.

Strategies:

1.9.1 Work cooperatively with the U.S. 

Army Corps of Engineers to breach the 

flood control levees on Refuge lands west 

of the San Joaquin River as part of a nonstructural flood alternative program and to 

facilitate natural flood events and restore 

natural floodplain function. (Same as 

strategy 1.1.3.)

1.9.2 Finalize and implement the restoration 

plan to create riparian habitat and restore 

natural floodplain function on the Mohler 

Tract. (Same as strategy 1.1.4.)

1.9.3 Develop and implement projects to 

protect and enhance riparian habitat at 

Christman Island and the Gardner’s Cove 

area, and restore eroded river stream 

banks to minimize erosion and subsequent 

sedimentation. (Same as strategy 1.1.6.)

1.9.4 Ascertain past and suitable fire 

regimes for habitat types at the San Joaquin 

River NWR to develop fire plans.

Great egret, a 

conspicuous species 

at the Refuge. 

Photo: Jerry Baldwin
68 San Joaquin River NWR Comprehensive Conservation Pla

1.9.5 Restore the role of fire through a 

prescribed fire program at the San Joaquin 

River NWR. 

1.9.6 Work with NRCS and upstream 

landowners to reduce sediment loads 

of drainwaters coming onto the Refuge 

through implementing recommendations 

outlined in the U.S. Dept. of Agriculture 

Sediment Reduction Plan (USDA 1992) 

and, where possible, implement those same 

recommendations on Refuge to further 

reduce sediment flow into the San Joaquin 

River. (Same as strategy 1.7.7.)

Goal 2 (Threatened and Endangered 

Species)

Contribute to the recovery of threatened/

endangered species, as well as the 

protection of populations of special 

status wildlife and plant species and their 

habitats.

Narrative: Federal and State threatened 

and endangered species and other special 

status species are a high priority for the 

management of the San Joaquin River 

NWR. The Refuge will aid in the protection 

and recovery of these species by maintaining 

and managing the habitats on which 

they depend, pursuing other measures, 

as needed, and participating in species 

recovery efforts. 

Objective 1. Reestablish two selfsustaining populations of riparian brush 

rabbits (Federal/State–Endangered) on 

Refuge lands within 10 years.

Narrative: The Riparian Brush Rabbit 

Working Group, comprised of the Service, 

BOR, CDFG, California Dept. of Parks and 

Recreation and CSU-Stanislaus Endangered 

Species Recovery Program is actively 

working to recover riparian brush rabbits 

from their endangered species status. With 

funding from the aforementioned Federal 

and State agencies, CSU-Stanislaus ESRP 

has conducted studies to better understand 

the ecology of the rabbit, established and 

run a captive propagation facility, released 

rabbits on the Refuge in 2002/03 to establish 

a population and is monitoring the status of 

the released rabbits. 

The Refuge is within the historic range of 

the riparian brush rabbit and is in proximity 

to an existing population at Caswell State 

Park. It has high potential to support the 

long term establishment of brush rabbit 

populations. The necessary habitat features 

required to enhance the area for this species 

include increasing the amount of California 

blackberry, California rose and other 

dense growing shrubs/forbs; expanding the 

riparian forest on the San Joaquin River 

floodplain; and creating vegetated, elevated 

mounds to provide refugia for the rabbits 

during flood events. 

Strategies:

2.1.1 Continue to work with ESRP and 

participate as a member of the Riparian 

Brush Rabbit Recovery Working Group 

to introduce captive-bred brush rabbits 

at two separate release sites and assist in 

monitoring their survival, productivity and 

distribution. 

2.1.2 Create elevated, earthen mounds in 

the floodplain to provide refugia during flood 

events and vegetate these areas with native 

blackberry, rose and herbaceous plants as 

escape cover.

2.1.3 Establish thick stands of native 

blackberry and rose along the banks of 

levees and ensure that patches of these 

plants are incorporated in riparian forest 

restoration plantings within the floodplain.

2.1.4 Increase the amount of riparian forest 

habitat and ensure that a mix of riparian 

forest growth stages exist on the Refuge. 

Objective 2. Maintain and enhance at 

least one self-sustaining population 

of San Joaquin Valley woodrats 

(Federal—Endangered) on Refuge lands 

consistent with recovery actions and 

other parameters established by the FWS 

Endangered Species Office.

Narrative: San Joaquin Valley woodrat 

recovery efforts are being conducted in 
San Joaquin River NWR Comprehensive Conservation Plan  

coordination with many of the participants of 

the riparian brush rabbit recovery program. 

CSU-Stanislaus ESRP is conducting 

research and monitoring at nearby Caswell 

State Park to better understand the 

ecology of the woodrat and the impacts 

of competition by non-native black rats. 

However, no direct management recovery 

actions are occurring for the species. The 

Refuge is within the historic range of 

the San Joaquin Valley woodrat, but it is 

unknown to what extent they presently 

occur at the Refuge. 

Strategies:

2.2.1 Determine the level of occurrence of 

the San Joaquin Valley woodrat at the San 

Joaquin River NWR.

2.2.2 Work with the FWS Endangered 

Species Office, ESRP and other partners 

to evaluate the suitability of habitat and 

feasibility, if needed, of reestablishing/

maintaining woodrats on the Refuge.

2.2.3 Participate in and foster any onRefuge population management projects 

initiated by the FWS Endangered Species 

Office.

Objective 3. Protect populations of 

vernal pool fairy shrimp (multiple species 

Federal–Endangered), vernal pool tadpole 

shrimp (Federal–Endangered) and 

California tiger salamander (Federal–

Candidate) by maintaining existing 

vernal pools (15 total; combined size < 1.0 

ac.), associated plant communities and 

surrounding micro-watersheds. 

Narrative: Multiple species of fairy 

shrimp, as well as vernal pool tadpole 

shrimp and California tiger salamanders, 

depend on vernal pools for survival. The 

most important components of preserving 

vernal pools are maintaining their natural 

hydrology. Vernal pools are supplied 

entirely by rainwater. To protect vernal pool 

habitats, the integrity of the underlaying 

claypan of the basin and topography of the 

micro-watershed must be preserved. An 

additional problem for vernal pools is that 

during dry years, upland plant species tend 

to encroach in the dry vernal pools, which 

results in thatch accumulation that hinders 

the growth of vernal pool plant species.

Strategies:

2.3.1 Map locations of vernal pools on the 

Refuge GIS database and document status 

of individual vernal pool communities. 

2.3.2 Continue the Complex-wide policy of 

no alteration of the topography of native 

uplands.

2.3.3 Use grazing to maintain short grass 

plant communities (3–6 in. high) and reduce 

thatch accumulation around vernal pool 

habitats.

Objective 4. Complete an abundance and 

distribution inventory of valley elderberry 

longhorn beetle (Federal–Endangered), 

giant garter snake (Federal–Threatened), 

willow flycatcher (State–Endangered) 

and western yellow-billed cuckoo (State–

Endangered) on the San Joaquin River 

NWR. Develop Refuge management 

plans for the species, if deemed necessary, 

within 10 years.

Narrative: Little is known regarding the 

status of these species on the Refuge. 

Information is required to determine if 

Refuge habitats are suitable for supporting 

populations of these species, and if they 

currently exist on the Refuge. Once their 

distribution and abundance on the Refuge 

is determined, restoration and management 

of habitats to meet species needs can 

be implemented, if needed and direct 

participation in recovery efforts initiated, as 

appropriate. 

Strategies:

2.4.1 Seek funding for species and habitat 

inventories through CALFED grants, FWS/

RONS projects, or other funding sources, 

and conduct inventories when funded.

2.4.2 Ascertain the distribution and 

abundance of valley elderberry longhorn 

beetle, giant garter snake, willow flycatcher 

and western yellow-billed cuckoo on the 

Refuge.
70 San Joaquin River NWR Comprehensive Conservation Plan

2.4.3 Incorporate the species and habitat 

inventories into the Refuge GIS database.

2.4.4 Develop and implement species 

management plans that incorporate habitat 

requirements from the literature and 

guidelines from species recovery plans.

Objective 5. Provide and enhance 

migration, spawning and rearing habitat 

for fall-run Chinook salmon Federal–

Threatened), Central Valley steelhead 

(Federal–Threatened), Sacramento 

splittail (Federal–Threatened), and any 

other listed fish species by establishing 

and maintaining a minimum of seven 

miles of shaded riverine aquatic habitat 

and 3,500 acres of floodplain habitat 

along the San Joaquin, Stanislaus and 

Tuolumne Rivers.

Narrative: The Refuge is downstream 

from tributaries where Chinook salmon and 

steelhead spawn and within the spawning 

area for Sacramento splittail. These species 

are currently excluded from most of the 

Refuge floodplain by the presence of flood 

control levees. Breaching on-Refuge levees 

as part of floodplain restoration and as an 

alternative flood control project will allow 

the river to assume a more natural pattern 

of flooding and inundation, giving these and 

other special status native fish species access 

to the floodplain during flood events. During 

periods of inundation, the restored floodplain 

can provide valuable spawning and rearing 

habitat for Sacramento splittail, and rearing 

habitat for salmon and steelhead smolts, 

thus contributing to the recovery these listed 

species. However, if designed or managed 

incorrectly, floodplain channels and wetlands 

could cause stranding and mortality of 

these same fish as the floodwater recedes. 

In addition, operation of any unscreened 

Refuge lift pumps along the San Joaquin, 

Tuolumne, and Stanislaus rivers could result 

in fish mortality. 

Strategies:

2.5.1 Coordinate with staff from the FWSAnadromous Fish Restoration Program 

and National Marine Fisheries Service to 

ensure that levee breaching and floodplain 

restoration is designed and implemented in 

ways that maximize spawning and rearing 

habitat benefits to listed and special status 

fish species, while minimizing potential for 

stranding. 

 

2.5.2 Implement levee breaching and 

riparian floodplain restoration as outlined 

in the CALFED ERP-01-N08 habitat 

restoration grant.

2.5.3 Develop a fisheries management 

strategy that is compatible with other 

Refuge management objectives and 

maximizes habitat benefits to listed and 

special status fish species. 

2.5.4 Work with partners to evaluate 

floodplain rearing potential, conduct 

monitoring to document actual use by and 

benefits to listed and special status species, 

and resolve any fisheries issues on Refuge 

lands.

2.5.5 Install fish screens on all Refuge 

riverine lift pumps to avoid entrapment 

of juvenile Chinook salmon, steelhead, 

Sacramento splittail or any other special 

status species of fish.

2.5.6 Seek funding sources and establish 

partnerships to continue additional riparian 

floodplain restoration and implement 

projects when funded.

Objective 6. Provide winter foraging 

and roost habitat for greater sandhill 

cranes (State–Threatened) by managing 

and enhancing 830 acres of irrigated 

pastures and native grasslands, 550 

acres of corn and cereal grain fields 

and 400 acres of roost pond habitat in 

conjunction with Aleutian Canada goose 

and other migratory bird management.

Narrative: Greater sandhill cranes 

winter on the Refuge in association with 

larger numbers of lesser sandhill cranes. 

Cranes are highly dependent on croplands 

and irrigated pasture, as well as native 

grasslands, for foraging habitat. They 

require shallow, open wetlands for use 

as mid-day loafing sites and night roosts. 
San Joaquin River NWR Comprehensive Conservation Plan 7

Cranes are less tolerant of disturbance 

than most other migratory birds using the 

Refuge. Management actions for greater 

sandhill cranes will be an integral part of the 

overall management of wetlands and uplands 

for migratory birds and other wildlife (See 

Goal 1, Objectives 2 and 4, and for Aleutian 

Canada geese see Goal 4.) 

Strategies:

2.6.1 Continue livestock grazing or other 

suitable methods on irrigated pasture and 

native grasslands to maintain short-cropped 

winter foraging habitat in accordance with 

annual grazing plans through a CLMA.

2.6.2 Continue growing corn and 

winter wheat for winter forage through 

sharecropping agreements and CLMAs.

2.6.3 Where compatible with other foraging 

habitat objectives, allow winter wheat to 

mature over the summer and then mow or 

disc down standing wheat to provide forage 

for cranes during autumn and early winter.

2.6.4 Manage wetlands to provide shallow 

(< 1 ft. deep) open loafing areas and roost 

sites.

2.6.5 Limit disturbance in crane roosts and 

foraging areas by maintaining sanctuaries.

2.6.6 Participate with other agencies 

and researchers in conducting Flyway-wide 

population surveys, population monitoring 

and other research. 

Objective 7: Provide habitat for and 

monitor least Bell’s vireo at the Refuge.

Narrative: This endangered species was 

first detected nesting on the refuge in 

2005. The vireo nested in recently restored 

riparian habitat. It is likely that the riparian 

habitat being restored at the Refuge 

will provide additional habitat for this 

endangered species as well as other riparian 

dependent wildlife.

Strategies:

2.7.1 Monitor presence and abundance 

of breeding pairs of least Bell’s vireo at the 

Refuge.

2.7.2 Document vegetation characteristics 

of vireo nesting habitat and use to guide 

riparian restoration and riparian woodland 

management.

2.7.3 Manage and restore 3,500 acres of 

riparian habitat at the Refuge.

 

Goal 3 (Aleutian Canada Goose)

Provide optimum wintering habitat for 

Aleutian Canada geese to ensure the 

continued recovery from threatened and 

endangered species status.

Narrative: Although Aleutian Canada 

geese have been delisted from threatened 

species status, they remain a species 

(subspecies) of special emphasis. Mandates 

of the Endangered Species Act and Service 

policies direct that management actions be 

taken to ensure that recovery is maintained. 

Because the Refuge continues to be the 

most important wintering area for Aleutian 

Canada geese and is critical for continued 

recovery, management to provide winter 

habitat will remain a priority of the Refuge. 

Objective 1. Manage and enhance a 

minimum of 500 acres of irrigated pasture 

and 350 acres of native grasslands as 

short grass foraging habitat (< 8 inches 

high) through grazing and other pasture 

management activities for Aleutian 

Canada geese and other wildlife. 

Narrative: Availability of short-cropped 

tender grasses is a critical component of 

the winter forage base for this small race 

of Canada goose. The birds feed on the 

fast-growing meristems (tips of the plants), 

which are the most tender portion of the 

plant and where the highest protein levels 

are concentrated. Aleutian Canada geese 

heavily use irrigated pasture during initial 

arrival in October and November, and 

irrigated pasture and native grasslands 

during late January until their departure 

in April. The availability of this habitat 

is especially important during the early 

spring months as the geese switch from 

a maintenance diet dominated by corn 

(high carbohydrate) to a higher protein 
72 San Joaquin River NWR Comprehensive Conservation Plan

grass diet to build fat reserves to meet 

the physiological needs associated with 

migration and subsequent reproduction. 

 

Grazing is the current, preferred method 

of maintaining short grass conditions 

rather than mowing, because grazing has 

proved to be compatible with goose use, 

is more economical than mowing and does 

not promote thatch build-up. Grazing 

is conducted at the Refuge by private 

individuals through a CLMA.

Strategies:

3.1.1 Continue grazing on irrigated pasture 

and native grasslands via a CLMA(s) as 

needed in accordance with annual grazing 

plans.

3.1.2 Use a combination of force account 

and CLMA operators to mow and apply 

herbicides to irrigated pasture, as necessary, 

to control weeds such as cockleburr, milk 

thistle and yellow starthistle. 

3.1.3 Work with CLMA operators to 

temporarily flood portions of pastures that 

receive high goose and other wildlife use 

during October and November to create wet 

meadow conditions.

3.1.4 Submit a FWS/RONS proposal to 

rehabilitate a rank pasture in the Johnson 

Corral Field and implement, if funded. 

Objective 2. Provide a minimum of 115 

acres of grain corn and 430 acres of winter 

wheat and maintain an additional 200 

acres of foraging habitat by 2004. 

Narrative: Most species of geese in North 

America, including Aleutian Canada geese, 

have become dependent on agricultural 

crops for their winter forage base. Growing 

grain (corn) and green forage (winter wheat 

and alfalfa) on the Refuge provides a high 

quality diet to meet the nutritional needs 

of wintering Aleutian Canada geese and 

reduces the amount of crop depredation 

caused by geese on nearby private lands. 

The carbohydrates provided by corn are 

important in maintaining body condition 

during the winter months and corn forms 

the major part of the diet from late 

November to early February. Winter wheat 

and alfalfa are heavily used by the geese 

from the time of initial arrival in October 

until final departure in April. As with grass, 

the higher protein levels associated with 

winter wheat and alfalfa are important in 

building fat reserves for spring migration 

and the subsequent reproductive cycle. Geese using crop 

field on Refuge.

Photo: Gary Powell
San Joaquin River NWR Comprehensive Conservation Plan 7

However, by late February, much of the 

winter wheat has been eaten out, or where 

not foraged upon, has grown too tall and 

rank to be attractive to geese. 

Strategies:

3.2.1 Continue growing corn and winter 

wheat on the East Unit through use of share 

cropping agreements and CLMAs.

3.2.2 Reduce reliance on share cropping of 

corn if the CLMA program is expanded (on 

any newly acquired lands or alfalfa fields) 

and sufficient CLMA credits are generated 

to allow direct funding of corn production.

3.2.3 Grow approximately 80 acres of winter 

wheat through a CLMA or force account on 

the West Unit.

3.2.4 Mow standing corn in sequential 

blocks from late November to early January 

to provide grain forage.

3.2.5 Assume management of alfalfa fields 

in the North/South Christman Fields after 

December 2003 through a CLMA. 

3.2.6 Maintain an additional 200 acres 

of goose foraging habitat by CLMA in 

the agricultural field north of Beckwith 

Road (Buffington property) if the parcel is 

acquired. 

Objective 3. Manage Page, Goose and 

Nelson Lakes (250 acres combined) as 

roosting and loafing habitat, and create 

a 60-acre roost pond in the Christman/

Colwell Fields area by 2010. 

Narrative: Shallow wetlands that provide 

areas for mid-day loafing and night roosts 

are a critical component of wintering habitat 

for Aleutian Canada geese. These areas are 

necessary for resting, preening, maintaining 

social bonds and providing security from 

predators. Important features of such 

roost ponds include an open aspect with 

limited emergent cover that has islands 

with low vegetative cover and having 

an open shoreline on at least part of the 

wetland. Page, Goose and Nelson Lakes 

have been the main roost pond sites to date, 

but additional roosting and loafing habitat 

will be necessary as the goose population 

increases. 

Strategies:

3.3.1 Maintain Page and Goose Lakes as 

open aspect seasonal wetlands and Nelson 

Lake as a permanent pond.

3.3.2 Graze or mow shorelines and islands 

of roost ponds prior to flood-up to provide 

loafing habitat for geese.

3.3.3 Create and subsequently manage as 

a seasonal wetland a 60-acre roost pond 

on the west side of the Christman/Colwell 

Field area adjacent to the San Joaquin River 

levee.

Objective 4. Provide 1,200 -1,400 acres 

of sanctuary in the foraging and roost 

areas of the East Unit by minimizing 

disturbance from public use and other 

disturbance factors in those areas. 

Narrative: Migratory birds, including 

Aleutian Canada geese, require disturbancefree areas in which to rest and feed. 

Although Aleutian Canada geese can be 

tolerant of human presence in certain 

feeding areas at the Refuge, excessive 

disturbance causes birds to flush and 

relocate to other areas, resulting in loss of 

feeding opportunity, expenditure of nutrient 

reserves and added stress. These impacts 

are especially critical in late winter and early 

spring, when geese are actively acquiring 

nutrient reserves for spring migration and 

the subsequent reproductive cycle.

Strategies:

3.4.1 Restrict public use in the Goose Lake/

Page Lake and Dairy Field/Page Field area 

to the viewing platform site along Beckwith 

Road. 

3.4.2 Design any photo blind or walking trail 

developed east of the Dairy Field so that 

disturbance to Aleutian Canada geese and 

other migratory birds is minimized.

3.4.3 Keep Johnson Corral fields, Beet 

Field, Maze Bottoms, 90-Acre Field and 
74 San Joaquin River NWR Comprehensive Conservation Plan

Colwell/Christman fields and bottoms closed 

to public use.

 

Objective 5. Minimize losses to avian 

cholera and other diseases by conducting 

regular disease monitoring annually 

from December through April and by 

management of roost pond water levels. 

Narrative: Avian cholera is the primary 

disease that affects waterbirds at the 

Refuge and in the Northern San Joaquin 

Valley. Recent research indicates that the 

bacterium is endemic in certain waterfowl 

populations and that outbreaks can be 

triggered by bird to bird transmission 

during periods of overcrowding and stress. 

Birds can die quickly after exposure and 

once an outbreak occurs, large numbers can 

die in a short period of time. Past outbreaks 

at the Refuge have coincided with the 

presence of large numbers of snow and Ross’ 

geese and periods of cold foggy weather.

Strategies:

3.5.1 Conduct weekly surveys for the 

presence of sick or dead geese around the 

roost ponds from December through April. 

Survey frequency will be increased during 

periods of cold, foggy weather or if diseased 

birds are encountered.

3.5.2 Monitor turbidity of water in roost 

ponds and provide flushing flows to maintain 

good water quality and clarity.

3.5.3 Implement disease outbreak 

notification and control activities procedures 

as outlined in the

San Luis NWR Complex Disease 

Contingency Plan and the Aleutian Canada 

Goose Disease and Contamination Hazard 

Contingency Plan. In the annual work 

plan, a Refuge staff member will be given 

responsibility for disease monitoring, 

notification and coordination of disease 

control activities

3.5.4 Submit specimens picked up in 

disease control activities to the National 

Wildlife Health Research Center for official 

confirmation of disease outbreaks. 

3.5.5 Incorporate documentation of disease 

losses and disease control activities into 

the San Luis NWR Complex-wide annual 

disease reports.

Objective 6. Manage habitat and 

populations in the context of FWS postdelisting obligations and Pacific Flyway 

management objectives.

Narrative: The Endangered Species Act 

requires that species be monitored for 

five years following delisting to ensure 

recovery goals remain accomplished. Once 

Aleutian Canada geese were delisted, 

management authority shifted from the 

Service’s Endangered Species Office to its 

Migratory Bird Management Office, and the 

species was incorporated into the Flyway 

Council process. An Aleutian Canada Goose 

Management Plan, which will be updated 

every five years, has been approved by the 

Pacific Flyway Council. Since most of the 

Aleutian Canada goose population winters 

on the Refuge, management and monitoring 

actions taken here will be coordinated with, 

and be an integral part of, larger scale 

population management of the subspecies. 

Strategies:

3.6.1 Coordinate with the FWS Region 7 

Endangered Species Office on recovery 

issues for the five years following delisting.

3.6.2 Participate as an advisor of the 

Aleutian Canada Goose Management 

Subcommittee of the Pacific Flyway Study 

Group. 

3.6.3 Monitor Aleutian Canada goose 

use of the Refuge and surrounding lands 

to determine numbers present, evaluate 

effectiveness of habitat management and 

document crop depredation issues. 

3.6.4 Band and neck-collar geese on an 

annual basis in partnership with California 

Department of Fish and Game.

3.6.5 Conduct population and off-Refuge 

distribution monitoring to the extent 

permitted by funding from the Endangered 

Species or Migratory Bird programs.
San Joaquin River NWR Comprehensive Conservation Plan 75

GOAL 4 (Ecosystem Management)

Coordinate the natural resource 

management of the San Joaquin River 

National Wildlife Refuge within the context 

of the larger Central Valley/San Francisco 

Ecoregion.

Narrative: Although the San Joaquin 

River NWR contains significant wildlife 

resources, including on a national level for 

species such as the Aleutian Canada goose 

and riparian brush rabbit, the surrounding 

land use and its management impacts 

the natural resources within the Refuge. 

Working cooperatively with both public and 

private entities provides the opportunity 

to affect natural resource management on 

a landscape or ecoregion level. Resources 

of the Refuge which can be addressed at 

this larger scale include migratory birds, 

anadromous fish, water issues, endangered 

and threatened species, contaminants, 

habitat patch size and riparian corridors, 

amongst others. 

The U.S. Fish and Wildlife Service has 

divided the nation into ecoregions to 

coordinate natural resource management. 

The San Joaquin River NWR is situated in 

the Central Valley/San Francisco ecoregion 

which includes the San Joaquin and 

Sacramento valleys and their drainages, 

as well as the Sacramento delta. This 

ecoregion contains significant wetland 

habitats which support some of the largest 

waterfowl and waterbird concentrations in 

the Pacific Flyway. 

Objective 1. Seek the acquisition of lands 

for the San Joaquin River NWR from 

within the approved Refuge boundary 

from willing landowners.

Narrative: Approximately half the acreage 

in the approved Refuge boundary has been 

purchased. The remaining lands are in 

private ownership. These lands have been 

previously identified as having suitable 

or potential significant wildlife values. 

Acquisition of lands within the approved 

Refuge boundary will enhance existing 

wildlife resources on present Refuge 

lands and enhance wildlife resources by 

increasing the land base; it will also provide 

for increased flexibility in the management 

of wildlife resources and offer greater 

opportunities for wildlife-dependent public 

use at the Refuge. 

Strategies:

4.1.1 Maintain a database of private lands 

within the approved Refuge boundary.

4.1.2 Work with the Service’s Region 1 

Realty Office on the acquisition of the 

Buffington parcel.

4.1.3 Work with the Service’s Region 1 

Realty Office on the acquisition of any 

private land parcels within the approved 

Refuge boundary as they become available 

from willing sellers.

Objective 2. Identify and acquire lands, 

outside the current acquisition boundary, 

with key natural resource features 

appropriate for inclusion into the San 

Joaquin River National Wildlife Refuge.

Narrative: Opportunities to benefit wildlife 

at the San Joaquin River NWR exist outside 

of the present Refuge acquisition boundary. 

Lands outside the 

current boundary 

offer the potential for 

increasing the amount 

of both wetland and 

riparian habitats, 

as well as offering 

the possibilities 

for increasing the 

connectivity of Refuge 

lands with similar 

wildlands in the San 

Joaquin Valley.

Strategies:

4.2.1 Expand the 

San Luis NWR 

Complex’s Geographic 

Information System 

(GIS) capabilities 

over the next ten 

years to include lands 

outside the acquisition 

White-crowned 

sparrow, a common 

winter songbird.
76 San Joaquin River NWR Comprehensive Conservation Pla

boundary of the San Joaquin River NWR, 

particularly in regards to riparian corridors.

4.2.2 Identify lands outside of the approved 

acquisition boundary for the San Joaquin 

River NWR which have key or the 

potential for key natural resources and/or 

would protect or enhance existing Refuge 

resources.

4.2.3 Work with the Service’s Region 

1 Realty Office to expand the Refuge’s 

acquisition boundary, if deemed appropriate, 

for the acquisition of land currently outside 

the boundary. 

Objective 3. Manage the U.S. Fish and 

Wildlife Service’s easement program on 

private lands for the benefit of wildlife 

within the acquisition boundary of the 

San Joaquin River NWR and explore the 

potential for additional wildlife easements 

in the vicinity of the Refuge.

Narrative: Service easements on private 

lands provide benefits to wildlife at lower 

cost than Refuge land acquisition, although 

they do not provide the same degree of 

flexibility of land management and overall 

benefit to wildlife. However, easements 

provide an opportunity to increase the 

level of protected habitats for wildlife 

surrounding Refuge lands and yield 

added benefits for wildlife when full land 

acquisition is neither feasible nor desirable. 

Strategies:

4.3.1 Monitor existing easement agreements 

with private landowners to ensure program 

compliance and wildlife benefits.

4.3.2 Identify and implement natural 

resource projects to benefit wildlife on 

easement lands to be funded through the 

Service’s Partners for Fish and Wildlife 

Program or other funding mechanisms.

4.3.3 Seek additional lands within the 

Refuge’s acquisition boundary for the 

Service easement program, if deemed 

appropriate. 

Objective 4. Create and cultivate 

partnerships, wherever possible, with 

other landowners including agencies, 

organizations, businesses, universities 

and/or private individuals, to coordinate 

and foster natural resource management 

in the ecoregion. 

Narrative: In addition to Refuge 

management, other ecosystem management 

efforts are being undertaken along this 

portion of the San Joaquin River. The U.S. 

Army Corps of Engineers’ Comprehensive 

Study (see Chapter 1, Other Projects), 

the San Joaquin River Management Plan, 

NRCS’ Wetlands Reserve Program and 

others are seeking to connect natural lands 

and foster natural resource management 

along the San Joaquin River. Refuge 

involvement with these initiatives will 

provide greater benefits for wildlife and the 

San Joaquin River NWR.

Strategies:

4.4.1 Provide natural resource information 

collected at the San Joaquin River NWR 

to other interested agencies, groups and 

researchers to foster collaborative efforts 

and support ecoregion-wide natural resource 

databases.

4.4.2 Participate in the regional planning 

for the conservation of the riparian brush 

rabbit, San Joaquin Valley woodrat, Aleutian 

Canada goose, California tiger salamander, 

vernal pool communities, San Joaquin kit fox 

and other species of special concern.

4.4.3 Participate in joint natural resource 

projects at the ecoregion level involving 

partners on issues pertaining to the 

management and protection of resources at 

the San Joaquin River NWR.

4.4.4 Develop a Refuge Friends group with 

interested parties for either the San Joaquin 

River NWR or the San Luis NWR Complex 

to promote and foster the natural resources 

of the Refuge and ecoregion. (Same as 

strategy 5.9.5.)
San Joaquin River NWR Comprehensive Conservation Plan 77

Objective 5. Foster natural resource 

research opportunities on the San Joaquin 

River National Wildlife Refuge for 

investigators involved in ecoregion-wide 

research efforts.

Narrative: Natural resource management 

direction and techniques employed at 

National Wildlife Refuges are developed 

through cooperative and coordinated 

research projects between the Refuge 

and investigators. All major advances 

and improvements in natural resource 

management at Refuges are developed 

through the research process. 

Strategies:

4.5.1 Encourage universities and 

researchers conducting ecoregion natural 

resource investigations to include the San 

Joaquin River NWR. 

Goal 5 (Public Use of the Refuge)

Provide the public with opportunities for 

compatible, wildlife-dependent visitor 

services to enhance understanding, 

appreciation and enjoyment of natural 

resources at the San Joaquin River NWR.

Narrative: Wildlife-dependent recreational 

activities, as identified in the Refuge 

Improvement Act, were given primary 

consideration over all other public uses. 

These wildlife-dependent priority public 

uses were considered and analyzed for 

implementation at the Refuge. These 

six priority uses include hunting, fishing, 

wildlife observation, wildlife photography, 

environmental education and interpretation. 

Existing public uses for the Refuge are 

limited to wildlife viewing and photography 

from an observation platform, occasional 

interpretive walks or programs, and guided 

visits for schoolchildren.

Planning for visitor services is influenced 

by other criteria, including wildlife needs, 

land use, habitat and wildlife protection, 

as well as accommodating the public’s 

desire for different types of recreational 

activities and the potential for one activity 

to impact others. The Refuge’s relatively 

small size and site specific issues that guided 

the development of habitat management 

required a similarly habitat-driven 

development for visitor services.

Objective 1: Implement a wildlife 

observation and photography program for 

the public on the San Joaquin River NWR 

by developing five public use facilities 

within the next five years and within the 

following five years, develop an additional 

five public use facilities.

Narrative: The Refuge’s proximity to and 

access from major California highways 

and population centers provides numerous 

and constant opportunities for the general 

public and groups to visit, enjoy and learn 

about the Refuge and its wildlife resources. 

Two major highways flank the Refuge, 

providing convenient access for the public. 

Major population centers in proximity to 

the Refuge include Modesto, Stockton, 

Sacramento and San Francisco. 

The general area is lacking in other publicowned wildlands, where the public has the 

opportunity to enjoy and view wildlife, plants 

and habitats. A public use program at the 

Refuge will help to fill a regional need for 

outdoor recreation with a focus on wildlife. 

Strategies:

5.1.1 Prepare and begin implementation 

of a public use plan focusing on wildlife 

observation, photography, environmental 

education and nature interpretation at the 

San Joaquin River NWR. The plan will 

integrate all aspects of a public use program 

with the other programs at the Refuge. This 

plan will be completed within three years 

and provide specific guidance for program 

implementation.

5.1.2 Construct either an auto-tour route or 

foot-trail that features wildlife observation 

and photographic opportunities for the 

public through a diverse array of habitats on 

the west side of the San Joaquin River. The 

tour route or foot-trail will include route/trail 

surface modification, signage, information 

kiosk, observation platform(s), side foottrails, brochures and maps, among other 

features.
78 San Joaquin River NWR Comprehensive Conservation Plan

5.1.3 Complete the wildlife observation 

platform and kiosk on Beckwith Road 

(landscaping, interpretive panels, parking lot 

improvements and signage). 

5.1.4 Develop and construct two wildlifephotography blinds at the Refuge.

5.1.5 Develop part of Christman Island as 

a free-roaming birding and wildlife viewing 

area. Construct a trail from a developed 

parking area to the wildlife viewing area and 

develop signage and maps to restrict public 

access from sensitive natural resource areas 

on Christman Island.

5.1.6 Develop one or more walk-in car-top 

boat launching facilities to facilitate the 

public’s ability to view wildlife from small 

watercraft and to promote recreational 

angling.

5.1.7 Develop the Gardener’s Cove area as 

a visitor use area (i.e., wildlife observation 

and photography as well as recreational 

angling), if deemed safe and compatible with 

the proposed Caltrans expansion of Highway 

132. The current roadway is not safe; before 

this area can be opened to the public, the 

Refuge must complete coordination with 

Caltrans designers and engineers to create a 

safe entrance and exit. 

5.1.8 Develop maps and guides showing 

visitor facilities and wildlife viewing areas at 

the Refuge. Develop interpretive materials 

to promote public use and understanding 

of the Refuge and the role it plays in the 

Central Valley Ecosystem and Pacific 

Flyway.

Objective 2. Within 10 years, develop a 

visitor contact station and trailhead in 

proximity to and in coordination with 

development of the Refuge’s headquarters 

area on Dairy Road.

Narrative: A visitor contact station will 

be a center for visitor orientation and 

information at the Refuge. The contact 

station will provide visitors their first 

impression of the Refuge and parking, 

access to an auto tour route and/or nature 

trails, and a locale to begin their wildlife 

observation hikes, garner information about 

opportunities on the Refuge, and learn about 

the Refuge from interpretive displays and 

materials.

The main administrative headquarters for 

the Refuge are in the buildings of a former 

dairy. This existing complex is close to the 

center of the Refuge and provides easy 

access and security for visitor services 

activities and opportunities to coordinate 

visitor services with Refuge maintenance 

and management programs. Visitor access 

to many parts of the Refuge will be possible 

after restoration and maintenance programs 

have been developed for the West Unit.

Strategies:

5.2.1 Construct and install an informational 

and interpretive kiosk at Dairy Road, 

serving as the main visitor contact station on 

the Refuge. Provide an associated 20 vehicle 

parking lot (with the capacity for two school 

buses).

5.2.2 Develop and install entrance, 

directional and regulatory signs at public 

access areas.

5.2.3 Construct restroom facilities adjacent 

to the visitor contact station.

5.2.4 Ensure the main auto-tour route or 

foot-trail (strategy 5.1.2) is in proximity to 

and accessible via the main visitor contact 

station.

Objective 3. Within five years, develop 

and implement a recreational hunt 

program.

 

Narrative: Recreational hunting is one of 

the six priority public uses for the National 

Wildlife Refuge System. Recreational 

waterfowl hunting has a long tradition in 

California’s Central Valley. A step-down 

management plan will be prepared prior 

to implementing hunting of migratory and 

upland birds after population monitoring 

indicates a hunting program could be 

sustained. This plan would identify suitable 
San Joaquin River NWR Comprehensive Conservation Plan 79

hunting areas and game species on the 

Refuge and the means to implement a hunt 

program on those areas. If conditions 

warrant, opportunities to hunt waterfowl 

would be available in select wetland areas 

and opportunities to hunt dove, quail 

and/or other species would be available in 

upland areas. Hunting opportunities may 

be limited by time of day, season, game 

species, numbers of permits issued and 

may also include a youth and/or disabilities 

component. Special consideration will be 

taken to ensure that the recently delisted 

Aleutian Canada goose population is not 

adversely affected by hunting on the Refuge. 

Strategies:

5.3.1 Evaluate the potential for a 

recreational hunt program at the San 

Joaquin River NWR and if warranted 

develop and implement the step-down hunt 

management plan. 

5.3.2 Coordinate with the California 

Department of Fish and Game (CDFG) in 

the development and administration of a 

recreational hunt program on the Refuge.

5.3.3 Develop maps showing facilities and 

hunt areas and distribute Refuge program 

pamphlets to participating sportsmen during 

the process of implementing a recreational 

hunting program.

5.3.4 Develop seasonal parking areas, travel 

routes and provide comfort stations for the 

hunt program.

5.3.5 Provide sanctuaries for the Aleutian 

Canada geese and ensure the protection of 

all threatened and endangered species, as 

well as other resources.

Objective 4. Develop and implement a 

recreational fishing program at the San 

Joaquin River NWR within 10 years.

Narrative: The presence of three rivers 

on the San Joaquin River NWR offers a 

variety of fishing opportunities. Gardner’s 

Cove provides one good possibility for bank 

fishing. Safe access will be available to the 

site once the Caltrans extension of Highway 

132 is completed. Boat and bank fishing 

opportunities are also possible in the West 

Unit along the San Joaquin River.

Strategies:

5.4.1 Work and coordinate with CDFG and 

the FWS Stockton Fishery Office to develop 

a recreational fishing program on the Refuge. 

Develop and implement a recreational fishing 

and boating section in the step-down Public 

Use Plan for the San Joaquin River NWR 

(See strategy 5.1.1.)

5.4.2 Develop one or more walk-in car-top 

boat launching facilities (as per strategy 

5.1.6) to promote and facilitate recreational 

angling. 

5.4.3 Provide opportunities for both 

recreational angling from a boat and the 

shore after finding suitable locations for 

these activities that minimize shoreline 

damage and potential conflicts with sensitive 

natural resources, as well as other public use 

programs at the Refuge.

5.4.4 Develop access for recreational 

fishermen and other visitors at the Gardner’s 

Cove portion of the San Joaquin River NWR 

once the Caltrans expansion of Highway 132 

is completed.

5.4.5 Create and distribute a fact sheet on 

the Refuge fishing program to the public.

Objective 5. Within five years, establish 

four interpretive programs, facilities, or 

publications for a diverse audience that 

reveals the natural and cultural history of 

the Refuge, migratory birds, endangered 

species, natural habitats, habitat 

restoration programs, wetland ecosystems 

amongst other topics. Establish an 

additional four programs, facilities, or 

publications during the following five 

years.

Narrative: Organized, well-managed, 

effective interpretive programs greatly 

enhance the quality of the public’s wildlife 

experience during their visits and field trips 

to National Wildlife Refuges.
80 San Joaquin River NWR Comprehensive Conservation Plan

Strategies:

5.5.1 Develop interpretive programs and 

events that incorporate Refuge themes and 

reveal the natural and cultural history of the 

area.

5.5.2 Construct interpretive kiosks at the 

observation platform on Beckwith Road and 

the headquarters’ visitor contact station.

5.5.3 Develop and provide maps, brochures 

and other interpretive materials showing 

visitor facilities. Distribute Refuge 

pamphlets at entrance stations to help 

visitors orient and appreciate the Refuge 

and the role it plays in the Central Valley 

ecosystem and the Pacific Flyway.

Objective 6. Develop and implement an 

environmental education program at the 

San Joaquin River NWR. Facilitate the 

use of the Refuge by educational groups.

Narrative: Environmental education serves 

many purposes including showcasing the 

Refuge’s unique resources in a controlled 

setting and fostering public education of 

the Refuge, wildlife and natural resources. 

Students provided environmental educational 

opportunities frequently understand the 

uniqueness of the Refuge and its fish and 

wildlife and develop a greater appreciation 

and sense of ownership for the Refuge. School 

groups and other educational groups from 

San Joaquin, Stanislaus and Merced counties 

will be encouraged to use the Refuge.

Strategies: 

5.6.1 Develop an educator-led ageappropriate curriculum for school children 

that is specific to the resources and goals of 

the San Joaquin River NWR.

5.6.2 Develop outdoor educational facilities, 

restroom facilities, parking, guides and other 

infrastructure necessary to accommodate 

school groups and buses.

5.6.3 Create an outreach program to recruit 

and educate teachers to use the Refuge for 

their environmental education programs. 

5.6.4 Expand school use of the San Joaquin 

River NWR within five years to include 

four college or university groups and four 

secondary/primary school groups per 

annum.

5.6.5 Promote partnerships with educational 

groups (i.e., such as the existing partnership 

with the Modesto Rotary Club) to foster 

and facilitate environmental education 

opportunities at the San Joaquin River 

NWR. 

Objective 7. Ensure public safety and 

security at the San Joaquin River NWR.

Narrative: A law enforcement presence 

at National Wildlife Refuges is crucial for 

the protection of the public and natural 

resources. Refuge law enforcement 

programs are proactive and seek to inform 

the public regarding Refuge regulations 

and prevent problems, rather than only 

enforcing statutes. 

Strategies:

5.7.1 Use signs, brochures/fact sheets and 

the Complex’s website to provide Refuge 

regulations to the visiting public. 

5.7.2 Conduct periodic patrols by Refuge 

law enforcement staff at the San Joaquin 

River NWR to ensure compliance with 

Refuge regulations, public safety and 

natural resource protection.

Environmental 

education at the 

Refuge. 

Photo: USFWS
San Joaquin River NWR Comprehensive Conservation Plan 8

5.7.3 Routinely examine and maintain public 

use facilities at the San Joaquin River NWR 

to determine and remedy unsafe conditions.

5.7.4 Extinguish all wildfires immediately 

on the San Joaquin River NWR by following 

the San Luis NWR Complex dispatch plan. 

Evacuate the public from the Refuge in the 

event of wildfire in public use areas. 

Objective 8. Develop a public outreach 

program to provide information on the San 

Joaquin NWR, San Luis NWR Complex, 

National Wildlife Refuge System and the 

U.S. Fish and Wildlife Service.

Narrative: An outreach program is a key 

component in helping the public become 

aware of the Refuge, its resources and the 

public use programs developed for their use 

and enjoyment. An outreach program would 

also inform the public about the National 

Wildlife Refuge System and the Service. 

Strategies:

5.8.1 Develop and install entrance and 

regulatory signs on all public access points 

to the San Joaquin River NWR.

5.8.2 Work with Caltrans to develop and 

install directional signs on public roads 

directing visitors to the San Joaquin River 

NWR. 

5.8.3 Work with the news media to highlight 

the programs at the San Joaquin River 

NWR.

 

5.8.4 Conduct outreach activities regarding 

the San Joaquin River NWR at local 

festivals and events.

5.8.5 Develop and produce products to 

conduct public outreach for the San Joaquin 

NWR, including a new Complex general 

brochure, trail guides, posters, fact sheets 

and other items. 

Objective 9. Establish both a volunteer 

program and Friends group to benefit the 

San Joaquin River NWR, its resources 

and its programs.

Narrative: Volunteer programs provide the 

capacity, at low economic cost, to benefit the 

Refuge in many different facets. Refuge 

volunteers can provide valued services 

in many programmatic areas, including 

biological monitoring, resource management, 

administration, nature interpretation, 

maintenance, and other areas. Volunteers 

frequently increase the productivity of a 

station, particularly when it is limited by 

staffing and funding shortages. A volunteer 

program also provides avenues for greater 

community involvement with the Refuge. A 

Friends group includes community residents 

who serve as advocates for the Refuge, 

sharing their enthusiasm about the Refuge 

with staff and the public. A Friends group 

typically focuses on conducting or facilitating 

some large-scale projects at the Refuge each 

year. 

Strategies:

5.9.1 Develop a protocol for a San 

Joaquin River NWR volunteer program 

and integrate it with the San Luis NWR 

Complex’s program.

5.9.2 Determine tasks and projects suitable 

for the volunteer program on a quarterly 

basis and implement.

5.9.3 Actively recruit volunteers through the 

media and via Refuge facilities.

5.9.4 Hold a volunteer recognition event 

annually for the San Luis NWR Complex. 

5.9.5 Develop a Refuge Friends group with 

interested parties for either the San Joaquin 

River NWR or the San Luis NWR Complex 

to promote and foster the natural resources 

of the Refuge and ecoregion. (Same as 

strategy 4.4.4.)
82 San Joaquin River NWR Comprehensive Conservation Plan
San Joaquin River NWR Comprehensive Conservation Plan 8

This CCP will serve as the primary 

reference document for San Joaquin 

River NWR planning, operations and 

management for the next 15 years or 

until it is formally revised or amended 

within that period. The Service will 

implement the CCP with assistance from 

existing and new partner agencies and 

organizations and the public. The timing 

and achievement of the management 

strategies proposed in this document 

are contingent upon a variety of factors, 

including:

n	Funding & Staffing

n	Step Down Plans 

n	Compliance Requirements

n	Adaptive Management

n	Plan Amendment and Revision 

Each of these factors is briefly discussed 

as it applies to the CCP.

Funding & Staffing

The funding required to operate any 

national wildlife refuge includes initial 

capital outlay for equipment, facilities, 

labor and other expenditures, as well as 

annual, ongoing costs for staff, contracts, 

supplies, management, maintenance and 

other recurring expenses (See Table 

2: Estimated Initial Capital Outlay to 

Implement the CCP). Initial expenditures 

for the Refuge as described in the 

CCP would cost approximately eight 

million dollars. Not all of these capital 

expenditures would accrue during the first 

year of implementation. For example, 

habitat development and research would 

be implemented over the entire length of 

the plan and select equipment, vehicles 

and staff may be borrowed or shared from 

other refuge units of the San Luis NWR 

6 Management Plan 

Implementation

Complex. The largest costs for this initial 

outlay are for habitat restoration and 

implementation of a public use program. 

Funding for many of these individual 

projects will be sought through grants and 

cooperative partnerships.

At full staffing, personnel dedicated to the 

Refuge would include a refuge manager, 

maintenance worker, tractor operator 

and wildlife biologist. A new public use 

specialist would be shared with the other 

units comprising the San Luis NWR 

Complex. The other staff positions of 

the Complex are also shared among the 

different refuge units. Annual contracts 

or cooperative agreements will be issued 

for additional law enforcement, fire 

protection, invasive pest control and other 

activities as needed. These recurring 

costs are expected to annually total 

over half a million dollars (See Table 3: 

Estimated Annual Cost to Implement the 

CCP).

Step-Down Management Plans 

Some projects or types of projects require 

more in-depth planning than the CCP 

process is designed to provide. For these 

projects, the Service prepares step-down 

management plans. In essence, stepdown management plans provide the 

additional details necessary to implement 

management strategies identified in a 

CCP (See Appendix G: Step-Down Plans).

The National Wildlife Refuge System 

Manual lists more than 25 Step-Down 

Management Plans that might be 

needed at a refuge. These step-down 

management plans are typically revised at 

a more frequent interval than a CCP.
84 San Joaquin River NWR Comprehensive Conservation Plan

Table 2. Estimated Initial Capital Outlay to Implement the CCP

Expenditure Unit Cost Unit Quantity Total Cost

Office Rehabilitation $50,000 ea 1 $50,000

Maintenance Shop Construction $250,000 ea 1 $250,000

Parking Lot $5,000 ea 3 $15,000

Replace Fencing $10,000 l.m. 2 $20,000

Replace Gates $1,000 ea 7 $7,000

Install Automatic Entrance Gate $10,000 ea 1 $10,000

Erosion Control Materials/Supplies $10,000 NA 1 $10,000

Habitat Restoration (Upland & Wetland) $6,000,000 NA NA $6,000,000

Brush Rabbit Habitat Restoration $40,000 NA NA $40,000

Lift Pump Rehabilitation & Fish Screens $100,000 ea 3 $300,000

Pasture Rehabilitation $200 ac 150 $30,000

Refuge GIS Capability $30,000 NA NA $30,000

Public Tour Route and/or Trails $250,000 NA NA $250,000

Photography Blinds $12,000 ea 2 $24,000

Public Restrooms $20,000 ea 2 $40,000

Information Kiosks & Display Panels $50,000 ea 3 $150,000

Boundary Posting $30,000 NA NA $30,000

Refuge and Regulatory Signs $3,000 ea 6 $18,000

Boat Launch Facilities $25,000 ea 2 $50,000

Structure Removal $20,000 ea 10 $200,000

Recreational Hunt Infrastructure $10,000 ea 1 $10,000

Recreational Fishing Infrastructure $40,000 ea 2 $80,000

Concrete Removal $100,000 NA NA $100,000

Dairy Waste Lagoon Cleanup $35,000 ea 1 $35,000

Tractor $150,000 ea 1 $150,000

Tractor Implements $8,000 ea 3 $24,000

All Terrain Vehicle $6,000 ea 1 $6,000

Misc. Fire Equipment $10,000 NA NA $10,000

Security Alarms for Buildings $1,500 ea 3 $4,500

Maintenance Equipment misc misc misc $10,000

Environmental Education Equipment misc misc misc $10,000

Grand Total: $7,963,500
San Joaquin River NWR Comprehensive Conservation Plan 85

Table 3. Estimated Annual Cost to Implement the CCP

Expenditure Unit Cost Unit Quantity Total Cost

Salaries and Benefits

 Complex Project Leader—GS 14 $109,040 ea 0.2 $21,808

 Deputy Complex Project Leader—GS 13 $92,270 ea 0.2 $18,454

 Refuge Manager—GS 12 $83,000 ea 1.0 $83,000

 Complex Admin. Assistant—GS 9 $50,164 ea 0.2 $10,032

 Complex Budget Technician—GS 6 $34,070 ea 0.2 $6,814

 Engineering Equipment Operator—WG 9 $61,100 ea 1.0 $61,100

 Tractor Operator—WG 6 $57,200 ea 1.0 $57,200

 Complex Supervisory Wildlife Biol.—GS 12 $83,000 ea 0.2 $16,600

 Complex Wildlife Biologist—GS 11 $60,696 ea 0.2 $12,139

 Complex Wildlife Biologsit—GS 11 $60,696 ea 0.2 $12,139

 Complex Wildlife Biologist—GS 9 $50,164 ea 0.2 $10,032

 Refuge Wildlife Biologist—GS 9 $50,164 ea 1.0 $50,164

 Complex Public Use Specialist—GS 12 $83,000 ea 0.2 $16,600

 Complex Public Use Specialist—GS 9 $50,164 ea 0.3 $15,049

 Complex Park Ranger—GS 9 $50,164 ea 0.2 $10,032

 Complex Fire Mgmt. Officer—GS 11 $60,696 ea 0.2 $12,139

 Complex Fire Specialist—GS 9 $50,164 ea 0.2 $10,032

 Complex Lead Forest Tech—GS 8 $45,417 ea 0.2 $9,083

 Complex Perm. Seas. Forest Tech—GS6 $34,070 ea 0.1 $3,407

 Complex Perm. Seas. Forest Tech—GS5 $33,107 ea 0.1 $3,311

 Complex Perm. Seas. Forest Tech—GS5 $33,107 ea 0.1 $3,311

 Complex Temp. Seas. Forest Tech—GS5 $25,467 ea 0.1 $2,547

 Complex Temp. Seas. Forest Tech—GS4 $22,762 ea 0.1 $2,276

 Complex Temp. Seas. Forest Tech—GS3 $20,277 ea 0.1 $2,027

Maintenance $50,000 ea 1.0 $50,000

Invasive Weed Program $20,000 ea 1.0 $20,000

Water/Pumping Costs $25,000 ea 1.0 $25,000

Riparian Brush Rabbit Monitoring $10,000 ea 1.0 $10,000

Water Quality Monitoring $10,000 ea 1.0 $10,000

Travel/Training $5,000 NA 1.0 $5,000

Supplies $25,000 ea 1.0 $25,000

Printing $5,000 ea 1.0 $5,000

Pump-out for restroom $5,000 ea 4.0 $20,000

Grand Total: $619,296

 
86 San Joaquin River NWR Comprehensive Conservation Pla

Current or anticipated step-down 

plans for the San Joaquin River NWR 

include: 

Plans that are current and up-to-date:

n	Fire Management Plan (2001)

n	Spill Response Plan (2003)

n	Safety Management Plan (2000)

n	Continuity of Operations Plan (1999)

Plans that exist but need to be updated:

n	Disease Management Plan (1983)

n	Emergency Management Plan (1993)

Plans that need to be initiated:

n	Water Management Plan

n	Law Enforcement Plan

n	Public Use Management Plan

n	Upland Management Plan

n	Fisheries Management Plan

n	Invasive Exotic Plant Control Plan

Compliance Requirements 

This CCP was developed to comply 

with all applicable Federal laws, 

executive orders, and legislative acts. 

Some activities, particularly those that 

involve revising an existing step-down 

management plan or preparing a new 

one, will need to comply with additional 

laws or regulations besides NEPA and the 

National Wildlife Refuge Improvement 

Act. In addition to these acts, full 

implementation of all components of this 

CCP requires compliance with other laws 

and mandates (See Appendix J: Relevant 

Federal Laws and Mandates).

Adaptive Management & Monitoring

Evaluation

Adaptive management is the process 

of implementing policy decisions as 

scientifically driven experiments that 

test predictions and assumptions about 

management plans, using the resulting 

information to improve the plans. 

Management direction is periodically 

evaluated via a system of applying several 

options, monitoring the objectives, and 

adapting original strategies to reach 

desired objectives. Habitat, wildlife 

and public use management techniques 

and specific objectives will be regularly 

evaluated as results of a monitoring 

program and other new technology and 

information become available. These 

periodic evaluations would be used over 

time to adapt both the management 

objectives and strategies to better achieve 

management goals. Such a system 

embraces uncertainty, reduces option 

foreclosure, and provides new information 

for future decision-making while allowing 

resource use. At a minimum, each year 

a checklist of the goals, objectives and 

management strategies of this CCP will 

be completed to assist in tracking and 

evaluating progress (Appendix P).

Monitoring

Monitoring is an essential component 

of the CCP. Monitoring strategies have 

been integrated into many of this plan’s 

goals and objectives. Specific details, 

including monitoring strategies, methods, 

techniques and locations, will be outlined 

in a step-down Monitoring Plan. In this 

CCP, habitat monitoring receives an 

important emphasis. 

All habitat management activities will be 

monitored to assess whether the desired 

effects on wildlife and habitat components 

have been achieved. Baseline surveys 

will be conducted for wildlife species for 

which existing or historical numbers and 

occurrences are not well known. Studies 

will also monitor wildlife responses to 

increased public use of the Refuge for 

fishing, hunting, wildlife observation and 

environmental education.

Monitoring will be designed and developed 

in cooperation with universities and 

non-governmental organizations to the 

greatest extent possible. Applied research 

can provide insight into ecological 

questions concerning habitat, wildlife and 

public use management. Refuge staff 

would work with researchers to ensure 

that investigations are applicable and 

compatible with Refuge objectives.
San Joaquin River NWR Comprehensive Conservation Plan 87

Maintaining and restoring habitat 

quality and quantity are a major means 

of accomplishing Refuge goals and 

objectives. Monitoring would focus 

on measuring vegetative diversity and 

abundance, water quality and quantity 

and wildlife response to management 

practices. Baseline surveys would be 

established for other species for which 

existing or historical numbers are not 

established.

Progress toward Refuge goals and 

objectives will be evaluated based on 

the results of this station’s monitoring 

activities.

Plan Amendment and Revision

This CCP is intended to evolve as the 

Refuge changes, and the Improvement 

Act specifically requires formal revision 

and updating of CCPs at least every 15 

years. The formal revision process would 

follow the same steps as the CCP creation 

process. In the meantime, the Service 

would be reviewing and updating this 

CCP periodically based on the results of 

its adaptive management program. This 

CCP would also be informally reviewed by 

Refuge staff while preparing annual work 

plans and updating Refuge databases. 

It may also be reviewed during routine 

inspections or programmatic evaluations. 

Results of any or all of these reviews may 

indicate a need to modify the plan. 

The goals described in this CCP would 

not change until they are reevaluated as 

part of the formal CCP revision process. 

However, the objectives and strategies 

may be revised to better address changing 

circumstances or to take advantage of 

increased knowledge of the resources 

at the Refuge. If changes are required, 

the level of public involvement and 

associated NEPA documentation would be 

determined by the Refuge Manager.

Refuge objectives and strategies are 

intended to be attained over the next 15 

years. Management activities would be 

phased in over time and implementation is 

contingent upon and subject to results of 

monitoring and evaluation, funding levels 

and staffing.
88 San Joaquin River NWR Comprehensive Conservation Plan