San Luis NWR Complex

947-C West Pacheco Blvd.

Los Banos, CA 93635

Telephone: 209/826-3508

Fax: 209/826-1445

U.S. Fish and Wildlife Service

1 (800) 344-WILD

June 2007

Photo: USFWS/L. Eastman

SJFCCP-cover_final.indd 1 

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San Joaquin River NWR Comprehensive Conservation Plan i

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. Response to Comments on Draft CCP/EA .........................................................................109

C. Public Scoping and Involvement Process ............................................................................111

D. Compatibility Determinations...............................................................................................119

E. Species List..............................................................................................................................159

F. Intra-Service Section 7 Consultation ...................................................................................167

G. Step Down and Other Plans ..................................................................................................175

H. Levee Breach Study ...............................................................................................................177

I. References and Literature Cited..........................................................................................179

J. Relevant Federal Laws and Mandates.................................................................................185

K. Mailing List..............................................................................................................................195

L. List of Preparers.....................................................................................................................199

M. Wilderness Review..................................................................................................................201

N. Estimate of Refuge Water Needs .........................................................................................205
San Joaquin River NWR Comprehensive Conservation Plan 1

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 
2 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, 

San Joaquin River NWR and adjacent lands 

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 3

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:

Q 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.

Q Provide a scientific foundation for Refuge 

management.

Q Provide a clear vision statement of 

the desired future conditions when 

Refuge purposes and goals have been 

accomplished.

Q Provide visitors with a clear 

understanding of the reasons for 

management actions on the Refuge.

Q Ensure the compatibility of current and 

future uses of the Refuge.

Q Provide long-term continuity in Refuge 

management.

Q Provide a basis for operation, 

maintenance and development budget 

requests.

The CCP 

will guide 

management 

decisions for 

the next 15 

years.
4 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 5

San Joaquin River from just south of the 

confluence with the Tuolumne River, then 

north to the south bank of the Stanislaus 

River. The Mohler Tract of the Refuge is a 

noncontiguous parcel situated on the north 

bank of the Stanislaus River three miles east 

from the main portion of the Refuge. The 

Refuge’s landscape represents a locally—as 

well as regionally—significant remnant of 

the once broad floodplain of these three 

major rivers of California’s Central Valley 

(Figure 1–Watershed/ Ecosystem Map 

and Figure 2–Regional & Project Location 

Map). Surrounding lands are largely used in 

agricultural production.

Ownership 

Lands within the Refuge boundary have 

been acquired in both fee title (outright 

purchases) and through easements (See 

Figure 3–Land Status Map). All acquisitions 

were on a willing-seller basis. Fee title 

lands are owned by the Service and serve as 

the core of Refuge lands. These lands are 

managed for wildlife as the priority. 

Easement lands are privately-owned lands, 

where a willing owner has sold restricted 

land-use rights to the Service to protect or 

enhance wildlife habitats on these private 

lands. Typically, Service easement lands 

occur in proximity to fee title lands. The 

Service perpetual conservation easements 

were established to protect existing 

resource habitat values while retaining 

land in private ownership. In addition, the 

U.S. Department of Agriculture National 

Resource Conservation Service (NRCS) 

holds both Wetland Reserve Program and 

floodplain easements on some parcels of the 

Service-owned lands. The NRCS Wetland 

Reserve Program and floodplain easements 

were a funding partnership to acquire fee 

title land for the Service, whereby the 

NRCS purchased easements on the land 

and the Service paid the landowner the 

remaining fee title value. The land is then 

owned and managed in perpetuity by the 

Service with an underlying NRCS easement.

Refuge Acquisition History

The Service became interested in the 

present Refuge locale in 1976 when the 

federally-listed Aleutian Canada goose 

was discovered using the Faith Ranch and 

Mapes Ranch as winter habitat. At that 

time, the Faith Ranch was owned by the 

Paul Davies family and the Mapes Ranch 

by the Bill Lyons, Sr. family. Both ranches 

were primarily beef cattle operations, 

although the Mapes Ranch also had a small 

amount of row crop agricultural production. 

Although bounded by riparian habitat to the 

north, west and south, the uplands of both 

ranches were dominated by short-cropped 

irrigated pasture, scattered wetlands and 

stock ponds. This complex of habitats 

formed optimum foraging and roosting 

habitat for wintering Aleutian Canada geese. 

Subsequent monitoring revealed that more 

than 98 percent of the Aleutian Canada 

goose population wintered on these lands. 

The open terrain of the ranches provided 

high quality habitat for other geese, lesser 

and greater sandhill cranes, as well as 

other wildlife. The Service established the 

San Joaquin River NWR in 1987 for the 

primary purpose of meeting the wintering 

habitat objectives of the Aleutian Canada 

Goose Recovery Plan. At that time, the 

approved Refuge acquisition boundary (the 

area within which the Service could acquire 

and manage land) totaled 10,295 acres, and 

included primarily the Faith Ranch and 

Mapes Ranch east of the San Joaquin River, 

and a portion of another property west of the 

river. Initially, all Refuge land acquisition 

was planned as fee title purchase. 

The first land acquisition occurred in 

1988 when the Service purchased the 777 

acre Christman Island from the National 

Audubon Society. Christman Island, 

formerly part of the Mapes Ranch, had 

been purchased by the Audubon Society 

in 1986 through a donation from Joseph 

M. Long and Don Lundberg, with the 

intent of reselling it the Service. During 

this time, the Service Realty Office was 

meeting with the Davies family landowners 

to pursue purchase of other lands within 

the acquisition boundary. For a variety 
6 San Joaquin River NWR Comprehensive Conservation Plan

Fresno

Sacramento

San Francisco

San Joaquin River

National Wildlife Refuge

Redding

Bakersfield

Modesto

101

101

99

5

80

580

99

5

O r e g o n

N e v a d a

C a l i f o r n i a

P

a

c

i

f

i

c

O

c

e

a

n

SACRAMENTO

RIVER NWR

SAN LUIS

NWR

BITTER

CREEK

NWR

STONE

LAKES

NWR

KERN

NWR

SAN

PABLO

BAY

NWR

DON EDWARDS

SAN FRANCISCO

BAY NWR

SACRAMENTO

NWR

MODOC

NWR

PIXLEY

NWR

SUTTER

NWR

BLUE

RIDGE

NWR

MARIN

ISLANDS

NWR

ANTIOCH

DUNES

NWR

MERCED

NWR

GRASSLANDS

WMA

COLUSA

NWR

BUTTE SINK

WMA

DELEVAN

NWR

WILLOW CREEK -

LURLINE WMA

Figure 1. 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 7

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
8 San Joaquin River NWR Comprehensive Conservation Plan

Beckwith Rd. Gates Rd.

Shoemake Rd.

Dairy Rd.

Center Rd.

Orchard Rd.

River Rd.

Stanislaus Rd.

132 132

33

Miller Lake

Tuolumne River

San

Joaquin

River

Stanislaus

River

San Joaquin County

Stanislaus County

Mohler Tract

Figure 3. Land Status

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

Miles

NRCS Wetland Reserve

Program Easements

Approved Refuge

Boundary

FWS Lands

FWS Conservation Easement

Private

Figure 3: Land Status
San Joaquin River NWR Comprehensive Conservation Plan 9

of reasons these negotiations were 

unsuccessful. 

In 1990, the Robert Gallo family purchased 

the Faith Ranch. The new landowners were 

not interested in selling the ranch to the 

Service, but were willing to enroll the ranch 

in a conservation easement in the future. 

From 1990 to 1992, the Lyons family stopped 

negotiations with the Service because the 

Mapes Ranch was being considered as 

one of several potential locations for the 

site of a future University of California 

campus. After the Mapes Ranch was 

eliminated from consideration as a campus 

site, the landowners reentered acquisition 

negotiations with the Service; however, by 

that time, funding that would have allowed 

purchase of the entire Mapes Ranch in a 

single acquisition action had been redirected 

to other projects. Subsequent acquisition 

proceeded on a parcel-by- parcel basis as 

funds became available. Fee-title purchases 

were made of 861 acres in 1993, 662 acres in 

1996, and 577 acres in 1997 using Migratory 

Bird Conservation Act funds. By 1997, 

the Service owned 2,877 acres within the 

Refuge.

In January 1997, a catastrophic flood 

occurred on the lower San Joaquin River 

system. Flood control levees failed and 

most of the Refuge and Faith Ranch, and 

much of the Mapes Ranch, were inundated 

by floodwaters. Other private lands west 

of the designated Refuge boundary also 

received extensive flooding. In all, the 

areas surrounding the Refuge suffered 

more than $2 billion in property damages. 

Subsequently, several landowners in 

the floodplain west of the San Joaquin 

River approached the Service with the 

intent of selling their flood-prone land for 

inclusion within the existing Refuge. This 

coincided with a Congressional mandate 

for the U.S. Army Corps of Engineers to 

explore nonstructural alternatives for flood 

protection; the same time period produced 

statewide initiatives, such as the San 

Joaquin River Management Plan, to restore 

riparian habitat and hydrologic function and 

provide alternate methods of flood control. 

In support of these efforts, the Service 

proposed a nonstructural flood protection 

demonstration project in which it would 

acquire those flood-prone properties, breach 

or remove the existing flood control levee, 

and allow periodic floodwaters to spread 

over the Refuge-owned floodplain to reduce 

downstream flooding. This proposal grew 

into a multi agency effort, with the Service 

partnering with NRCS, U.S. Army Corps 

of Engineers, U.S. Bureau of Reclamation 

and the California Department of Water 

Resources. In 1997, the Service completed 

an environmental assessment and Land 

Protection Plan to expand the approved 

Refuge boundary to 12,887 acres. Following 

approval, in 1999 the Service acquired 2,037 

acres of floodplain and riparian habitat 

west of the San Joaquin River in fee title, 

using a combination of Service (Emergency 

Flood Appropriations) and NRCS (Wetland 

Reserve Program) funds. In 2000, an 

additional 210 acres of floodplain habitat 

immediately south of and adjacent to the 

Refuge were acquired with CALFED funds, 

and 35 acres of riparian habitat along the 

Stanislaus River north of the Refuge were 

purchased by the Service Anadromous Fish 

Restoration Program and turned over to 

the Refuge for management. By 1998, the 

owners of the Mapes Ranch had reversed 

their original decision to sell their entire 

ranch in fee title, and instead, were willing 

to sell only a small portion of the remaining 

ranch lands in fee title and enroll the rest 

in perpetual conservation easements. 

Accordingly, the Service purchased 

Mapes Ranch lands both in fee title and 

in easement, and purchased a perpetual 

conservation easement on most of the Faith 

Ranch. 

Fee Title Lands

Purchase of fee title land began in 1988 and 

is ongoing. The past five years have yielded 

the greatest increase in land acquisition for 

the Refuge. Figure 3 (Land Status Map) 

illustrates the approved Refuge boundary 

for acquisition, totaling close to 13,000 acres, 

and the current land ownership status. 

As of 2004, Fee title lands comprise 51 

percent of the approved Refuge boundary. 

Sources of acquisition funds have included 
10 San Joaquin River NWR Comprehensive Conservation Plan

the Land and Water Conservation Fund, 

Migratory Bird Conservation Act Fund, 

CALFED Bay-Delta Program, emergency 

flood control appropriations, Anadromous 

Fish Restoration Program and the State of 

California. 

Easement Lands

Easements are legal agreements whereby 

one party has binding authority regarding 

some aspect(s) of a property owner’s land. 

Easements will influence the management 

activities and opportunities at the Refuge. 

In some cases, the Service has easements 

on adjacent private property; in other 

instances, other agencies have easements on 

Refuge lands.

Perpetual Conservation Easements 

(USFWS)

The Service acquired perpetual conservation 

easements on 1,834 acres of the 2,050 acre 

Faith Ranch in 2001, and 1,112.9 acres of 

the 4,000 acre Mapes Ranches in 2002. 

Additional funding is currently being 

sought to enroll much of the rest of the 

Mapes Ranch into the easement program. 

Both properties are within the Service’s 

acquisition boundary for the Refuge. The 

purpose of the easements is to protect 

critical wintering habitat for Aleutian 

Canada geese, State threatened greater 

sandhill cranes, other threatened and 

endangered species, and migratory birds. 

The authority to acquire these easements 

comes from the 1997 Environmental 

Assessment for the expansion of the Refuge. 

These easements are subject to all Federal 

laws pertaining to those rights being 

acquired through the easement. Locally, 

the easements are administered by the San 

Luis NWR Complex under the guidance of 

the Easement Program Manager to ensure 

the ecological integrity of the easements are 

met.

The specific terms of the easements guide 

the landowners and the Service in protecting 

the integrity of the agricultural operations 

(irrigated and native pasture and cereal 

grains) while sustaining critical habitat for 

migratory wildlife. In addition, the Service 

acquired the right to continue providing 

wildlife habitat on the property if the 

landowner can no longer sustain a viable 

agricultural operation.

The Service is considering an acquisition 

boundary expansion concurrent with this 

CCP that would extend along the San 

Joaquin River floodplain from the southern 

boundary of the Refuge southward to the 

existing Grasslands Wildlife Management 

Area in Merced County. Under this 

proposal, most acquisitions would be 

perpetual conservation easements developed 

in conjunction with other agency easement 

programs. The Service has prepared a 

Study Report and drafted a Preliminary 

Project Proposal, and is seeking the 

authority to study land acquisition in this 

area. The Study Report is currently being 

reviewed within the Service. 

Floodplain Warranty Easement 

Program (NRCS)

This NRCS easement applies to San 

Joaquin River NWR lands that the Service 

purchased from J. P. Lara and the El Solyo 

Ranch. This easement requires the Service 

and any subsequent landowner, to protect 

the floodplain and restore and manage for 

native habitats and natural resource values. 

The Lara and Vierra Units of the Refuge are 

both enrolled in this program and comprise 

515.69 and 632.65 acres, respectively. The 

landowner (i.e., Refuge) is required to 

provide for “the unimpeded reach and flow of 

any waters in, over, or through the easement 

area; to retard runoff and prevent soil 

erosion through the restoration, protection, 

or enhancement of the floodplain; to restore, 

protect, manage, maintain, and enhance the 

functional values of wetlands, riparian areas, 

conservation buffer strips, and other lands; 

to conserve natural values including fish and 

wildlife habitat, water quality improvement, 

flood water retention, groundwater 

recharge, open space, aesthetic values, and 

environmental education; and to safeguard 

lives and property from floods, drought, and 

the products of erosion” in perpetuity. 

To ensure the enrolled easement lands 

meet the program’s purposes and goals, the 

management of these lands must conform 
San Joaquin River NWR Comprehensive Conservation Plan 11

to the Planned Conservation Treatment 

and Compatible Use Permit of NRCS. This 

permit between the NRCS and landowner 

addresses short-term management practices 

that would be applied until fulfilling the 

long-term goal of restoring riparian/wetland 

habitat and natural floodplain hydrology 

to maintain the ecological integrity of the 

easement are. The permit applies to both 

the Floodplain Warranty Easement and 

Wetlands Reserve Program Easements. 

Wetland Reserve Easement Program 

(NRCS)

This NRCS-administered easement 

applies to lands west of the San Joaquin 

River that the Service purchased from 

Mr. Ed Hagemann (Mehlhaff and Hay, 

1999). It requires the owner to “restore, 

protect, manage, maintain, and enhance 

the functional values of wetlands and other 

lands, and for the conserving of natural 

values including fish and wildlife habitat, 

water quality improvement, flood water 

retention, groundwater recharge, open 

space, aesthetic values, and environmental 

education” for 30 years. The Hagemann 

tract of the Refuge is part of this program 

and comprises 2,017.8 acres. These 

lands are also required to conform to the 

Planned Conservation Treatment and 

Compatible Use Permit of NRCS, which is 

described above. 

Refuge Management and Monitoring 

History

The level and type of management activities 

applied to the Refuge have evolved over 

time. Beginning in 1976, prior to Refuge 

establishment, graduate students or 

contract researchers were present 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 Plan

provide needed forage habitat, the Refuge 

entered into a cooperative agreement with 

the Lyons family. Under this agreement, 

the Cooperator planted and grew corn on a 

sharecrop basis and then harvested a share 

as silage. The Refuge’s share of corn was 

grown to maturity, and then mowed down by 

the Cooperator on a schedule developed by 

the Refuge to provide forage for the geese. 

Cattle grazing was allowed on Refuge-owned 

irrigated pasture and uplands to create the 

short-grass foraging habitat preferred by 

Aleutian Canada geese and other arctic 

nesting geese, once they arrived in autumn/

winter. The Cooperator compensated the 

Refuge for the value of grazing by planting 

winter wheat on Refuge lands to provide 

green forage for the geese (where the silage 

corn was harvested), and providing water 

to flood and maintain seasonal wetlands and 

roost ponds on the Refuge.

The amount of habitat available for goose 

and sandhill crane management increased 

as new lands were acquired from the Mapes 

Ranch. The existing Page Lake roost pond 

was enhanced through a cooperative project 

in 1996 by the Service, the Lyons family, and 

Ducks Unlimited, and additional roosting 

habitat (Goose Lake) was developed by 

the Service in 1999. By 1999, 335 acres 

of corn and winter wheat fields, 469 acres 

of irrigated pasture, 371 acres of native 

uplands, and 191 acres of roost ponds/

wetlands were actively managed for Aleutian 

Canada geese, sandhill cranes, and other 

migratory birds on the Refuge. Although 

increasing numbers of geese made use of 

Refuge lands, there continued to be goose 

use at the Faith and Mapes Ranches.

In 1995, responsibility for monitoring 

wintering Aleutian Canada geese for 

the recovery program shifted to Region 

1, Division of Refuges. Since that time, 

seasonal biologists of the San Luis NWR 

Complex have been based at the Refuge each 

winter to monitor Aleutian Canada geese and 

cackling Canada geese (Branta canadensis 

minima). While Refuge staff maintained 

the same level of goose monitoring as 

did the previous researchers, they were 

also available to perform other Refuge 

management activities. The staff increased 

disease control activities, took more control 

of water management, and initiated biological 

inventories, such as Refuge species lists, 

heron/egret rookery counts, sandhill crane 

counts, and vernal pool surveys. 

Since 1996, a permanent Refuge staff 

member has been assigned the oversight 

and day-to-day management of the Refuge 

as a primary duty. This, and assistance from 

other San Luis NWR Complex staff, has 

allowed for an expansion of management 

activities at the Refuge. Management has 

included removing debris and unneeded 

facilities on new Refuge lands; demolishing 

buildings, including asbestos removal in 

Gardner’s Cove and the former El Solyo 

Dairy site; repairing and upgrading lift 

pumps, pipelines, water control structures, 

and other water delivery facilities; 

developing new wetlands on former 

agricultural fields; initiating volunteer 

projects; constructing a cooperatively-funded 

observation tower for public use; preparing 

habitat restoration plans; and submitting 

major land acquisition and habitat 

restoration grant funding requests.
San Joaquin River NWR Comprehensive Conservation Plan 13

San Joaquin River on the Refuge. 

Photo: USFWS
14 San Joaquin River NWR Comprehensive Conservation Plan

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San Joaquin River NWR Comprehensive Conservation Plan 15

The purpose of the Comprehensive 

Conservation Plan (CCP) for the San 

Joaquin River National Wildlife Refuge is 

to guide the management of the Refuge. 

The CCP provides managers with a 15-year 

strategy for achieving Refuge purposes 

and contributing toward the mission of the 

National Wildlife Refuge System, consistent 

with sound principles of fish and wildlife 

conservation and legal mandates. A CCP is 

needed 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 CCP, 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 selected 

management alternative for the Refuge; 

other management alternatives were 

developed and considered as part of this 

planning process, and are found in Appendix 

B of the Draft Comprehensive Conservation 

Plan and Environmental Assessment.

The Planning Process

Part of comprehensive conservation 

planning includes preparation of a NEPA 

document. Key steps in the CCP and the 

parallel NEPA process are listed below:

1. Preplanning and team formation

2. Public scoping and involvement

3. Identifying issues, opportunities, and 

concerns

4. Defining and revising vision statement 

and Refuge goals

5. Developing and assessing alternatives

6. Identifying preferred alternative plan

7. Draft CCP and EA

8. Revising draft documents and releasing 

final CCP

9. Implementing the CCP

10. Monitoring/feedback

Figure 4 shows the overall CCP steps and 

process in a linear cycle, but the planning 

process is actually a non-sequential 

movement among the steps, with many 

revisions occurring during the development 

of the plan. The following sections provide 

additional detail on individual steps in the 

planning process. 
16 San Joaquin River NWR Comprehensive Conservation Plan

Final

CCP

Prepare Draft

CCP

Develop

Alternative Objectives

And Strategies

Implement CCP

And Monitor

Review and

Revise the CCP

Public Scoping &

Identify Issues

Develop Vision

Statement & Goals

Initiate Study

Preplanning

Public

Input

Public

Input

Public

Input

Final

CCP

Prepare Draft

CCP

Develop

Alternatives

Implement CCP

and Monitor

Review and

Revise the CCP

Public Scoping &

Identify Issues

Develop Vision

Statement & Goals

Initiate Study

Preplanning

Public

Input

Public

Input

Public

Input

CCP

Process

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 public involvement process for 

the San Joaquin River CCP is summarized 

below and describe in detail in Appendix C. 

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. 

The draft CCP and EA were provided to 

other agencies and the public for review and 

comment. Responses to comments on the 

draft CCP and EA are included in Appendix 

B.

Overview of Public Scoping Comments 

and Discussions

The planning team identified issues, 

concerns and opportunities internally and 
San Joaquin River NWR Comprehensive Conservation Plan 17

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 e-mail. 

The following key issues, concerns and 

opportunities were identified during the 

planning process and compiled by the 

Service. Resource issues and opportunities 

were also identified during this process: 

Q Wildlife Management and Restoration

Q Recreation and Public Use

Q Refuge Staffing and Resources

Q Flood Management

Q Wetland and Water Management

Q Refuge Proximity to Private Lands

Development of Alternatives 

The development of management 

alternatives 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 of the Draft 

Comprehensive Conservation Plan and 

Environmental Assessment. The final 

CCP highlights the selected management 

alternative for the Refuge.
18 San Joaquin River NWR Comprehensive Conservation Plan

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San Joaquin River NWR Comprehensive Conservation Plan 19

Flyway Setting

The San Joaquin River NWR is situated 

within the Pacific Flyway. The flyway 

extends from the crest of the Rocky 

Mountains west to the Pacific Ocean within 

North America. It is used by millions of 

waterfowl and shorebirds for migration to 

and from wintering and breeding grounds. 

California’s Central Valley is the largest 

watered flatland in the flyway, providing 

critical winter habitat for waterfowl, in 

particular. Autumn/winter rains and melting 

snow from the Sierra Nevada and Coast 

ranges provide water for wetlands, and mild 

winters make this area a major center for 

wintering waterfowl. Approximately 60 

percent of the flyway’s waterfowl winter 

in the Central Valley, with wintering duck 

populations ranging from two to five 

million birds. Common valley waterfowl 

species include the snow goose (Anser 

caerulescens), Ross’ goose (Anser rossii), 

white-fronted goose (Anser albifrons), 

Aleutian Canada goose, green-winged teal 

(Anas crecca), northern shoveler (Anas 

clypeata), mallard (Anas platyrhynchos), 

northern pintail (Anas acuta), cinnamon teal 

(Anas cyanopters), gadwall (Anas strepera), 

American widgeon (Anas americana), 

canvasback (Aythya valisinieria), 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 in the 

ecoregion. Today, the ecoregion has been 

converted into one of the most productive 
20 San Joaquin River NWR Comprehensive Conservation Plan

agricultural areas in the world (Schoenherr 

1992). With this increase in land devoted 

to agricultural use there was an associated 

loss of wildlands. The valley grasslands 

dominated by native perennial grasses that 

once covered all well-drained areas now 

only occur in a pristine condition on just one 

percent of the ecoregion (Schoenherr 1992). 

Likewise, approximately 94 percent of the 

wetlands and 89 percent of the riparian 

woodlands/forests have also disappeared 

(Schoenherr 1992). Despite these losses, 

the remaining wildlands in the ecoregion 

still provide significant habitats for unique 

Central Valley wildlife communities; they 

also offer critical habitat for many wildlife 

species both regionally and nationally, 

particularly waterfowl and other waterbirds.

Historic Refuge Environment

Refuge lands were historically a mosaic of 

riverine channels, broad riparian floodplains, 

wetlands and grassland savannas dominated 

by valley oaks. This area was bisected by 

the main stem of the San Joaquin River and 

was bounded to the north by the Stanislaus 

River and to the south by the Tuolumne 

River. Historically, the San Joaquin River 

and its tributaries would overtop natural 

levees and inundate the floodplain following 

winter rains and Sierra snow melt. This 

system was dynamic, depositing rich 

alluvium, creating and cutting streambanks, 

creating and maintaining riparian forests, 

creating oxbow lakes and backwater sloughs 

by changing the rivers’ course, clearing and 

depositing debris, scouring streambeds, 

and exposing and depositing gravel and 

sand. The resulting floodplain corridor was 

vegetated by trees, such as button willow, 

black willow and sandbar willow in the lower 

areas. The upper areas were dominated by 

box-elder, Fremont’s cottonwood, Oregon 

ash, arroyo willow and valley oak. The 

most common mid- and ground-story 

shrubs included California rose, California 

blackberry, elderberry and wild grape. 

Dominant grasses and forbs included 

creeping wild rye, basket sedge, mugwort 

and goldenrod. The uplands adjacent to the 

floodplain were less frequently inundated 

by floods and were dotted with valley oaks 

with an understory of perennial grasses 

and forbs, such as creeping wild rye, 

saltgrass, alkali sacaton, gum plant and 

spikeweed. Wetlands and vernal pools were 

abundant throughout the upland savannahs. 

These habitats supported a wide array of 

migratory birds, salmonids and other fish, 

large herbivores and other wetland and 

upland associated wildlife. 

American Indians lived in permanent 

villages on elevated locations above the 

floodplain. These native people, the Yokuts, 

made their homes along the San Joaquin 

River and its tributaries in part, because of 

the abundance of natural resources in the 

area. When Lieutenant Gabriel Moraga led 

the Spanish cavalry into the San Joaquin 

Valley in 1805, the explorers were astonished 

by the abundance of wildlife. The Spaniards 

saw ducks, geese, cranes, herons, pelicans, 

curlews, pronghorn antelope, tule elk and 

grizzly bears, in large numbers.

Conditions began to rapidly change by the 

1850s, following European settlement and 

development. Pronghorn antelope were 

extirpated, tule elk were nearly made extinct 

and other wildlife were diminished by 

commercial hunting that was driven by the 

meat markets of San Francisco and mining 

camps of the California Gold Rush. Valley 

oaks and riparian forests were cut down 

for lumber and firewood to fuel steamboat 

traffic on the rivers. By the late 1800s and 

early 1900s, wetlands were being drained, 

creeks channelized and floodplains cleared of 

trees to create farmland. 

During the 1940s and 1950s, Friant Dam and 

other water storage/flood control facilities 

were built on the San Joaquin River and 

its major tributaries, and water diversions 

were made for agricultural, industrial and 

metropolitan uses. Flood control levees 

were constructed along the river’s course to 

contain and greatly narrow the floodplain. 

Nearly two centuries after Moraga’s 

expedition, the San Joaquin Valley landscape 

is dominated by agriculture and is now one 

of the most intensively farmed regions in 

North America. 

Refuge 

lands were 

historically 

a mosaic 

of riverine 

channels, 

broad 

riparian 

floodplains, 

wetlands and 

grassland 

savannas 

dominated 

by valley 

oaks.
San Joaquin River NWR Comprehensive Conservation Plan 21

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.

Soils and Geology

Schoenherr (1992) provides a broad 

overview of the soils and geology of 

California’s Central Valley:
22 San Joaquin River NWR Comprehensive Conservation Plan

“The Central Valley is a huge basin filled 

with sediments. The deepest parts of the 

gravels and sands are marine sediments 

that have accumulated since the late 

Jurassic—145 million years ago. The 

sea retreated from the Central Valley at 

about the same time that the southern 

Coast Ranges were uplifted, and during 

the long history of accumulation of marine 

sediments in the valley, the basement 

rock continued to subside. During most 

of the Pleistocene the area was occupied 

by shallow brackish and freshwater lakes. 

During the last 5 million years, sediments 

accumulated as alluvial deposits washed 

out of the mountains. These deposits are 

only a few thousand feet deep over most 

of the valley floor.” 

 

Physical conditions at the Refuge, especially 

the geology of the watersheds, are different 

on lands east or west of the San Joaquin 

River. A soil survey for eastern and western 

Stanislaus County used the San Joaquin 

River to delineate a boundary (McLauglin 

and Huntington 1968). Refuge lands on 

both sides of the river consist primarily of 

recent alluvial floodplains and basin lands. 

Soil types are often mixed alluvium mapped 

as soil associations. Basin soils are affected 

by high water tables from river water 

seepage, as well as saturation of the land 

by deep penetration of rain and irrigation 

water. Most soils exhibit very poor drainage, 

with a high water table at a depth of just 

three to six feet from December through 

April (Arkley 1964). If the land is irrigated, 

it provides prime farmland, although it 

floods every few years. 

Topography and River Geomorphology

Elevations on the Refuge vary from 20 feet 

along the edge of the San Joaquin River to 

40 feet in several locations near the eastern 

boundary. The Refuge is bisected by the San 

Joaquin River, which has flood control levees 

on both banks. Most of the Refuge lands 

along the river have been laser-leveled and 

intensively farmed in the past for row crops 

and irrigated pasture. Small parcels that 

retain the natural topography are present 

on the East Unit (for Refuge management 

purposes the area east of the San Joaquin 

River is referred to as the East Unit and 

lands west of the river as the West Unit). 

The riparian corridors inside the levees 

were not intensively developed and retain 

their natural topography. Within the levees, 

the sizes of the riparian areas range from 

narrow corridors to large floodplains of 900 

acres or more (i.e., Christman Island and 

Gardner’s Cove areas). A remnant of what 

used to be the main river channel is present 

on the West Unit and forms the western 

boundary of Christman Island. 

Two major tributaries of the San Joaquin 

River occur on the East Unit. The 

Stanislaus River is located along part of 

the Refuge’s north boundary where it flows 

into the San Joaquin River. The Tuolumne 

River forms the southern boundary of the 

East Unit and flows into the San Joaquin 

River near the Refuge’s southern end. Both 

rivers contribute significant flows to the San 

Joaquin River system and both have been 

modified by levees, gravel mining and water 

diversions, but to a lesser extent than the 

San Joaquin River. 

Eight smaller tributaries cross western 

Stanislaus County, draining from the eastern 

slopes of the Diablo Range to the San 

Joaquin River. From north to south they 

are: Hospital, Ingram, Kern, Del Puerto, 

Salado, Crow, Orestimba and Garzas creeks. 

These creeks have watersheds of similar 

size and are spaced three to five miles apart. 

Though rainfall is infrequent in these creek 

watersheds, it is often heavy, making them 

prone to erosion. None of the creeks flow 

continuously. Two of these, Hospital and 

Ingram creeks, cross the West Unit of the 

Refuge. Both have been heavily channelized 

on farmland located upslope from the Refuge 

and essentially, act as agricultural drains. 

Agricultural tailwater makes up the largest 

contribution of flows entering the Refuge 

from the watersheds of these two creeks.

 

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 
San Joaquin River NWR Comprehensive Conservation Plan 23

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. 

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).
24 San Joaquin River NWR Comprehensive Conservation Plan

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 

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. 
San Joaquin River NWR Comprehensive Conservation Plan 25

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 

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, 

Beaver crossing 

waterway; good 

water quality is a 

critical issue for 

many wildlife at the 

Refuge. 

Photo: Jerry Baldwin
26 San Joaquin River NWR Comprehensive Conservation Plan

Figure 5: Land Cover Map

Beckwith Rd. Gates Rd.

Shoemake Rd.

Dairy Rd.

Center Rd.

Orchard Rd.

River Rd.

Stanislaus Rd.

132 132

33

Miller Lake

Tuolumne River

San

Joaquin

River

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

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 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 

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

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.

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 

Shorebirds are 

dependent on 

wetlands such as 

this black necked 

stilt. 

Photo: Jerry Baldwin
San Joaquin River NWR Comprehensive Conservation Plan 29

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 pools for the 

presence of tadpole and fairy shrimp, but it 

is believed that the aquatic and terrestrial 

invertebrate fauna is representative for 

the Central Valley. Non-systematic field 

observations have detected the presence of 

representatives from nine of the thirteen 

insect orders with aquatic species (Merritt 

and Cummins 1996), as well as two types of 

native bees. Future work on invertebrates 

is dependent on funding and may include 
30 San Joaquin River NWR Comprehensive Conservation Plan

surveys for the endangered valley 

elderberry longhorn beetle (Desmocerus 

californicus dimorphus) and native bee 

inventories. 

Fish 

Habitats for fish on the Refuge include 

rivers, permanent wetlands, oxbows and 

sloughs. Three major rivers (i.e., San 

Joaquin, Tuolumne and Stanislaus) join 

on the Refuge and provide an important 

nexus for migratory fish. The stretch of the 

San Joaquin River and tributaries on the 

Refuge provide habitat and connectivity 

to aquatic habitats for a wide range of 

fish, including fall-run chinook salmon 

(Oncorhynchus tshawytscha), steelhead 

(Oncorhynchus mykiss) and Sacramento 

splittail (Pogonichthys macrolepidotus)—all 

species which are or proposed for federal 

listing under the Endangered Species Act. 

Appendix E provides the species list of fish 

known to occur or have the potential to occur 

at the Refuge.

Historically, California supported over 90 

freshwater species of native fishes; the 

Sacramento-San Joaquin Valley sustained 

approximately 60 native species (Schoenherr 

1992). Although there is still a diversity 

of aquatic habitats in the Central Valley, 

the natural assemblages of Central Valley 

fish communities have been degraded by 

altered flow regimes, levee construction/

maintenance and associated loss of 

floodplain, reduction in riparian habitats, the 

introduction of exotic fish species and other 

factors. At San Joaquin River NWR, many 

native fish species have been extirpated or 

are severely reduced in number, but several 

still occur, including fall-run chinook salmon, 

steelhead, Pacific lamprey (Lamptera 

tridentata), river lamprey (Lamptera 

ayresi), hitch (Lavinia exilicauda), 

Sacramento splittail, Sacramento blackfish 

(Orthodon microlepidotus), Sacramento 

sucker (Catostomus occidentalis), tule perch 

(Hysterocarpus traski), and prickly sculpin 

(Cottus asper). Some of these species are 

dependent on large river systems while 

others use sloughs and other backwater 

habitats. Introduced species now dominate 

many of the aquatic habitats of the Central 

Valley, including those at San Joaquin River 

NWR. Thirty-six introduced fish species are 

present in the Central Valley (Schoenherr 

1992). Refuge aquatic habitats are now 

dominated by the following non-native 

species: black bass (Micropterus salmoides), 

carp (Cyprinus carpio), bluegill (Lepomis 

macrochirus), threadfin shad (Dorosoma 

petenese), red shiner (Cyprinella lutrensis) 

and striped bass (Morone saxatilis).

Although the Refuge was originally 

established to benefit endangered and other 

migratory birds, it has the potential to 

benefit and enhance populations of native 

fish. The restoration of floodplain habitats 

on the Refuge, including riparian forest, 

and a return to more natural water regimes 

have the potential to benefit many natives 

dependent on floodplains for spawning and 

rearing purposes (Moyle 2002).

Amphibians and Reptiles

San Joaquin River NWR has the potential 

for twenty-seven species of reptiles and 

amphibians to occur (Appendix E). 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 

(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.
San Joaquin River NWR Comprehensive Conservation Plan 31

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). Compared to other 

habitats, oak woodlands and riparian 

habitats, which support multiple 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 

Drake northern 

shoveler. 

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

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) 

and mule deer (Odocoileus hemionus), and 

several domestic mammals which either 

trespass onto the Refuge or are used in the 

Refuge’s grazing program. A permanent 

mule deer population does not exist at the 

San Joaquin River NWR, although transient 

deer are periodically observed.

Threatened and Endangered Species 

Several threatened and endangered 

species occur or have the potential to occur 

on the San Joaquin River NWR. The 

Refuge was originally established for the 

Aleutian Canada goose, which was listed as 

endangered in 1967. Much of the population 

had been ravaged by arctic foxes introduced 

onto the Aleutian Islands in Alaska where 

this subspecies breeds (USFWS 1991). The 

population numbered 800 birds when the 

Coyote, a 

conspicuous 

predator at the 

Refuge.

Photo: Gary Powell
San Joaquin River NWR Comprehensive Conservation Plan 33

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 

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.
34 San Joaquin River NWR Comprehensive Conservation Plan

State of California listed endangered and 

threatened species which occur on the 

Refuge include the greater sandhill crane, 

yellow-billed cuckoo, Swainson’s hawk, 

willow flycatcher and bank swallow. The 

greater sandhill crane annually winters on 

and around the Refuge. Existing pastures, 

agricultural lands, and wetlands are used 

for foraging and roosting (Lewis 1979, 

Reinecke and Drapu 1979, Iverson et al. 

1982, Walker and Schemnitz 1987). Unlike 

lesser sandhill cranes, greater sandhill 

cranes within the Pacific Flyway have shown 

precipitous population declines because of 

destruction of wetlands and riparian habitat, 

lack of nesting habitat, and low productivity 

(Pogson and Lindstedt 1991). This area 

is one of eight geographic regions in which 

greater sandhill cranes winter in the Central 

Valley. The yellow-billed cuckoo, which relies 

upon riparian woodland, and the willow 

flycatcher, which depends on wet, shrubby 

habitat, have not recently been documented 

on the Refuge, although planned habitat 

restoration activities will likely create 

additional habitat for these species. The 

bank swallow require large cut banks for 

its breeding colonies; although such areas 

exist at the Refuge, there have been no bank 

swallow colonies during the last decade. 

The Swainson’s hawk is conspicuous at the 

Refuge, which provides habitat for several 

breeding pairs.

Historical and Cultural Resources

Cultural resources are physical remains, 

sites, objects, records, oral testimony and 

traditions that connect us to our nation’s 

history and the land’s past. Cultural 

resources include archaeological and 

historical artifacts, sites, landscapes, plants, 

animals, sacred locations and cultural 

properties that play an important role 

in the traditional and continuing life of a 

community.

Little formal cultural resources survey 

work has been conducted on the Refuge. 

The known cultural resources in and within 

one mile of the acquisition boundary of the 

San Joaquin River NWR consist of eight 

prehistoric sites and two historic sites. 

Cultural resources, especially archaeological 

sites, are fragile and nonrenewable. Most 

consist of worked stone, fire-altered rocks 

and organically enriched soil on or close 

to the surface. When compared to the 

surrounding landscape and contemporary 

cultural features, such as roads, ditches and 

structures, archaeological sites are small 

and subtle.

Prehistory

The Refuge is in the homeland of several 

Indian groups collectively known as the 

Northern Valley Yokuts. Within the Refuge, 

one group, the Tuolumnes aboriginal group, 

has been identified. The Tuolumnes’ home 

was east of the San Joaquin River, between 

the Stanislaus and Tuolumne rivers (True 

1981). The Refuge borders the territory 

of, and at various times, was probably 

occupied by, the Miwok tribe (Silverstein 

1978). As neighbors, the Yokuts and Miwok 

traded, intermarried and shared many 

cultural practices. Acorns (valley oak) and 

salmon were dietary staples, as were tule 

elk, antelope and jackrabbit (Levy 1995). 

Major Northern Valley Yokuts settlements 

were located within a short distance of 

the San Joaquin River banks and along 

major tributaries. As the San Joaquin 

and Tuolumne rivers have changed and 

meandered considerably over the years, 

these sites may appear most anywhere on 

the Refuge. Villages were typically built on 

ground higher than the surrounding area, 

situated to best exploit the rich subsistence 

resources without being consistently flooded. 

Yokuts would mainly congregate in the 

winter; during spring, summer and fall, 

groups would disperse to gather different 

resources (Jensen 1996). Villages were 

typically a scatter of four or five to several 

dozen structures. Each house served as a 

home to one family. Large villages might 

also have a great communal earth lodge for 

ceremonial use.

History

Spanish colonization of California began 

with the readily accessible coastal areas, 

avoiding the interior valleys during the 

18th century. Early in the 19th century, 

military explorers and missionaries moved 

away from the coast and to the inland 
San Joaquin River NWR Comprehensive Conservation Plan 35

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 

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 
36 San Joaquin River NWR Comprehensive Conservation Plan

Figure 6: Refuge Roads and Facilities

Beckwith Rd. Gates Rd.

Shoemake Rd.

Dairy Rd.

Center Rd.

Orchard Rd.

River Rd.

Stanislaus Rd.

132 132

33

San Joaquin County

Stanislaus County

Hanger

Two Houses

Lagoon/Pond

3 Barns

Small Barn

Large Barn

Green House

White House

Figure 6. Refuge Roads and Facilities

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

Miles

Barn

Hanger

House

Pond

Refuge Boundary

Private Roads

Public Roads

Refuge Roads

FWS Lands
San Joaquin River NWR Comprehensive Conservation Plan 37

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 

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 
38 San Joaquin River NWR Comprehensive Conservation Plan

Figure 7: Wetland Units

Lower

White

Lake

River

 Bend

Oxbow

Field

Food

Plot

Chrisman

Island

Riley

 Slough

Goose Lake

Nelson

Lake

Mid Lateral 4

Ingram Creek

Mid Lateral 3

Mid Main Drain

Mid Lateral 7

Ringneck

Wetland Beckwith Rd. Gates Rd.

Shoemake Rd.

Dairy Rd.

Center Rd.

Orchard Rd.

River Rd.

Stanislaus Rd.

132 132

33

Creekside

Pond

Upper

White

Lake

Miller Lake

Tuolumne River

San Joaquin

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 39

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 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 
40 San Joaquin River NWR Comprehensive Conservation Plan

Figure 8: Refuge Management Units

Beckwith Rd. Gates Rd.

Shoemake Rd.

Dairy Rd.

Center Rd.

Orchard Rd.

River Rd.

Stanislaus Rd.

132 132

33

Miller Lake

Tuolumne River

San

Joaquin

River

Stanislaus

River

San Joaquin County

Stanislaus County

Mohler Tract

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 41

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 

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 
42 San Joaquin River NWR Comprehensive Conservation Plan

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. 

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. 
San Joaquin River NWR Comprehensive Conservation Plan 43

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 

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 
44 San Joaquin River NWR Comprehensive Conservation Plan

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. 

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 
San Joaquin River NWR Comprehensive Conservation Plan 45

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 Plan

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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 51

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, as 

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 53

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 Plan

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

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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: 

Q Provide feeding and resting habitat for 

wintering waterfowl;

Q Provide habitat and manage for 

5 Management Goals, 

Objectives, and Strategies

endangered, threatened and/or sensitive 

species of concern;

Q Protect and provide habitat for 

neotropical migratory landbirds;

Q Preserve a natural diversity and 

abundance of plants and animals;

Q Provide an area for compatible, wildlifeoriented research; and

Q 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 

Refuge purposes. Each goal is supported 
60 San Joaquin River NWR Comprehensive Conservation Plan

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 61

Figure 9: Proposed Habitat Management for San Joaquin River NWR

Beckwith Rd. Gates Rd.

Shoemake Rd.

Dairy Rd.

Center Rd.

Orchard Rd.

River Rd.

Stanislaus Rd.

132 132

33

Miller Lake

Tuolumne River

San

Joaquin

River

Stanislaus

River

San Joaquin County

Stanislaus County

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 Plan

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 Maintain 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.

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 63

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 Plan

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 Continue growing alfalfa 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 65

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 Plan

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 67

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 Plan

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 69

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 71

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 condition. Coordinate pasture 

flooding with neighboring landowners to 

ensure an optimal amount of 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. Maintain a minimum of 115 

acres of grain corn, 430 acres of winter 

wheat, and 200 acres of foraging habitat. 

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 Geese using crop 

field on Refuge.

Photo: Gary Powell
San Joaquin River NWR Comprehensive Conservation Plan 73

building fat reserves for spring migration 

and the subsequent reproductive cycle. 

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. Review the mowing 

sequence and timing annually to meet 

program needs

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 
74 San Joaquin River NWR Comprehensive Conservation Plan

other migratory birds is minimized.

3.4.3 Keep Johnson Corral fields, Beet 

Field, Maze Bottoms, 90-Acre Field and 

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 
San Joaquin River NWR Comprehensive Conservation Plan 75

permitted by funding from the Endangered 

Species or Migratory Bird programs.

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 Realty Office 

on the acquisition of the Buffington parcel.

4.1.3 Work with the Service’s Realty Office 

on the acquisition of any private land parcels 

within the approved Refuge boundary as 

they become available from willing sellers.

Objective 2. Work with partners to protect 

other high value habitat along the San 

Joaquin River corridor.

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 

boundary of the San 

Joaquin River NWR, 

particularly in regards 

White-crowned 

sparrow, a common 

winter songbird.
76 San Joaquin River NWR Comprehensive Conservation Plan

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 Refuge Planning 

Office to prepare and process a boundary 

expansion proposal. 

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.)

Objective 5. Foster natural resource 

research opportunities on the San Joaquin 

River National Wildlife Refuge for 
San Joaquin River NWR Comprehensive Conservation Plan 77

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.

5.1.3 Complete the wildlife observation 

platform and kiosk on Beckwith Road 
78 San Joaquin River NWR Comprehensive Conservation Plan

(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 

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 
San Joaquin River NWR Comprehensive Conservation Plan 79

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.

Strategies:

5.5.1 Develop interpretive programs and 

events that incorporate Refuge themes and 

reveal the natural and cultural history of the 

area.
80 San Joaquin River NWR Comprehensive Conservation Plan

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.

5.7.3 Routinely examine and maintain public 

use facilities at the San Joaquin River NWR 

to determine and remedy unsafe conditions.

Environmental 

education at the 

Refuge. 

Photo: USFWS
San Joaquin River NWR Comprehensive Conservation Plan 81

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

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San Joaquin River NWR Comprehensive Conservation Plan 83

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:

Q Funding & Staffing

Q Step Down Plans 

Q Compliance Requirements

Q Adaptive Management

Q 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 

Complex. The largest costs for this initial 

outlay are for habitat restoration and 

6 Management Plan 

Implementation

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, step-down 

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.

Current or anticipated step-down 

plans for the San Joaquin River NWR 

include: 

Plans that are current and up-to-date:

Q Fire Management Plan (2001)
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 Plan

Q Spill Response Plan (2003)

Q Safety Management Plan (2000)

Q Continuity of Operations Plan (1999)

Plans that exist but need to be updated:

Q Disease Management Plan (1983)

Q Emergency Management Plan (1993)

Plans that need to be initiated:

Q Water Management Plan

Q Law Enforcement Plan

Q Public Use Management Plan

Q Upland Management Plan

Q Fisheries Management Plan

Q 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 stepdown 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 nongovernmental 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.

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.
San Joaquin River NWR Comprehensive Conservation Plan 87

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

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San Joaquin River NWR Comprehensive Conservation Plan 89

Appendices
90 San Joaquin River NWR Comprehensive Conservation Plan

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San Joaquin River NWR Comprehensive Conservation Plan 91

Appendix A: Glossary of Terms

Abiotic Factors. The non-living parts of an ecosystem, such as light, temperature, water, 

oxygen, and other nutrients or gases.

Accumulation. The build-up of a chemical in an organism due to repeated exposure (Henry 

and Hickey 1991).

Acorn. Fruit of an oak.

Acre-feet (AF). An acre-foot of water is the amount of water required to cover 1 acre of 

land to a depth of 1 foot; it is the equivalent of 325,851 gallons.

Adaptive Management. The rigorous application of management, research, and monitoring 

to gain information and experience necessary to assess and modify management activities. 

A process that uses feedback from refuge research and monitoring and evaluation of 

management actions to support or modify objectives and strategies at all planning levels. 

Alkalinity. Refers to the extent to which water or soils contain soluble mineral salts. 

Waters with a pH greater than 7.4 are considered alkaline.

Alluvial Fan. Accumulation of sediment where a stream moves from a steep gradient to a 

flatter gradient and suddenly loses transporting power.

Alluvium. Clay, sand, or other sediment that is gradually deposited by moving water (see 

also alluvial-fan).

Alternatives. Different sets of objectives and strategies or means of achieving refuge 

purposes and goals, helping fulfill the Refuge System mission, and resolving issues. (1) 

A reasonable way to fix the identified problem or satisfy the stated need. (40 CFR 150.2) 

(2) Alternatives are different means of accomplishing refuge purposes and goals and 

contributing to the System mission (Draft Service Manual 602 FW 1.5).

Animal Unit Month (AUM). The amount of forage necessary to maintain one 1,000-pound 

animal for one month.

Appropriated Water. Surface water in an irrigation district that has been assigned or 

allocated to owners of water rights.

Appurtenant Land. The land base to which water rights legally pertain or belong.

Aquatic. Pertaining to water, in contrast to land. Living in or upon water.

Aquatic Habitat. The physical, chemical, and vegetative features that occur within the 

water of lakes, ponds, reservoirs, rivers, irrigation canals, and other bodies of water.

Aquifer. An underground layer of porous rock, sand, or gravel containing large amounts of 

water.

Artifact. An object made by humans; usually in reference to primitive tools, vessels, 

weapons, etc.

ATV. All Terrain Vehicle ( either 3 or 4-wheeled vehicles).
92 San Joaquin River NWR Comprehensive Conservation Plan

Backward Linkages. The impacts associated with the purchase of inputs needed to 

produce a good whose output will change as a direct consequence of the water rights 

acquisition program.

Bank. The rising ground bordering a body of water or forming the edge of a cut or hollow.

Basin. A depressed area with little or no surface water; an area where water flows in, but 

where surface water does not flow out.

Bench Land. Eligible land with a water duty of 4.5 AF/acre/year.

Berries. Pulpy fruit of relatively small size.

Biodiversity (biological diversity). Refers to the full range of variability within and among 

biological communities, including genetic diversity, and the variety of living organisms, 

assemblages of living organisms, and biological processes. Diversity can be measured in 

terms of the number of different items (species, communities) and their relative abundance, 

and it can include horizontal and vertical variability. The variety of life, including the variety 

of living organisms, the genetic differences among them, and the communities in which they 

occur. 

Biological Control. The use of organisms or viruses to control weeds or other pests.

Biological Integrity. Biotic composition, structure, and functioning at the genetic, 

organism, and community levels consistent with natural conditions, including the natural 

biological processes that shape genomes, organisms, and communities. 

Biosphere. Synonym: ecosphere. Literally, the “living circle.” The portion of our planet (or 

any other, should life be discovered elsewhere) that contains and supports life. On Earth, 

this layer is roughly 7 to 8 miles high and, at the deepest depths of the oceans, about 7 

miles (a little more than 38,000 feet) deep. All life exists within this thin veneer circling 

the globe. The biosphere is subdivided into three main sections: lithosphere (the solid part 

of the planet’s surface), hydrosphere (the water on and under the planet’s surface), and 

atmosphere (the mass of air surrounding the planet).

Biome. A broad category of habitat; a type of ecosystem. Often characterized by a 

particular type of climax vegetation. May also be characterized by crucial abiotic factors, 

such as rainfall or temperature (both of which greatly influence what kind of climax 

vegetation will be present) values.

Biota. The plant and animal life of a region.

Biotic Factors. All the living organisms—fungi, protists, vertebrate, invertebrate, plants, 

etc.—and their impacts on other living things within an ecosystem.

Bogs. Low-lying and inadequately drained areas rich in plant residues.

Bottom Land. Eligible land with a water duty of 3.5 AF/acre/year.

Canal Losses. Seepage, evaporation, and operational spills from main-line canals and 

regulatory reservoirs.

Carbon Banking. The storage of atmospheric carbon in living tissues. Carbon is the most 

fundamental element of organic chemistry, so it is a major component of all living organisms. 
San Joaquin River NWR Comprehensive Conservation Plan 93

The largest “banks” are primary growth forests, especially tropical forests. The value of 

carbon banking is the removal of carbon from the atmosphere, where it contributes to the 

greenhouse effect.

Carcinogenic. Any substance that produces or causes cancer.

Carnivore. An animal that kills and eats other animals.

Categorical Exclusion (CE, CX, CATEX, CATX). A category of actions that do not 

individually or cumulatively have a significant effect on the human environment and have 

been found to have no such effect in procedures adopted by a Federal agency pursuant to the 

National Environmental Policy Act (40 CFR 1508.4).

CFR. Code of Federal Regulations.

Community. The combined populations of all organisms in a given area, and their 

interactions. For example, the frogs, fish, algae, cattails, and lily pads in a backyard pond 

make up a community.

Compatible Use. A wildlife-dependent recreational use or any other use of a refuge that, 

in the sound professional judgment of the Director, will not materially interfere with or 

detract from the fulfillment of the Mission of the System or the purposes of the refuge (Draft 

Service Manual 603 FW 3.6).

Comprehensive Conservation Plan (CCP). A document that describes the desired 

future conditions of the refuge or planning unit; and provides long-range guidance and 

management direction to accomplish the purposes of the refuge, helps fulfill the mission 

of the Refuge System; maintains and, where appropriate, restores the ecological integrity 

of each refuge and the Refuge System; helps achieve the goals of the National Wilderness 

Preservation System; and meets other mandates.

Concern. See Issue.

Cones. Ovule-bearing mass of scales or bracts of gymnosperm trees.

Coordination Area. A wildlife management area made available to a State, by “(A) 

cooperative agreement between the United States Fish and Wildlife Service and the State 

fish and game agency pursuant to Section 4 of the Fish and Wildlife Coordination Act (16 

U.S.C. 664); or (B) by long-term leases or agreements pursuant to the Bankhead-Jones 

Farm Tenant Act (50 Stat. 525; 7 U.S.C. 1010 et seq.).” States manage Coordination Areas, 

but they are part of the Refuge System. We do not require CCPs for Coordination Areas.

Cultural Resource. The physical remains of human activity (artifacts, ruins, burial mounds, 

petroglyphs, etc.) and conceptual content or context (as a setting for legendary, historic, or 

prehistoric events, such as a sacred area of native peoples) of an area. It includes historical, 

archaeological and architectural significant resources.

Cultural Resource Inventory. A professionally conducted study designed to locate 

and evaluate evidence of cultural resources present within a defined geographic 

area. Inventories may involve various levels, including background literature search, 

comprehensive field examination to identify all exposed physical manifestations of cultural 

resources, or sample inventory to project site distribution and density over a larger area. 

Evaluation of identified cultural resources to determine eligibility for the National Register 

follows the criteria found in 36 CFR 60.4 (Service Manual 614 FW 1.7).
94 San Joaquin River NWR Comprehensive Conservation Plan

Cultural Resource Overview. A comprehensive document prepared for a field office that 

discusses, among other things, its prehistory and cultural history, the nature and extent of 

known cultural resources, previous research, management objectives, resource management 

conflicts or issues, and a general statement on how program objectives should be met and 

conflicts resolved. An overview should reference or incorporate information from a field 

offices background or literature search described in Section VIII of the Cultural Resource 

Management Handbook (Service Manual 614 FW 1.7).

Delivery. The amount of irrigation water delivered to a water-users head gate during the 

irrigation season. 

Demand. The amount of water that a water-right holder calls for or requests in any one 

irrigation season. Under Nevada State law demand should not exceed entitlement. 

Deposits. Material that is laid down through the actions of wind, water, ice, or other natural 

process.

Designated Wilderness Area. An area designated by the United States Congress to be 

managed as part of the National Wilderness Preservation System (Draft Service Manual 

610 FW 1.5).

Detritus. An accumulation of decomposing plant and animal remains.

Dissolved-Solids. Particles that are dissolved and suspended in water. See also total 

dissolved solids.

Diversion. A structure in a river or canal that diverts water from the river or canal to 

another water course.

Downzoning. The act of reclassifying a land use of a particular area or property to a lower 

development-intensity land use classification; such as from moderate density residential to 

agriculture.

Drain. A canal that collects and transports excess water from irrigated farmland.

Drainwater. See irrigation drainwater.

Easement. A privilege or right that is held by one person or other entity in land owned by 

another.

Ecological Integrity. The integration of biological integrity, natural biological diversity, and 

environmental health; the replication of natural conditions. 

Ecology. The branch of biology that studies the interactions of organisms within an 

environment, either with other organisms (biotic factors) or with the non-living components 

(abiotic factors) of that ecosystem.

Ecosystem. The sum of all interacting parts of the environment and associated ecological 

communities within a particular area; an ecological system. Many levels of ecosystems 

have been recognized. Very few, if any ecosystems are self-contained; most influence, or 

are influenced by, components or forces outside the system. For administrative purposes, 

we have designated 53 ecosystems covering the United States and its possessions. These 

ecosystems generally correspond with watershed boundaries, and their sizes and ecological 

complexity vary. 
San Joaquin River NWR Comprehensive Conservation Plan 95

Ecosystem Approach. Protecting or restoring the natural function, structure, and species 

composition of an ecosystem, recognizing that all components are interrelated. 

Effect. A change in a resource, caused by a variety of events including project attributes 

acting on a resource attribute (direct), not directly acting on a resource attribute (indirect), 

another project attributes acting on a resource attribute (cumulative), and those caused by 

natural events (e.g., seasonal change).

Efficiency. With reference to an irrigation water delivery system, the proportion of the 

amount of water delivered for irrigation use compared to the total amount of water released 

to meet that delivery (i.e., amount of delivery divided by amount of release).

Effluent. Waste material discharged into the environment from a wastewater treatment 

facility.

Emergent Vegetation. Rooted, aquatic plants that have most of their vegetative (nonroot) 

parts above water.

Endemic Species. Plants or animals that occur naturally in a certain region and whose 

distribution is relatively limited to a particular locality.

Endangered Species. Any species that is in danger of extinction throughout all or a 

significant portion of its range and listed as such by the Secretary of the Interior in 

accordance with the Endangered Species Act of 1973. Endangered species are afforded 

protection under the Act as amended and under various State laws for State-listed species.

Entitlement. The annual maximum amount of water which can be delivered to a parcel of 

land, a product of eligible acres and water duty (expressed in acre-feet).

Environment. The sum total of all biological, chemical, and physical factors to which 

organisms are exposed; the surroundings of a plant or animal.

Environmental Assessment (EA). A concise public document, prepared in compliance 

with the National Environmental Policy Act, that briefly discusses the purpose and need 

for an action, alternatives to such action, and provides sufficient evidence and analysis of 

impacts to determine whether to prepare an environmental impact statement or finding of 

no significant impact (40 CFR 1508.9).

Environmental Health. Abiotic composition, structure, and functioning of the environment 

consistent with natural conditions, including the natural abiotic processes that shape the 

environment

Environmental Impact Statement (EIS). A detailed written statement required by 

section 102(2)(C) of the National Environmental Policy Act, analyzing the environmental 

impacts of a proposed action, adverse effects of the project that cannot be avoided, 

alternative courses of action, short-term uses of the environment versus the maintenance 

and enhancement of long-term productivity, and any irreversible and irretrievable 

commitment of resources (40 CFR 1508.11).

Ephemeral. Pertains to streams, lakes and wetlands that exist temporarily each year. 

Ethnography. The branch of anthropology that deals descriptively with specific cultures, 

especially those of non-literate peoples.
96 San Joaquin River NWR Comprehensive Conservation Plan

Evapotranspiration. The collective processes by which water is transferred from the 

surface of the earth, including from the soil and the surface of water-bodies (through 

evaporation) and from plants (through transpiration).

Exotic and Invading Species (Noxious Weeds). Plant species designated by Federal or 

State law as generally possessing one or more of the following characteristics: aggressive 

or difficult to manage; parasitic; a carrier or host of serious insects or disease; or nonnative, 

new, or not common to the United States, according to the Federal Noxious Weed Act (PL 

93-639), a noxious weed is one that causes disease or has adverse effects on man or his 

environment and therefore is detrimental to the agriculture and commerce of the Unite 

States and to the public health.

Fallow. Allowing land that normally is used for crop production to lie idle.

Farm Profits. Sales minus fixed and variable costs.

Fauna. All the plant species of a determined area.

Federal Trust Resources. A trust is something managed by one entity for another who 

holds the ownership. The Service holds in trust many natural resources for the people of 

the United States of America as a result of Federal Acts and treaties. Example are species 

listed under the Endangered Species Act, migratory Birds protected by the Migratory Bird 

Treaty Act and other international treaties, and native plant or wildlife species found on the 

Refuge System.

Ferns. Spore-forming vascular plants with leaf-like fronds.

Finding of No Significant Impact (FONSI). A document prepared in compliance with the 

National Environmental Policy Act, supported by an environmental assessment, that briefly 

presents why a Federal action will have no significant effect on the human environment 

and for which an environmental impact statement, therefore, will not be prepared 

(40 CFR 1508.13).

Flyway. A route taken by migratory birds between their breeding grounds and their 

wintering grounds. Four primary migration routes have been identified for birds breeding 

in North America: the Pacific, Central, Mississippi, and Atlantic Flyways.

Foraging. The act of feeding; another word for feeding.

Forbs. Herbaceous dicotyledonous plants.

Forward Linkages. Impacts that are associated with the use of goods whose production 

will change as a direct consequence of the water rights acquisition program. For instance, 

if additional cost to an alfalfa producer is incurred due to water rights acquisitions, this cost 

will be passed on to dairy producers by forward linkages. 

Fragmentation. The process of reducing the size and connectivity of habitat patches.

Friable Soil. Easily crumbled or pulverized soil.

Fruit. Pulpy fruit reproductive body of a seed plant.

Fungi. Saprophytic spore-forming, nonvascular plants such as mushrooms, molds, etc.
San Joaquin River NWR Comprehensive Conservation Plan 97

GIS. Geographic Information System. Refers to such computer mapping programs as 

ArcView, ArcInfo, ERDAS, etc.

Goal. Descriptive, open-ended, and often broad statement of desired future conditions that 

conveys a purpose but does not define measurable units (Draft Service Manual 620 FW 1.5).

Grain. A single, hard seed of a cereal grass.

Graminoids. Grasses and grass-like plants.

Gravely Soil. Soil dominated by gravel size grains 2 to 75 mm (.08 to 3.0) in diameter).

Greenhouse Effect. Warming of the surface and lower atmosphere of a planet caused by 

conversion of solar radiation into heat. The process of gases trapping heat from the sun in 

the Earth’s atmosphere is called the greenhouse effect.

Habitat. Suite of existing environmental conditions required by an organism for survival 

and reproduction. The place where an organism typically lives.

Habitat Restoration. Management emphasis designed to move ecosystems to desired 

conditions and processes, and/or to healthy forestlands, rangelands, and aquatic systems.

Head gate. The control works or gate at the entrance to a canal or conduit system.

Head gate entitlement. The amount of water/AF/year to which a particular water right is 

entitled.

Humus. The nutrient-rich, dark dirt found in areas with lots of decaying organic material 

suspended in the soil. Commonly referred to as “topsoil.” Humus is generally rich in 

saprobes and saprophytes (things that get their nutrients by decomposing dead organic 

materials, thereby speeding the nutrient cycles and making the soil richer).

Hydrologic Regime. The local pattern and magnitude of water flow influenced by season.

Hydrology. The science dealing with the properties, distribution, and circulation of water on 

and below the earth’s surface and in the atmosphere. The distribution and cycling of water 

in an area.

Hydrothermal. Relating to hot water-especially to the formation of minerals by hot 

solutions rising from a cooling magma. Underwater volcanoes can form hydrothermal 

chimneys.

Impoundment. A body of water created by collection and confinement within a series of 

levees or dikes thus creating separate management units although not always independent 

of one another.

Impact. See effect.

Informed Consent. The grudging willingness of opponents “to go along” with a course of 

action that they actually oppose (Bleiker).

Indigenous. Native to the area.
98 San Joaquin River NWR Comprehensive Conservation Plan

Industry Outputs. The estimated value of commodities produced in any given year.

Integrated Pest Management (IPM). Methods of managing undesirable species, such as 

weeds, including education; prevention, physical or mechanical methods or control; biological 

control; responsible chemical use; and cultural methods.

Invertebrate. Animals that do not have backbones. Included are insects, spiders, mollusks 

(clams, snails, etc.), and crustaceans (shrimp, crayfish, etc.).

Irrigated Acreage. The amount of land that is irrigated.

Irrigation Delivery. Refers to the delivery of water for irrigation purposes.

Irrigation Drainwater. Ideally, subsurface water which flows from irrigated land and 

generally transports higher concentrations of dissolved salts than the water applied to the 

land.

Irrigation Return Flow. Water which reaches surface drainage by overland flow or 

through groundwater discharge as a result of applied or natural irrigation.

Issue. Any unsettled matter that requires a management decision, e.g., an initiative, 

opportunity, resource management problem, threat to the resources of the unit, conflict in 

uses, public concern, or the presence of an undesirable resource condition. 

Lacustrine. Of or pertaining to lakes. More specifically, this term refers to permanent, 

seasonal, and intermittent lakes and reservoirs that typically have depths exceeding 6 feet 

and are larger than 20 acres, and that have less than 30 percent of their area covered by 

emergent wetlands vegetation.

Landowner. A person or entity indicated as the owner of property on the various ownership 

maps maintained by the Office of the County Assessor.

Lease. A legal contract by which water rights are acquired for a specified period of time for 

a specified rent or compensation.

Levee. An embankment along the river to prevent water from overbank flooding. 

Lichens. Algal-fungal symbiotic associations on solid surfaces.

Linear Regression. A mathematical technique used to determine the functional 

relationship between two variables; the resulting model can be used to predict the values of 

one variable when values of the other variable are given.

Lithic. A scatter of rocks less than 254 mm (10 in) in diameter on the ground.

Management Alternative. See Alternative.

Management Concern. See Issue.

Management Opportunity. See Issue.

Marsh. A periodically wet or continually flooded area where the water is shallow enough to 

allow the growth of emergent vegetation such as sedges, rushes, and cattails.
San Joaquin River NWR Comprehensive Conservation Plan 99

Marsh Habitat. Habitat that is characterized by shallow water and emergent vegetation. 

Unless otherwise specified, this term does not apply to similar habitat found in rivers, 

drains, or canals.

Migration. The seasonal movement from one area to another and back.

Migratory Bird. A bird that seasonally moves between geographic areas. In reference to 

birds in the Great Basin, a bird that breeds in Great Basin and subsequently moves south of 

the Great Basin for the winter months. Birds that migrate south of Mexico for the winter 

are considered neotropical migrants.

Mission Statement. Succinct statement of the unit’s purpose and reason for being 

(Region 7 Planning Staff).

Mitigation. To avoid or minimize impacts of an action by limiting the degree or magnitude 

of the action; to rectify the impact by repairing, rehabilitating, or restoring the affected 

environment; to reduce or eliminate the impact by preservation and maintenance operations 

during the life of the action.

Mobilization. Transport or movement of an element or other substance into the water 

column.

Model. A mathematical formula that expresses the actions and interactions of the elements 

of a system in such a manner that the system may be evaluated under any given set of 

conditions.

Moist-Soil. A process where water is drawn down intentionally or naturally to produce 

mudflats (i.e., moist soil) that are required for germination of many desirable plants.

Moss. Bryophytic plants.

Mud Flat. Expanses of mud contiguous to a water body often covered and exposed by tides.

Multiplier. A number by which another number is multiplied. Used in economic analysis to 

show linkages.

National Environmental Policy Act (NEPA). An act which encourages productive and 

enjoyable harmony between humans and their environment, to promote efforts that will 

prevent or eliminate damage to the environment and atmosphere, to stimulate the health 

and welfare of humans. The act also established the Council on Environmental Quality 

(CEQ). Requires all agencies, including the Service, to examine the environmental impacts 

of their actions, incorporate environmental information, and use public participation in the 

planning and implementation of all actions. Federal agencies must integrate NEPA with 

other planning requirements, and prepare appropriate NEPA documents to facilitate better 

environmental decision making (from 40 CFR 1500).

National Wildlife Refuge (Refuge or NWR). A designated area of land or water or an 

interest in land or water within the system, including national wildlife refuges, wildlife 

ranges, wildlife management areas, waterfowl production areas, and other areas (except 

coordination areas) under the Service jurisdiction for the protection and conservation of fish 

and wildlife. A complete listing of all units of the Refuge System may be found in the current 

Report of Lands Under Control of the U.S. Fish and Wildlife Service.
100 San Joaquin River NWR Comprehensive Conservation Plan

National Wildlife Refuge System, Refuge System, or System. Various categories of 

areas that are administered by the Secretary for the conservation of fish and wildlife, 

including species that are threatened with extinction; all lands, waters, and interest therein 

administered by the Secretary as wildlife refuges; areas for the protection and conservation 

of fish and wildlife that are threatened with extinction; wildlife ranges; game ranges; wildlife 

management or waterfowl production areas.

National Wildlife Refuge System Mission (mission). “The mission of the System is to 

administer a national network of lands and waters for the conservation, management, and, 

where appropriate, restoration of the fish, wildlife, and plant resources and their habitats 

within the United States for the benefit of present and future generations of Americans.” 

Native Species. Species that normally live and thrive in a particular ecosystem.

NEPA. National Environmental Policy Act of 1969.

Nectar. The sweet fluids secreted by flowers.

Nest Box. A box constructed to provide secondary cavity nesters a nesting site.

Nest Platform. An elevated platform constructed as a large bird nesting site.

Nest Island. An island constructed for bird nesting.

Niche. An organism’s “place,” or role, in an ecosystem. This involves many components 

of the organism’s life: where it lives (habitat), what it eats, by whom it is eaten, when it 

migrates or breeds, etc. All of these factors combine to determine the role of the organism in 

its ecosystem.

No Action Alternative. An alternative under which existing management would be 

continued. 

Non-Priority Public Uses. Any use other than a compatible wildlife-dependent recreational 

use.

Non-Structural Alternative: A hydraulically based flood control design alternative versus 

an engineered “hard” solution for control of flood waters.

Notice of Intent (NOI). A notice that an environmental impact statement will be prepared 

and considered (40 CFR 1508.22). Published in the Federal Register.

Nuts. Hard-shelled, dry fruit.

NWR. National Wildlife Refuge.

Objective. A concise statement of what we want to achieve, how much we want to achieve, 

when and where we want to achieve it, and who is responsible for the work. Objectives 

derive from goals and provide the basis for determining strategies, monitoring refuge 

accomplishments, and evaluating the success of strategies. Make objectives attainable, timespecific, and measurable. 

Operation and Maintenance (O&M) Costs. Charges paid by water users for delivery 

of water in the Newlands Project that are paid to the Newlands Project operator for 

reasonable and customary operation and maintenance of the delivery system.
San Joaquin River NWR Comprehensive Conservation Plan 101

Opportunities. Potential solutions to issues.

Organic Soil. Soil which contains greater than 20 percent of organic matter by weight.

Overbank Flooding. River flows that exceed the boundaries of the existing river channel 

and flood the adjacent riparian areas and bottomlands.

Palustrine. Of or pertaining to marshes or marsh habitat. More specifically, for this 

document, this term refers to permanently, seasonally, and intermittently flooded areas that 

typically have depths less than six feet and that have more than 30 percent of their area 

covered by emergent wetland vegetation. 

Passerine Bird. A songbird or other perching bird that is in the order Passeriformes. 

Blackbirds, crows, warblers, sparrows, and wrens for example.

Perennial. In reference to a body of water, one that contains water year-to-year and that 

rarely goes dry.

Pasture Land. Eligible land with a water duty of 1.5 AF/acre/year.

Peak Flow. The maximum discharge of a stream during a specified period of time.

Permeability. The property or capacity of porous rock, sediment, or soil to transmit water.

Phenology. Life cycle of particular species.

Phreatophytes. Plants whose roots penetrate to the water table.

Physiographic. Physical geography of a particular region of the U.S.

PILT. Payment-in-Lieu-of-Taxes.

Planning Area. The area upon which the planning effort will focus. A planning area may 

include lands outside existing planning unit boundaries currently studied for inclusion in 

the Refuge System and/or partnership planning efforts. It also may include watersheds 

or ecosystems outside of our jurisdiction that affect the planning unit. At a minimum, the 

planning area includes all lands within the authorized boundary of the refuge.

Planning Team. A team or group of persons working together to prepare a document. 

Planning teams are interdisciplinary in membership and function. Teams generally consist 

of a Planning Team Leader, Refuge Manager and staff biologists, a state natural resource 

agency representative, and other appropriate program specialists (e.g., social scientist, 

ecologist, recreation specialist). We also will ask other Federal and Tribal natural resource 

agencies to provide team members, as appropriate. The planning team prepares the CCP 

and appropriate NEPA documentation.

Planning Team Leader. The Planning Team Leader typically is a professional planner 

or natural resource specialist knowledgeable of the requirements of NEPA and who has 

planning experience. The Planning Team Leader manages the refuge planning process and 

ensures compliance with applicable regulatory and policy requirements. 

Planning Unit. A single refuge, an ecologically or administratively related refuge complex, 

or distinct unit of a refuge. The planning unit also may include lands currently outside 

refuge boundaries.
102 San Joaquin River NWR Comprehensive Conservation Plan

Plant Community. An assemblage of plant species of a particular composition. The term 

can also be used in reference to a group of one or more populations of plants in a particular 

area at a particular point in time; the plant community of an area can change over time due 

to disturbance (e.g., fire) and succession.

Playa. A shallow basin where water collects and is evaporated.

Pollutant. Any introduced gas, liquid, or solid that makes a resource unfit for a specific 

purpose.

Population. All the members of a single species coexisting in one ecosystem at a given time.

Preferred Alternative. This is the alternative determined (by the decision maker) to best 

achieve the Refuge purpose, vision, and goals; contributes to the Refuge System mission, 

addresses the significant issues; and is consistent with principles of sound fish and wildlife 

management. The Service’s selected alternative at the Draft CCP stage.

Prescribed Fire. The skillful application of fire to natural fuels under conditions of weather, 

fuel moisture, soil moisture, , etc., that allows confinement of the fire to a predetermined 

area and produces the intensity of heat and rate of spread to accomplish planned benefits to 

one or more objectives of habitat management, wildlife management, or hazard reduction.

Prescribed Natural Fires. A fire ignited by natural process (usually lightning) and allowed 

to burn within specified parameters of fuels, weather, and topography to achieve specified 

resource management objectives.

Primary Wetland Habitat. Habitat provided by shallow or deep water (up to 6-feet deep), 

with or without emergent and aquatic vegetation. Primary wetland habitat only exists when 

and where a primary wetland or portion of a primary wetland is flooded with water (visible 

surface water). Consequently, the size and shape of “primary wetland habitat” will fluctuate 

from season-to-season and year-to-year while the size and shape of the “primary wetland” 

within which primary wetland habitat occurs will remain constant from season to season 

and from year to year. Primary wetlands only provide habitat for waterfowl, shorebirds, 

muskrats, aquatic insects, and other wetland-dependent wildlife when they contain surface 

water (i.e., when they provide wetland habitat).

Prime Farmland. Farmland in an area or region that is considered to be the most ideal 

farmland based on several criteria; usually soil types and land productivity of the land are 

two of the most important criteria.

Prime Water. Any water delivered via a canal to a head gate.

Priority Public Uses. Compatible wildlife-dependent recreation uses (hunting, fishing, 

wildlife observation and photography, and environmental education and interpretation).

Proposed Action. The Service’s proposed action for Comprehensive Conservation Plans is 

to prepare and implement the CCP.

Public. Individuals, organizations, and groups; officials of Federal, State, and local 

government agencies; Indian tribes; and foreign nations. It may include anyone outside 

the core planning team. It includes those who may or may not have indicated an interest in 

Service issues and those who do or do not realize that Service decisions may affect them. 
San Joaquin River NWR Comprehensive Conservation Plan 103

Public Involvement. A process that offers impacted and interested individuals and 

organizations an opportunity to become informed about, and to express their opinions 

on Service actions and policies. In the process, these views are studied thoroughly 

and thoughtful consideration of public views is given in shaping decisions for refuge 

management.

Public Involvement Plan. Broad long-term guidance for involving the public in the 

comprehensive planning process. 

Public Scoping. See public involvement.

Purposes of the Refuge. “The purposes specified in or derived from the law, proclamation, 

executive order, agreement, public land order, donation document, or administrative 

memorandum establishing, authorizing, or expanding a refuge, refuge unit, or refuge 

subunit.” For refuges that encompass congressionally designated wilderness, the purposes 

of the Wilderness Act are additional purposes of the refuge. .

Purveyor. A private land owner or association that controls water rights for the ability to 

use the water.

Raptor. A bird of prey, such as a hawk, eagle, or owl.

Recommended Wilderness. Areas studied and found suitable for wilderness designation 

by both the Director and Secretary, and recommended for designation by the President to 

Congress. These areas await only legislative action by Congress in order to become part of 

the Wilderness System. Such areas are also referred to as “pending in Congress” (Draft 

Service Manual 610 FW 1.5).

Record of Decision (ROD). A concise public record of decision prepared by the Federal 

agency, pursuant to NEPA, that contains a statement of the decision, identification of all 

alternatives considered, identification of the environmentally preferable alternative, a 

statement as to whether all practical means to avoid or minimize environmental harm from 

the alternative selected have been adopted (and if not, why they were not), and a summary 

of monitoring and enforcement where applicable for any mitigation (40 CFR 1505.2).

Recreation Day. A standard unit of use consisting of a visit by one individual to a recreation 

area for recreation purposes during any reasonable portion or all of a 24-hour period.

Refuge. Short of National Wildlife Refuge.

Refuge Goal. See goal.

Refuge Operating Needs System (RONS). The Refuge Operating Needs System is a 

national database that contains the unfunded operational needs of each refuge. We include 

projects required to implement approved plans and meet goals, objectives, and legal 

mandates. 

Refuge Purposes. The purposes specified in or derived from the law, proclamation, 

executive order, agreement, public land order, donation document, or administrative 

memorandum establishing, authorizing, or expanding a refuge, a refuge unit, or refuge 

subunit (Draft Service Manual 602 FW 1.5).

Refuge Revenue Sharing Program or RRSP. Proves payments to counties in lieu of taxes 

using revenues derived from the sale of products from refuges.
104 San Joaquin River NWR Comprehensive Conservation Plan

Refuge Use. Any activity on a refuge, except administrative or law enforcement activity 

carried out by or under the direction of an authorized Service employee.

Remediation. The act or process of correcting a problem.

Reservoir. An artificially created lake in which water is collected and stored for future use.

Reservoir Storage. The volume of water held in a reservoir at any particular time.

Return Flow. See irrigation return flow. 

Riparian Area. The land adjacent to rivers, streams, and irrigation canals and drain ditches 

where vegetation is influenced by higher amounts of water than the surrounding lands. For 

the purpose of this EIS, riparian areas do not include the land surrounding lakes and basin 

marshes.

Riverine. Living or situated on the banks of a river; related to, formed by, or resembling a 

river.

RMIS. Refuge Management Information System database

Roots. The underground parts of plants.

Sales. Gross cash receipts.

Saline Soil. Soils which are saline or alkaline, supporting vegetation which is salt tolerant 

(e.g., pickleweed, salt grass, shadscale, iodine bush).

Salinity. An expression of the amount of dissolved solids in water.

Sand Dune. A hill or ridge of sand piled up by the wind.

Sandy Soil. Soil dominated by sand grain .05 to 2 mm (.002 to .08 in) in diameter.

Sap. The fluid part of a plant.

Secretary. Short of the Secretary of the Interior.

Sediment. Any material, carried in suspension by water, which ultimately settles to the 

bottom of water courses. Sediments may also settle on stream banks or flood plains during 

high water flow.

Seeds. The ovules of plants.

Service. Or USFWS. Short for U.S. Fish and Wildlife Service.

Shorebirds. Long-legged birds, also known as waders, belonging to the Order 

Charadriiformes that use shallow wetlands and mud flats for foraging and nesting.

Shrubs. Woody plants of smaller stature than trees when fully grown.

Soil Erosion. The wearing away of the land’s surface by water, wind, ice, or other physical 

process.
San Joaquin River NWR Comprehensive Conservation Plan 105

Sound Professional Judgement. A finding, determination, or decision that is consistent 

with principles of sound fish and wildlife management and administration, available science 

and resources, and adherence to the requirements of the Refuge Administration Act and 

other applicable laws.

Spatial Distribution. The pattern of frequency of a specific habitat type over a larger area.

Species. A distinctive kind of plant or animal having distinguishable characteristics, and 

that can interbreed and produce young. A category of biological classification. 

Species Composition. A group of species that inhabit a specific habitat type in its healthy 

state. To enhance species composition is to ensure that all or as many species as possible 

inhabit the appropriate habitat by improving the quality of that habitat.

Spill. With reference to a reservoir operations, water that is released, either inadvertently 

or through precautionary releases, in excess of that required to compensate for delivery 

system losses and to meet irrigation demand.

Spillway. The overflow channel of a dam.

Step-Down Management Plan. A plan that provides specific guidance on management 

subjects (e.g., habitat, public use, fire, safety) or groups of related subjects. It describes 

strategies and implementation schedules for meeting CCP goals and objectives. 

Strategy. A specific action, tool, or technique or combination of actions, tools, and techniques 

used to meet unit objectives (Draft Service Manual 602 FW 1.5).

Submergent Vegetation. Plants that grow completely submerged except when flowering.

Sub-surface Drainage. Irrigation water that percolated into the soil and subsequently 

flows under the surface of irrigated farmland into drains.

Surface Water. A body of water that has its upper surface exposed to the atmosphere.

System or Refuge System. National Wildlife Refuge System.

Talus. A slope formed by an accumulation of rock debris, often at the base of a cliff.

Targeting. A technique for acquiring or protecting water-rights whereby specific areas 

could be targeted, based on soil type classification or other relevant variables.

Terminus. In reference to a stream or river, its end point; where it flows into a lake or other 

basin.

Threatened Species. Any species that is likely to become an endangered species within the 

foreseeable future throughout all or a significant portion of its range, and one that has been 

designated as a threatened species in the Federal Register by the Secretary of the Interior. 

Threatened species are afforded protection under the Endangered Species Act of 1973.

Tiering. The coverage of general matters in broader environmental impact statements with 

subsequent narrower statements of environmental analysis, incorporating by reference, the 

general discussions and concentrating on specific issues (40 CFR 1508.28).
106 San Joaquin River NWR Comprehensive Conservation Plan

Total Dissolved-Solids (TDS). The total concentration of solids (or salts) dissolved in 

water; specific conductance is a surrogate measure of dissolved solids. More specifically, 

total dissolved-solids is an aggregate of carbonates, bicarbonates, chlorides, sulfates, 

phosphates, nitrates, etc. of calcium, magnesium, manganese, sodium, potassium, and other 

cations that form salts.

Trace Elements. Metallic elements (with atomic number >21) generally occurring in trace 

amounts in water, including iron, manganese, copper, chromium, arsenic, mercury, and 

vanadium.

Transfer Rate. The use-rate for a water right that is transferred from an owner to a buyer 

during a transaction.

Transient Species. Animals that migrate through a locality without breeding or 

overwintering.

Trust Species. Species for which the U.S. Fish and Wildlife Service has primary 

responsibility, including, most federally listed threatened and endangered species, 

anadromous fishes once they enter inland U.S. waterways, migratory birds, and certain 

marine mammals. 

Turbidity. Cloudiness of a water body caused by suspended silt, mud, pollutants, or algae.

Understory. Shrubs and herbaceous plants that typically grow beneath larger trees in a 

woodland.

Unit Objective. See objective. 

Unconsolidated. A geological term that describes soil that is not compacted.

Upland. An area where water normally does not collect and where water does not flow on 

an extended basis. Uplands are non-wetland areas.

Use-rate. The amount of water/AF/year to which a particular water right is entitled.

USFWS or Service. Short for U.S. Fish and Wildlife Service.

U.S. Fish and Wildlife Service Mission. Our mission is working with others to conserve, 

protect, and enhance fish, wildlife, and plants and their habitats for the continuing benefit of 

the American people.

Vegetation Community. See plant community.

Vegetation Type or Habitat Type. A land classification system based upon the concept of 

distinct plant associations.

Vernal Pool. Seasonally flooded depressions found on ancient soils with an impermeable 

layer such as a hardpan, claypan, or volcanic basalt. The impermeable layer allows the 

pools to retain water much longer then the surrounding uplands; nonetheless, the pools are 

shallow enough to dry up each season. Vernal pools often fill and empty several times during 

the rainy season. Only plants and animals that are adapted to this cycle of wetting and 

drying can survive in vernal pools over time.
San Joaquin River NWR Comprehensive Conservation Plan 107

Vertebrate. An animal having a segmented backbone or vertebral column; includes 

mammals, birds, fish, amphibians, and reptiles.

Vision Statement. A concise statement of what the planning unit should be, or what we 

hope to do, based primarily upon the Refuge System mission and specific refuge purposes, 

and other mandates. We will tie the vision statement for the refuge to the mission of 

the Refuge System; the purpose(s) of the refuge; the maintenance or restoration of the 

ecological integrity of each refuge and the Refuge System; and other mandates. 

VOW. Valley oak woodland habitat

Water Duty. The maximum rate at which water can legally be delivered to a farm head gate 

to satisfy a water right, usually expressed in AF/acre/year.

Water Year. That period of time between October 1 of one calendar year and September 

30 of the next calendar year. Traditionally, hydrologic data (i.e., stream flows, precipitation, 

etc.) was summarized or totaled for this period of time.

Waterfowl. A group of birds that include ducks, geese, and swans (belonging to the order 

Anseriformes).

Water-righted Acreage. The land base for which there are water rights.

Water Rights. A grant, permit, decree, appropriation, or claim to the use of water for 

beneficial purposes, and subject to other rights of earlier date of use, called priority, or prior 

appropriation.

Watershed. The entire land area that collects and drains water into a river or river system.

Wetland. Land that is transitional between upland (terrestrial) and aquatic systems 

(greater than about 6-feet deep) where the water table is usually at or near the surface or 

the land is covered by shallow water... wetlands must have one or more of the following three 

attributes: (1) at least periodically, the land supports predominantly hydrophytes (plants 

that require wet conditions); (2) the substrate is predominantly undrained hydric soil; and 

(3) the substrate is nonsoil and is saturated with water or covered by shallow water at some 

time during the growing season of each year (Cowardin and others, 1979).

Wetland Habitat. Habitat provided by shallow or deep water (but less than 6-feet deep), 

with or without emergent and aquatic vegetation in wetlands. Wetland habitat only exists 

when and where a wetland or portion of a wetland is covered with water (visible surface 

water). Consequently, the size and shape of “wetland habitat” will fluctuate from seasonto-season and year-to-year while the size and shape of the “wetland” within which wetland 

habitat occurs will remain constant from season to season and from year to year. Wetlands 

only provide habitat for waterfowl, shorebirds, muskrats, aquatic insects, and other wetlanddependent wildlife when they contain surface water (i.e., when they provide wetland habitat).

Wilderness Review. The process we use to determine if we should recommend Refuge 

System lands and waters to Congress for wilderness designation. The wilderness review 

process consists of three phases: inventory, study, and recommendation. The inventory is 

a broad look at the refuge to identify lands and waters that meet the minimum criteria for 

wilderness. The study evaluates all values (ecological, recreational, cultural), resources 

(e.g., wildlife, water, vegetation, minerals, soils), and uses (management and public) within 

the Wilderness Study Area. The findings of the study determine whether or not we will 

recommend the area for designation as wilderness.
108 San Joaquin River NWR Comprehensive Conservation Plan

Wilderness Study Areas. Lands and waters identified through inventory as meeting the 

definition of wilderness and undergoing evaluation for recommendation for inclusion in the 

Wilderness System. A study area must beet the following criteria: (1) generally appears 

to have been affected primarily by the forces of nature, with the imprint of man’s work 

substantially unnoticeable; (2) has outstanding opportunities for solitude or a primitive and 

unconfined type of recreation; (3) has at least 5,000 contiguous roadless acres or is sufficient 

in size as to make practicable its preservation and use in an unimpaired condition (Draft 

Service Manual 610 FW 1.5).

Wilderness. See designated wilderness.

Wildfire. A free-burning fire requiring a suppression response; all fire other than 

prescribed fire that occurs on wildlands (Service Manual 621 FW 1.7).

Wildland fire. Every wildland fire is either a wildfire or a prescribed fire (Service Manual 

621 FW 1.3)

Wildlife. All nondomesticated animal life; included are vertebrates and invertebrates.

Wildlife Corridor. A landscape feature that facilitates the biologically effective transport 

of animals between larger patches of habitat dedicated to conservation functions. Such 

corridors may facilitate several kinds of traffic, including frequent foraging movement, 

seasonal migration, or the once in a lifetime dispersal of juvenile animals. These are 

transition habitats and need not contain all the habitat elements required for long-term 

survival of reproduction of its migrants.

Wildlife-Dependent Recreational Use. “A use of a refuge involving hunting, fishing, 

wildlife observation and photography, or environmental education and interpretation.” These 

are the six priority public uses of the Refuge System as established in the National Wildlife 

Refuge System Administration Act, as amended. Wildlife-dependent recreational uses, other 

than the six priority public uses, are those that depend on the presence of wildlife. We also 

will consider these other uses in the preparation of refuge CCPs; however, the six priority 

public uses always will take precedence.

Zoning. The act of dividing a city or county into zones, and assigning particular, allowable 

land uses for each of the defined zones; also used in reference to the end product of such a 

process.

Zooplankton. Small animals free-floating in the oceans and lakes of the world. Unable to 

control their movements through the oceans, they are at the mercy of the currents and tides. 

They feed on smaller zooplankton or on phytoplankton. Examples of zooplankton would 

include true plankton (animals that will remain planktonic all their lives) such as jellyfish, 

ctenophores, chaetognaths, and—the most important of all plankton—the shrimp-like krill 

of the south oceans. Zooplankton also includes transient plankton (organisms that will not 

remain planktonic for their whole lifecycle) such as baby crabs and lobsters, newly hatched 

fish, coral larvae, etc.
San Joaquin River NWR Comprehensive Conservation Plan 109

Appendix B: Response to Comments on the Draft CCP/EA

Comments by the public, organizations, and agencies on the draft Comprehensive 

Conservation Plan (CCP) of the San Joaquin River National Wildlife Refuge (NWR) were 

solicited during July 2006. Electronic and hard copies of the draft CCP were placed in four 

local libraries, and were made available at the main office of the San Luis NWR Complex, 

for the convenience of the public. The document was also available to the public on the U.S. 

Fish and Wildlife Service’s California-Nevada Operations Planning Office’s website. A 

FWS press release was issued regarding the opportunity for public comment on the CCP in 

July 2006. A local newspaper (Patterson Irrigator) printed a story on the CCP during this 

process to encourage public comment. In addition, 150 hard copies and 150 compact disks of 

the CCP were mailed to individuals, organizations, and agencies listed on the CCP mailing 

list (Appendix K).

A limited number of comments (less than ten) were received from this effort. Several phone 

calls from the public or organizations/agencies were also received regarding the CCP; all 

were in favor of the preferred management alternative in the CCP. The California State 

Clearinghouse, which includes all state agencies including the California Department of Fish 

and Game, indicated they had no comments regarding the draft CCP. All written and or oral 

comments were grouped by category for response. Most of these issues had previously been 

identified during the planning process and addressed in the CCP.

Selection of Alternative

All respondents which indicated a preference selected the Service’s preferred alternative 

– Alternative D: Biodiversity Focus. All felt this alternative met the broadest needs of the 

resources and a public use program at the San Joaquin River NWR.

Wetland Management

One respondent was unclear on the definition of the different wetland types mentioned 

in the CCP. These are defined in Chapter 3 – Refuge Settings. The need for shorebird 

management on the Refuge was also expressed; FWS agrees, and this need is included 

under Goal 1 (Biological Diversity), Objective 1 (management of wetlands), Objective 2 

(management of seasonal wetlands), and Objective 8 (developing a Refuge inventory and 

monitoring plan).

Upland and Cropland Management

One reviewer stressed the need to not only control invasive weeds on pasture/grasslands as 

listed in Goal 3 (Aleutian Canada Goose), Objective 1; but also to control these invasives in 

winter wheat. This issue is covered in Goal 3 (Aleutian Canada Goose), Objective 2.

It was also suggested that Goal 3 (Aleutian Canada Goose), Objective 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 be done in conjunction 

with neighboring landowners rather than on the Refuge. The Service agrees with part of 

this suggestion and has modified Objective 3.1.3 to read “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 condition. Coordination of pasture flooding 

with neighboring landowners will be conducted to ensure an optimal amount of wet meadow 

conditions.”
110 San Joaquin River NWR Comprehensive Conservation Plan

It was also suggested for Goal 3 (Aleutian Canada Goose), Objective 2.4 that standing corn 

mowing be reviewed annually and modified as necessary. This strategy was changed by 

adding the following sentence to Objective 2.4A: Review the mowing sequence and timing 

annually to meet program needs.

Public Use Activities

Most respondents agreed with the Service’s preferred alternative of focusing the Refuge’s 

public use program on the Service’s six priority public use activities: wildlife observation, 

nature interpretation, photography, hunting, fishing, and environmental education.

Several respondents indicated that the different public use activities should not conflict 

with one another. In order to reduce and/or eliminate potential conflicts, the CCP indicates 

several step-down plans will be prepared; these plans will address any concerns including 

potential conflicts of different public use activities. Any hunting program implemented 

will be developed to eliminate/reduce conflicts with other public use activities, and will be 

designed to reduce disturbance to sensitive wildlife -- including greater sandhill cranes. One 

strategy of the CCP (Objective 2.6.5) is to limit disturbance in crane roosts and foraging 

areas by maintaining sanctuaries.

One respondent indicated a visitor center should be constructed by Dairy Road on the 

Refuge. Because the Refuge is in its early stages of developing a public use program it was 

felt that instead of a visitor center a visitor contact station be developed first as indicated in 

Goal 5 (Public Use of the Refuge), Objective 2.

One comment indicated that no boat launching facilities should be developed on the Refuge 

because enough launch facilities already exist in proximity to the Refuge. The Service’s 

original scoping process indicated that suitable launch facilities did not exist; however, the 

issue will be re-examined when the Refuge prepares a step-down public use plan.

Water Supplies and Infrastructure

One letter indicated a local irrigation district’s concerns regarding water conveyance 

infrastructure and water supplies. The CCP indicates a water management plan for the 

Refuge will be prepared which will address water needs and issues. No impacts will occur to 

any non-Refuge water conveyance system and any needed water supplies will be sought only 

through identified willing sellers and existing procedures.

Refuge Complexing

The San Joaquin River NWR is one of four Refuge units comprising the San Luis NWR 

Complex. The other units include San Luis NWR, Merced NWR, and Grasslands Wildlife 

Management Area. One comment indicated that the San Joaquin River NWR should not 

be part of the Complex, but should be a stand-alone Refuge because of its size, complexity, 

and resource value; ensuring that it receives the needed attention it deserves. The reason 

the Refuge is part of the Complex is to make it more efficient and more productive. More 

activities can be and are accomplished at the Refuge by it being part of a Complex than 

would be accomplished if it were not part of a Complex. The San Joaquin River NWR was 

made part of a Complex to help reduce costs, including annual operation, by being able to 

share staff and other resources with other units to provide effective law enforcement, public 

use, administrative, fire, and resource management programs. Due to budget constraints, 

refuges are being complexed nationwide expressly for the purpose of such cost-effectiveness 

and efficiency.
San Joaquin River NWR Comprehensive Conservation Plan 111

Appendix C: Public Scoping & Involvement Process

The Planning Process

The planning process followed for the development of this CCP was guided by the Refuge 

Planning Chapter of the Fish and Wildlife Manual (Part 602 FW 2.1, November 1996) 

and evolving policy related to the Refuge System Improvement Act of 1997. Key steps 

have included: (1) preplanning, (2) identifying issues and developing vision; (3) gathering 

information; (4) analyzing resource relationships; (5) developing alternatives and assessing 

environmental effects; (6) identifying a preferred alternative; (7) publishing the draft plan; 

8) documenting public comments on the draft plan; (9) preparing the final plan; (10) securing 

approval of the Regional Director; and finally (11) implementing the plan. The life-span 

of the plan is 15 years, but the Service will review the CCP periodically. The CCP may be 

amended as necessary at anytime under the adaptive management strategy. 

The Refuge held quarterly Community Forum Meetings to develop components of the 

draft plan, identify issues, concerns, and opportunities, and update the public on refuge 

operations. 

In a Federal Register Notice dated February 23, 1999, the Service announced that it was 

preparing a plan for the Refuge. A series of planning updates were used to inform the 

public of the CCP Process and potential refuge operations. These updates were a forum 

to announce upcoming public workshops and meetings, as well as update the public on the 

progress the CCP team was making. These updates were mailed to interested and affected 

parties. The first planning update for the Refuge was released in March 1999 . This update 

informed the public about the Refuge and Refuge planning process and announced a public 

workshop to be held to identify issues, concerns, and described preliminary goals and 

key areas of management focus to be discussed in a management plan and environmental 

assessment. The planning update also encouraged the public to provide comments and 

concerns about Refuge management via e-mail, phone, and US Postal Service. The second 

planning update, released in October 1999, described the issues, concerns, and opportunities 

identified at the public workshop. The Refuge held quarterly Community Forum Meetings 

during this time. The third planning update released January 2000, reported on issues 

identified by the Community Forum. A fourth planning update released in April 2006 

announced the pending release of the Draft CCP and EA.

Public input received in response to these updates, workshops and briefings is incorporated 

into the CCP and EA, and a summary of comments is included in this appendix. The original 

comments are being maintained in planning team files at the California/Nevada Refuge 

Planning Office in Sacramento, CA, and are available for review upon request.

The Service published a Notice of Availability of the draft CCP and EA in the Federal 

Register on June 22, 2006. The Draft CCP and EA were distributed to Refuge partners, 

adjacent landowners, government agencies, local jurisdictions, community groups and 

private citizens. The 30-day comment period closed on July 24, 2006. A total of seven 

comment letters were received during the review period. Our response to these comments is 

included in Appendix B of the final CCP. 

CCP implementation began with the signing of the Finding of No Significant Impact. The 

CCP will be reviewed by Refuge staff while preparing annual work plans and updating the 
112 San Joaquin River NWR Comprehensive Conservation Plan

Refuge Management Information System (RMIS) database. RMIS is a master database 

that contains refuge realty information, operation needs, maintenance needs, as well as CCP 

schedules. It may also be reviewed during routing inspections or programmatic evaluations. 

Results of the reviews may indicate a need to modify the plan. The periodic review of the 

objectives and strategies is an integral part of plan implementation, and management 

activities may be modified if the desired results are not achieved. If minor changes are 

required, the level of public involvement and NEPA documentation will be determined by 

the Project Leader. The CCP will be formally revised about every 15 years. 

Detailed Listing of all Issues, Concerns, and Opportunities and Service Responses 

to Each Item

Issues, concerns, and opportunities were identified through early planning discussions 

and through the public scoping process, which began with the mailing of the first planning 

update in March 1999 The planning team held a public open house in March 1999 and a 

second open house in April 2000. The first meeting was a scoping meeting held to gather 

the public’s issues and concerns about the refuge. The Core team presented preliminary 

alternatives at the second meeting. In addition, Service staff held quarterly Community 

Forums to meet with the public and discuss concerns in further detail. Other comments 

were received orally from meetings and in writing. 

The following issues, concerns, and opportunities are a compilation of information received 

by the Service throughout the planning process: 

Wildlife Management and Restoration:

One person stated that they support the concept of multiple use land management and 

considered cattle and cropping to be compatible with wildlife. They wanted the Service 

to consider strongly any decision to discount cattle on the Refuge. Others felt that the 

Refuge’s primary concern should be wildlife and that the Refuge should remain focused 

on what attracted geese and waterfowl to the area in the first place before making 

improvements. Others felt that the Refuge should have an interest in permanent wetlands 

in addition to other habitat types. Also, dairies to the east are concerned about crop 

depredation. One person suggested that the Refuge consider the reintroduction of Tule elk. 

Lastly, a comment was made that any environmental restoration that would involve levee 

breaching in the new Refuge land west of the San Joaquin River must consider potential fish 

entrapment.

One individual strongly advised the Service to pursue screening water diversions by the 

West Stanislaus Irrigation District to prevent fish from entering into the irrigation pumps 

and dying. Another suggested that the operator of the 262 cfs pump should screen their 

diversion on the new Refuge property to prevent fish entrainment and mortality and that the 

operator should be able to fund the screen to release them from their responsibility of their 

unscreened diversion. 

A duck club operator expressed that the Refuge was causing a disruption of waterfowl 

distribution because waterfowl would tend to migrate toward the Refuge, where there is no 

hunting, and abundant food.

Concern was expressed about the restoration of the new Refuge addition. Sacramento 

River Partners, a nonprofit organization, has been hired by the Refuge to prepare a prerestoration plan for the new Refuge lands west of the San Joaquin River. This plan has 

subsequently been sent to the USDA Natural Resources Conservation Service for review.
San Joaquin River NWR Comprehensive Conservation Plan 113

Visitor Services (Recreation and Public Use): 

Several comments were raised about public use. Many people felt that the Service should 

preserve the Refuge for wildlife and people to enjoy and that the Service should provide 

access which would provide something there for the people. It was felt that people would 

want to protect and support the Refuge if the Service provided them with access and 

educated them. One person felt that no public camping should be allowed at the Refuge, 

with the possible exceptions of the Boy Scouts and educational groups. 

Several people were concerned about the impact of visitors on the adjacent landowners. One 

individual said that an observation tower may bring in too many people. Another comment 

that the Service shouldn’t let too many people into the Refuge and that the Refuge should 

be kept as private as possible in the near term. Another commented that the Service should 

monitor public use. Local landowners have expressed that Refuge public access should not 

be located near private residences. 

Several people requested access to the Refuge, especially at Christman Island. Others 

wanted the Refuge to provide interior access where compatible with sensitive species and 

allow access to the river to show and educate students about the river and Refuge. Others 

requested canoeing access.

Members of the public suggested many non-consumptive activities and facilities, including 

a docent program so that volunteers could be trained to provide tours for adults, students, 

and families. Others requested that the program with the outdoor recreation specialist and 

school groups be allowed to continue to provide opportunities for community building and 

environmental education. Others requested birding and photography opportunities in the 

form of maps that identify good areas for these activities that minimize bird disturbance 

but provide viewing opportunities. Requested facilities include photography blinds with 

north, east, and west camera ports and a visitor education center needed. However, it was 

requested that the visitor center be located away from any houses.

Comments were made that were in favor and against hunting. Some felt that the Service 

should minimize hunting and promote non-consumptive activities such as catch and release 

fishing. Other individuals requested that there be no hunting on the Refuge, “even of birds.”

Others wanted the Refuge to include hunting opportunities, including waterfowl and upland 

game and felt that local support would increase if hunting were considered. One individual 

expressed concern that Refuge operations affects waterfowl distribution by attracting 

waterfowl away from hunting clubs onto the Refuge. Members of the Old Fisherman’s Club 

members expressed concern that the Service will acquire the club or limit their activities. 

However, the land on which the club is located is owned by the Lyon’s family, who have said 

that they weren’t interested in selling the land, and the Service is not interested in acquiring 

it.

Refuge Staffing: 

Members of the community said that they would feel better if one consistent person were 

available at the Refuge to communicate with, such as a full time Refuge Manager and that 

they would like to see continuity of Refuge management as well as an operational budget for 

the Refuge. Another individually felt strongly that the plan was like putting the cart before 

the horse and that the Service should not develop CCP before a manager is in place for the 

Refuge. A request was made for staff presence on weekends for public access
114 San Joaquin River NWR Comprehensive Conservation Plan

Flood Management: 

Some people offered support for Non-Structural Agreement (NSA). The Refuge staff 

expressed concern that the Corps has not signed their agreement to implement its portion 

of the NSA. Congressman Condit’s representative stated that their number one priority is 

the adjacent landowners’ desire to complete the NSA flood control project with the Corps. 

One individual felt that dredging San Joaquin River was not an appropriate method of flood 

control. Another was concerned about flood control at Red Bridge slough. Other landowners 

are concerned about flood control and their ability to continue to drain across the Refuge’s 

newly acquired property on the west side of the San Joaquin River. 

Modesto Irrigation District (MID) pays to operate Miller Lake pumps to prevent flooding in 

winter. Water is pumped into river when the water in Miller Lake is high, otherwise, Miller 

Lake water flows by gravity into the river. One individual expressed concern over who 

would pay for the pumping in the future and questioned whether MID or the Service would 

pay for the pumping or would the area flood instead.

Wetland and Water Management: 

One individual expressed concern that winter water storm drainage of probably poor quality 

drains from Modesto into Miller Lake. Another was concerned about the impacts of poor 

quality water from upstream on the Refuge and wondered what the Refuge would do to 

avoid attracting waterfowl to a site with poor water quality on the Refuge. 

Concern was expressed by a Community Forum participant that water management on 

the new Refuge lands west of the San Joaquin River was causing a rise in the groundwater 

level. Adjacent landowners expressed concern that an elevated groundwater level would 

make the lands surrounding the Refuge more difficult to farm. Refuge staff informed 

those attending the Community Forum that a letter had been sent to adjacent landowners 

requesting permission to establish observation wells on lands adjacent to the Refuge. These 

observation wells would monitor groundwater levels.

Refuge Proximity to Private Lands: 

Adjacent landowners are concerned that the Refuge will curtail their abilities to operate 

and use their lands. They are concerned that the Refuge will limit their use of chemicals, 

require adjacent landowners to have buffers, and/or fill their fields with endangered species. 

Landowners were also concerned about trespassing from the Refuge onto their property. 

Adjacent farmers to the west are concerned about additional restrictions on them that may 

be placed on them because of their proximity to the Refuge. 

Public Issues Pertaining to All Alternatives

There are certain issues addressed by the public that would remain consistent under all 

alternatives of the Environmental Assessment. The following describes issues and concerns 

received by the Service throughout the planning process, that will be addressed separately 

from the above:

Land Protection and Boundary Expansion:

Several people at the public workshop and in letters expressed a desire for the Refuge to 

expand its boundary as did other agencies and programs within the U.S. Fish and Wildlife 

Service such as the Anadromous Fish Restoration Program. Landowners outside the 

current Refuge boundary, up to several miles south of the Refuge, expressed an interest in 

either selling an easement on their property or selling their property in fee to the Service. 

Also, Stanislaus County is interested in complementing San Joaquin River NWR with 

mitigation banking proposal.
San Joaquin River NWR Comprehensive Conservation Plan 115

Transportation: 

California Department of Transportation (Caltrans) has been investigating the expansion 

and realignment of State Highway 132 since the 1980’s. One person commented that they 

did not want a freeway. Others complained about the danger of Highway 132, including 

people driving 65 - 100 mph, passing on double yellow lines, and 2 accidents per month at the 

intersection of Gates and 132. One person said that the Refuge should construct pullouts 

along 132, however others commented that Highway 132 is not safe for a pull out because 

traffic moves so fast. Another individual commented that it was very helpful to close Page 

Road because it resulted in much less traffic in the area. 

Mosquito Abatement: 

At one of the community forums, Turlock Mosquito Abatement District (TMAD) and East 

Side Mosquito Abatement District (ESMAD), were concerned that they will be unable to 

control mosquitoes produced on the Refuge the way they traditionally do. The Districts 

expressed their concern that people within their Districts may be exposed to mosquitotransmitted diseases. The Community of Grayson is concerned that mosquito levels will be 

higher than they have been in the past, should TMAD and ESMAD not be allowed to control 

mosquitoes in the traditional way on the Refuge. 

U.S. Fish and Wildlife Service Staff Key Issues

The following key issues, concerns and opportunities were identified during the planning 

process by FWS Staff:

Wildlife Management and Restoration:

Refuge staff commented that Aleutian Canada goose, anadromous fish, and other former 

and current endangered species should receive a high level of consideration in the CCP 

process. Goose flyway management and control of nonnative weeds, such as Arundo will 

continue to be an important issue for the Service.

Fish have a tendency to be come entrapped by unscreened diversions, adversely affecting 

fish resources.

Avian cholera is a disease that affects the birds on the Refuge. If it is uncontrolled, this 

disease has the potential to decimate the waterfowl population on the Refuge, including 

the Aleutian Canada geese. Furthermore, waterfowl using the Stanislaus County sewage 

treatment plant located about seven miles southeast of the Refuge are especially in danger 

of contracting avian cholera due to the high concentrations of birds using the area.

Nonnative weeds on the Refuge adversely affect native plants.

Recreation and Public Use:

The Service recognizes public access as an important issue to address in the CCP and sees 

uncontrolled access, or trespassing as an issue for the Refuge and adjacent landowners.

Refuge staff noted that they would like to avoid locating visitor facilities near adjacent 

private residences. 

Refuge staff have expressed that the hunting on the Refuge may not be of sufficient quality 

or quantity to justify a hunting program. Refuge staff have also expressed that fishing 

access must be controlled to prevent trespassing on other parts of the Refuge.
116 San Joaquin River NWR Comprehensive Conservation Plan

Refuge Staffing:

The lack of a Refuge Manager has been an ongoing issue. Law enforcement continues to be 

an issue for FWS staff with vandalism, illegal dumping of hazardous waste, trespass, theft 

included on the list of crimes committed at the Refuge. 

Flood Management: 

The Service is concerned that the Corps’ non-structural alternative for levees be 

implemented as soon as possible.

Wetland and Water Management: 

The Service is concerned about the water quality of the San Joaquin River since it has been 

designated as a water quality impairment area. The river carries a high load of sediment 

from the steeper gradient of the incoming Stanislaus and Tuolumne rivers which are 

sometimes exacerbated by human activity. The sediment carries contaminants.

The Service is also concerned that the Refuge has sufficient reliable water supply and rights 

for habitat management. 

Agricultural drainage has presented challenges for the Refuge. When the Refuge acquired 

the properties west of the Stanislaus River, it acquired two drainage systems that provide 

drainage for about 8,000+ acres of agricultural lands. The first system drains through 

what was formerly the Hagemann property. Agricultural lands southwest of the Hagemann 

property formerly drained through ditches running through the Hagemann property. 

Originally, these waters drained to the river with a gravity drainage system. Water would 

pool in Upper White Lakes, a low spot on the Hagemann property. Sometime in the 1930’s 

or 1940’s, a drainage system was constructed that allowed Upper White Lakes to drain 

via tile drains, and the drainwater was pumped into the San Joaquin River. The pumping 

lowered the water table enough so that the Upper White Lakes area could be farmed. 

After the Refuge acquired the Hagemann property, the pumps which drain agricultural 

water into the San Joaquin River broke, resulting in a rise in the water table. Since the 

flooding of Upper White Lakes was beneficial for wildlife, the Refuge opted to replace the 

pump drainage system to the original gravity drainage system. Nevertheless, adjacent 

landowners (Chunn and Bettencourt) complained that the increased water table adversely 

affected their farms. Neighbors are also concerned about their ability to continue to drain 

across the Refuge’s newly acquired property, particularly Chunn, Tosta, NASCA, Lopes and 

Bettencourt.

The Refuge inherited another drainage system north of the Hagemann system when it 

acquired the Lara, Hagemann, and Vierra properties. Hospital Creek provides drainage 

into the San Joaquin River for properties north of Ingram Creek, all of which are in the 

West Stanislaus Irrigation District (WSID). Hospital Creek has a tendency to accumulate 

silt. In the summer 1999, silt accumulation blocked a culvert, causing water to back up in 

Hospital Creek, flooding an adjacent landowner. Although WSID is responsible for clearing 

Hospital Creek, the Refuge opened a gate from Hospital Creek onto Refuge property so 

that Refuge, rather than private agricultural lands, would flood. The arrangement suited 

the farmer. However, the mosquito population in these temporarily flooded Refuge lands 

increased, drawing the attention of the local mosquito abatement district and the community 

of Grayson. 

Refuge Proximity to Private Lands:

FWS staff are concerned about land use changing on properties adjacent to the Refuge.
San Joaquin River NWR Comprehensive Conservation Plan 117

FWS Staff Issues Pertaining to All Alternatives

There are certain issues addressed by FWS staff that would remain consistent under all 

alternatives of the Environmental Assessment. The following describes issues and concerns 

received by the Service throughout the planning process, that will be addressed separately 

from the above:

Land Protection and Boundary Expansion:

Refuge staff have identified land acquisition as a beneficial and necessary tool for managing 

wildlife. However, other entities may have an issue with converting farmland to wildlife 

habitat.

Transportation:

Caltrans is investigating the expansion and realignment of State Highway 132. Refuge staff 

are concerned that the realignment and expansion of State Highway 132 realignment does 

not harm the Refuge.

Mosquito Abatement:

Same as public issues. A memorandum of understanding (MOU) is currently being 

developed by the Service with ESMAD and TMAD and should be completed. In response 

to a request from TMAD and ESMAD, the MOU and CCP will provide a written plan of 

Refuge management activities. 

Refuge Opportunities

Although there are may issues facing the Refuge, there are also opportunities. There are 

many opportunities to work with other entities. Through CALFED, restoration and land 

protection opportunities exist. The Anadromous Fish Restoration Program has funding 

to acquire land, but no funding or authority for management. They have approached 

the Refuge on several occasions to partner and manage lands that they acquire. The 

nonstructural project with the Corps provides the Refuge staff an opportunity to combine 

flood management with environmental restoration. The Endangered Species Recovery 

Program is also working with the Refuge to create habitat for the listed riparian brush 

rabbit and riparian wood rat. The Natural Resources Conservation Service’s Wetlands 

Reserve Program has been working with the Service on land protection and is active in the 

Merced area with Refuge expansion. The Nature Conservancy has also agreed to assist the 

Refuge with land protection (Mapes Ranch). The Sierra Club (observation platform), Safari 

Club (interpretive panels), and Ducks Unlimited (Page Lakes expansion) have participated 

in Refuge construction projects and may continue to do so. Audubon continues to provide 

political support for the Refuge.

There are also opportunities to open the Refuge to a variety of public uses, including 

volunteerism. With so many entities, such as the Sierra Club, and Old Fisherman’s Club, 

interested in the Refuge, there is a large pool of potential volunteers.
118 San Joaquin River NWR Comprehensive Conservation Plan

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San Joaquin River NWR Comprehensive Conservation Plan 119

Appendix D: Compatibility Determinations

COMPATIBILITY DETERMINATION for Recreational Waterfowl Hunting on the San 

Joaquin River National Wildlife Refuge

Use Considered: Recreational Waterfowl Hunting 

Refuge Name:

San Joaquin River National Wildlife Refuge (Refuge)—a unit of the San Luis National 

Wildlife Refuge (NWR) Complex. The Refuge is located in western Stanislaus and San 

Joaquin Counties, California. The Refuge presently consists of approximately 6,500 acres 

situated along the San Joaquin River from just south of the confluence with the Tuolumne 

River north to the north bank of the Stanislaus River. The approved boundary for the 

Refuge comprises 12,887 acres; land presently not part of the Refuge is proposed for the 

conservation easement program. 

Establishing and Acquisition Authority(ies):

The Refuge was established in 1987 to protect the, at the time, endangered Aleutian Canada 

goose, listed as endangered in 1967 and relisted as threatened in 1991. The Refuge was 

originally established under the authority of the Endangered Species Act. Other Refuge 

lands were acquired under the Migratory Bird Conservation Act and the Fish and Wildlife 

Act of 1956. 

Refuge Purpose(s):

The Refuge purposes 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)

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).

National Wildlife Refuge System Mission:

The mission of the National Wildlife Refuge System (NWRS) is “to administer a national 

network of lands and waters for the conservation, management, and where appropriate, 

restoration of the fish, wildlife, and plant resources and their habitats within the United 

States for the benefit of present and future generations of Americans.” 16 U.S.C. 668dd668ee (National Wildlife Refuge Administration Act of 1966, as amended).
120 San Joaquin River NWR Comprehensive Conservation Plan

Description of Use:

The Refuge would establish a recreational waterfowl hunt program for the public. No 

hunting activity is presently allowed at the Refuge. A waterfowl hunt program similar 

to programs at other Central Valley National Wildlife Refuges would be established and 

developed after significant progress in habitat restoration, particularly wetlands, on the 

Refuge has been accomplished and the necessary infrastructure for a waterfowl hunt 

program has been developed. It is expected that this will occur within the first five years of 

the Comprehensive Conservation Plan (CCP).

Hunting is identified as a priority public use of the National Wildlife Refuge System under 

the National Wildlife Refuge System Improvement Act of 1997 (Act). Other priority 

wildlife-dependent public uses identified by the Act include fishing, wildlife observation, 

photography, environmental education and interpretation. Hunting would be permitted 

on designated areas of the Refuge, pursuant to the conditions of a cooperative agreement 

with the State of California, Department of Fish and Game, during the established state 

waterfowl hunting season. The Refuge would remain closed to all other forms of hunting 

and target shooting. 

Before any hunt program is opened at the Refuge a waterfowl hunt plan and associated 

compliance documents will be developed. This plan will outline any proposed program 

including season, hunt areas, hunter carrying capacity, and procedures. Associated with 

the plan will be an environmental assessment to meet National Environmental Policy 

Act (NEPA) compliance which will address impacts to the environment and community. 

Interested individuals and agencies will have the opportunity for input into the plan and 

to comment on any proposed hunt program. Any waterfowl hunt program developed will 

conform to state and federal regulations and be similar to existing waterfowl hunt programs 

at other National Wildlife Refuges in the Central Valley of California. 

Availability of Resources:

Adequate funding and staff exist to manage a waterfowl hunt program at the Refuge. To 

facilitate this use, the Refuge can provide adequate staff which includes administrative, 

managerial, biological, and when available, a Refuge law enforcement officer to perform 

hunter compliance enforcement. Due to changes in Service policy regarding refuge law 

enforcement personnel, there may be times when a trained Service law enforcement officer 

(LEO) will not be available on the Refuge in a full time capacity. When this is the case, 

LEO’s from other refuges will be detailed to the Refuge to provide the necessary patrol 

activities. Additional law enforcement can be provided by California Department of Fish 

and Game wardens and on occasion, Fish and Wildlife Service special agents. 

The California Department of Fish and Game (CDFG) may provide employees to administer 

any waterfowl hunt program including staffing any hunter check station for the processing 

of hunters and monitoring of game taken. Public hunt programs on other NWRs in 

California are administered cooperatively with the California Department of Fish & Game 

under the provisions of a Cooperative Agreement last amended in 2001. This agreement 

details the responsibilities and costs associated with the implementation of the hunt program 

on each refuge and provides a detailed list of costs to be reimbursed to the Service by the 

State. Some of the cost items listed for reimbursement include: signs, brochures, permit 

compliance, access control, maintenance of the check station, blinds, and parking lots, and 

administrative functions such as managerial, biological and clerical support. In addition to 

staffing the hunter check station and performing Refuge clean-up duties, the CDFG staff 

also perform all Refuge sign posting tasks as directed by the Refuge Manager to conform 

with current habitat conditions.
San Joaquin River NWR Comprehensive Conservation Plan 121

Anticipated Impacts of the Use:

The proposed hunt program will be limited to waterfowl, coots, and moorhens only within 

portions of the wetland areas of the Refuge. Sportsmen associated with this activity may 

disturb or harm both target and non-target migratory birds but only in some riparian, 

and wetland habitats on the Refuge. Hunters may accidentally take non-target migratory 

birds due to misidentification, however, this is rare and usually reported to Refuge or 

CDFG staff by other hunters. A certain level of self enforcement is expected by the Refuge 

hunters. Select numbers of waterfowl belonging to target species would be taken by 

hunters each season, but this is not expected to result in significant adverse effects on their 

populations. Hunting regulation frameworks which include hunting limits are established 

annually through the adaptive harvest management process which includes factors 

such as anticipated hunter harvest of waterfowl. These guidelines are proposed for the 

Pacific Flyway and the State establishes hunting limits which fall within these framework 

guidelines. 

Litter discarded by Refuge visitors including sportsmen could entangle wildlife or possibly 

be ingested, resulting in death or injury. Litter control will be a major emphasis item in 

the routine maintenance of the Refuge public use areas. Trash cans and restrooms will 

be provided year round in parking areas for use by the public while involved in wildlife 

observation, photography, education, interpretation as well as hunting. 

Additional potential impacts to resident and migratory wildlife include the trespass of 

hunters outside the established hunt zone and dogs harassing wildlife. The hunt area will be 

patrolled on shoot days and Refuge employees performing routine work also actively watch 

for hunters outside of their assigned areas. While hunter trespass may cause a temporary 

disturbance to wildlife in the immediate vicinity of the activity, this violation is deemed 

rare and wildlife temporarily displaced have large areas closed to hunting in which to seek 

refuge. Dogs have not generally been observed harassing wildlife at other refuges with hunt 

programs and are normally kept under close control by the hunters themselves. 

Public Review and Comment:

The public was provided the opportunity to review and comment on current and potential 

Refuge programs as part of the Comprehensive Conservation Planning process for the 

Refuge. This process included three large mailings of plan updates encouraging public input 

on the development of Refuge programs as well as having the opportunity to participate at a 

public planning workshop. Main topics of public interest were visitor access and appropriate 

recreational or educational uses of the Refuge. Some public comments expressed interest in 

a waterfowl hunt program at the Refuge. A step-down public use plan or recreational hunt 

plan and supporting environmental assessment will be developed for any recreational hunt 

program at the Refuge. During this process, input will be sought from the public regarding 

proposed public use activities and hunting at the Refuge. 

Determination (check one below):

____ Use is Not Compatible

_X__ Use is Compatible with Following Stipulations

Stipulations Necessary to Ensure Compatibility:

The following stipulations are required to ensure compatibility of this activity: 

• When the draft CCP is finalized a Public Use Plan and/or a Refuge Hunt Plan will be 
122 San Joaquin River NWR Comprehensive Conservation Plan

developed as a step down along with associated compliance documents from the CCP that 

will provide management guidelines for operation of the Refuge hunting program. 

• Fallow agricultural lands at the Refuge will be restored to natural habitats before public 

use facilities/programs are fully developed.

• All Refuge rules and regulations must be followed unless otherwise excepted, in writing, 

by project leader. 

• All laws applicable to any refuge hunting program included in the Code of Federal 

Regulations and the State of California Fish and Game Code will be enforced. Law 

enforcement patrols will be conducted on a routine basis in cooperation with California 

Department of Fish and Game wardens to ensure regulation compliance and the 

protection of Refuge resources. The Refuge will increase law enforcement patrols when 

staff is available, particularly during opening weeks of waterfowl hunting season, to 

document hunter use and ensure compliance with Refuge and California regulations

• For any developed Refuge hunt program, regulatory directional signs, as well as maps, 

will clearly mark hunting areas (free roam and blind site units), closed areas, and available 

parking lots. Additional pamphlets at the Refuge headquarters will provide further 

information including special season restrictions, California, and Refuge regulations. Signs 

will be maintained and replaced on an as needed basis.

• When a recreational hunt program is established, annual monitoring of waterfowl hunter 

use and impacts will continue to be implemented. The information gathered will be used 

to review and possibly revise hunting regulations to enhance the quality and safety of the 

Refuge’s hunting program, and ensure hunting would continue to be compatible with the 

Refuge purpose and the mission of the National Wildlife Refuge System.

Justification:

The Refuge was established to conserve fish or wildlife which are listed as endangered 

species or threatened species or plants...; as an inviolate sanctuary, or for any other 

management purpose, for migratory birds; for the development, advancement, management, 

conservation, and protection of fish and wildlife resources; and for the benefit of the United 

States Fish and Wildlife Service, in performing its activities and services. Recreational 

waterfowl hunting by the public at the Refuge as indicated in this determination is 

compatible with the purposes for which the Refuge was established. Hunting is a high 

priority public use for the National Wildlife Refuge System. 

Mandatory Re-Evaluation Date:

___2021___ Mandatory 15 year Re-Evaluation Date (for priority public uses)

__________ Mandatory 10 year Re-Evaluation Date (for all uses other than priority public 

uses)
San Joaquin River NWR Comprehensive Conservation Plan 123

NEPA Compliance for Refuge Use Decision:

_________ Categorical Exclusion without Environmental Action Statement

_________ Categorical Exclusion and Environmental Action Statement

____X_____ Environmental Assessment and Finding of No Significant Impact

_________ Environmental Impact Statement and Record of Decision

Literature Cited:

Williams, B.K. and F.A. Johnson, 1995. Adaptive Management and the Regulation of 

Waterfowl Harvests. The Wildlife Society Bulletin, Vol. 23(3):430-436.

Refuge Determination: 

 

Prepared by: ______________________________________________

 (Signature and Date)

Refuge Manager Approval: ______________________________________________

 (Signature and Date)

Concurrence:

Refuge Supervisor: ______________________________________________

 (Signature and Date)

Assistant Manager,

National Wildlife

Refuge System ______________________________________________

 (Signature and Date)

California/Nevada

Operations Manager _______________________________________________

 (Signature and Date)
124 San Joaquin River NWR Comprehensive Conservation Plan

COMPATIBILITY DETERMINATION for Recreational Fishing on the San Joaquin 

River National Wildlife Refuge

Use Considered: Recreational Fishing 

Refuge Name:

San Joaquin River National Wildlife Refuge (Refuge)—a unit of the San Luis National 

Wildlife Refuge (NWR) Complex. The Refuge is located in western Stanislaus and San 

Joaquin Counties, California. The Refuge presently consists of approximately 6,500 acres 

situated along the San Joaquin River from just south of the confluence with the Tuolumne 

River north to the north bank of the Stanislaus River. The approved boundary for the 

Refuge comprises 12,887 acres; land presently not part of the Refuge is proposed for the 

conservation easement program. 

Establishing and Acquisition Authority(ies):

The Refuge was established in 1987 to protect the, at the time, endangered Aleutian Canada 

goose, listed as endangered in 1967 and relisted as threatened in 1991. The Refuge was 

originally established under the authority of the Endangered Species Act. Other Refuge 

lands were acquired under the Migratory Bird Conservation Act and the Fish and Wildlife 

Act of 1956. 

Refuge Purpose(s):

The Refuge purposes 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)

“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).

National Wildlife Refuge System Mission:

The mission of the National Wildlife Refuge System (NWRS) is “to administer a national 

network of lands and waters for the conservation, management, and where appropriate, 

restoration of the fish, wildlife, and plant resources and their habitats within the United 

States for the benefit of present and future generations of Americans.” 16 U.S.C. 668dd668ee (National Wildlife Refuge Administration Act of 1966, as amended).

Description of Use:

The Refuge would establish a recreational fishing program for the public. No fishing activity 

from the Refuge is presently allowed at the Refuge, however, the San Joaquin, Tuolumne 

and Stanislaus Rivers, which are all navigable waters, extend across the Refuge and it 

is legal for boaters to fish in these waters without accessing them through the Refuge. 

A recreational fishing program on the Refuge would include developing several bank 

sites where sportsmen could fish and a small boat launch area where they could launch 
San Joaquin River NWR Comprehensive Conservation Plan 125

watercraft. This program would be established and developed after significant progress in 

habitat restoration on the Refuge has been accomplished and the necessary infrastructure 

for a fishing program has been developed. It is expected that this will occur within the first 

five years of the Comprehensive Conservation Plan (CCP).

Recreational fishing is identified as a priority public use of the National Wildlife Refuge 

System under the National Wildlife Refuge System Improvement Act of 1997 (Act). Other 

priority wildlife-dependent public uses identified by the Act include hunting, wildlife 

observation, photography, environmental education and interpretation. Fishing would 

be permitted on designated areas of the Refuge. Game species found on the Refuge are 

American shad, rainbow trout, black crappie, white crappie, smallmouth and largemouth 

bass, striped bass, sunfish, bluegill, catfish, bullhead, and occasionally Chinook salmon. 

Before any fishing program is opened at the Refuge a public use plan and associated 

compliance documents will be developed. This plan will outline any proposed program 

including locations, roads, public carrying capacity, and procedures. Associated with 

the plan will be an environmental assessment to meet National Environmental Policy 

Act (NEPA) compliance which will address impacts to the environment and community. 

Interested individuals and agencies will have the opportunity for input into the plan and to 

comment on any proposed public use program. Any recreational fishing program developed 

will conform to state and federal regulations and be similar to existing fishing programs at 

other National Wildlife Refuges in the Central Valley of California. 

Availability of Resources:

Adequate funding and staff exist to manage a recreational fishing program at the Refuge. 

To facilitate this use, the Refuge can provide adequate staff which includes administrative, 

managerial, biological, and when available, a Refuge law enforcement officer to perform 

compliance enforcement. Additional law enforcement can be provided by California 

Department of Fish and Game wardens and on occasion, Fish and Wildlife Service special 

agents. 

Anticipated Impacts of the Use:

Short-term impacts for the recreational fishing program will be associated with the 

establishment of fishing sites, parking lots and a boat launch facility. These short-term 

impacts include increased noise from construction activities, an increase in the number of 

vehicles and people on the Refuge, and soil disturbance where signs, posts and the boat 

launch are situated. Wildlife will likely avoid areas where work is being conducted but 

are expected to resume normal activities and patterns when these facilities have been 

completed. Once these facilities are in place, we expect that terrestrial and aquatic animals 

will continue to use the fishing sites and surrounding areas. 

Litter discarded by Refuge visitors including sportsmen could entangle wildlife or possibly 

be ingested, resulting in death or injury. Litter control will be a major emphasis item in 

the routine maintenance of the Refuge public use areas. Trash cans and restrooms will 

be provided year round in parking areas for use by the public while involved in wildlife 

observation, photography, education, interpretation as well as hunting. 

Long-term impacts will be associated with the construction of a parking lot(s), boat launch 

facility, signs, and use of the roads. These include loss of habitat, increase in manmade 

permanent structures, and increased use by the public. The creation of the parking lots will 

result in the permanent loss of less than two acres of introduced grasses and will not impact 

any sensitive, threatened, or endangered plant or animal species. Terrestrial and burrowing 

animals will be displaced by this action but are expected to continue to use the area. The 
126 San Joaquin River NWR Comprehensive Conservation Plan

increase in permanent structures will add a vertical and human-made component to an 

otherwise natural and relatively flat environment. Disturbance to wildlife will be increased 

for select species at and along the developed facilities. The major anticipated impact of 

these activities is disturbance of wildlife and trampling of plants. However, the disturbance 

to wildlife including migratory birds will be minimal by keeping sportsmen confined to 

specific areas for fishing and confining their movement across the Refuge to specific trails/

roads. 

Public Review and Comment:

The public was provided the opportunity to review and comment on current and potential 

Refuge programs as part of the Comprehensive Conservation Planning process for the 

Refuge. This process included three large mailings of plan updates encouraging public input 

on the development of Refuge programs as well as having the opportunity to participate 

at a public planning workshop. Main topics of public interest were visitor access and 

appropriate recreational or educational uses of the Refuge. Few public comments were 

received regarding fishing at the Refuge. A step-down public use plan including a section on 

a recreational fishing program and supporting environmental assessment will be developed 

for any recreational fishing program at the Refuge. During this process, input will be sought 

from the public regarding proposed public use activities at the Refuge. 

Determination (check one below):

____ Use is Not Compatible

_X__ Use is Compatible with Following Stipulations

Stipulations Necessary to Ensure Compatibility:

The following stipulations are required to ensure compatibility of this activity: 

• When the draft CCP is finalized a Public Use Plan including a section on recreational 

fishing will be developed as a step down along with associated compliance documents from 

the CCP that will provide management guidelines for operation of the Refuge fishing 

program. 

• Fallow agricultural lands at the Refuge will be restored to natural habitats before public 

use facilities/programs including recreational fishing are fully developed.

• All laws applicable to any Refuge fishing program included in the Code of Federal 

Regulations and the State of California Fish and Game Code will be enforced. Law 

enforcement patrols will be conducted on a routine basis in cooperation with California 

Department of Fish and Game wardens to ensure regulation compliance and the 

protection of Refuge resources. 

• For any developed Refuge fishing program, regulatory directional signs, as well as 

maps, will clearly mark fishing areas, closed areas, and available parking lots. Additional 

pamphlets at the Refuge headquarters will provide further information including special 

fishing restrictions, California, and Refuge regulations. Signs will be maintained and 

replaced on an as needed basis.

• When a recreational fishing program is established, annual monitoring of angler use and 

impacts will be implemented. The information gathered will be used to review and possibly 

revise the fishing program to enhance the quality and safety of the Refuge’s fishing 

program, and ensure fishing would be compatible with the Refuge purpose and the mission 

of the National Wildlife Refuge System.
San Joaquin River NWR Comprehensive Conservation Plan 127

Justification:

The Refuge was established to conserve fish or wildlife which are listed as endangered 

species or threatened species or plants...; as an inviolate sanctuary, or for any other 

management purpose, for migratory birds; for the development, advancement, management, 

conservation, and protection of fish and wildlife resources; and for the benefit of the United 

States Fish and Wildlife Service, in performing its activities and services. Recreational 

fishing by the public at the Refuge as indicated in this determination is compatible with the 

purposes for which the Refuge was established. Fishing is a high priority public use for the 

National Wildlife Refuge System. 

Mandatory Re-Evaluation Date:

__2021___ Mandatory 15 year Re-Evaluation Date (for priority public uses)

_________ Mandatory 10 year Re-Evaluation Date (for all uses other than priority public 

 uses)

NEPA Compliance for Refuge Use Decision:

_________ Categorical Exclusion without Environmental Action Statement

_________ Categorical Exclusion and Environmental Action Statement

____X____ Environmental Assessment and Finding of No Significant Impact

_________ Environmental Impact Statement and Record of Decision

Refuge Determination: 

Prepared by: ______________________________________________

 (Signature and Date)

Refuge Manager Approval: ______________________________________________

 (Signature and Date)

Concurrence:

Refuge Supervisor: ______________________________________________

 (Signature and Date)

Assistant Manager,

National Wildlife

Refuge System ______________________________________________

 (Signature and Date)

California/Nevada

Operations Manager _______________________________________________

 (Signature and Date)
128 San Joaquin River NWR Comprehensive Conservation Plan

COMPATIBILITY DETERMINATION for Wildlife Observation, Nature Interpretation 

and Photography on the San Joaquin River National Wildlife Refuge

Use Considered: Wildlife observation, nature interpretation, and photography uses by the 

public. 

Refuge Name:

San Joaquin River National Wildlife Refuge (Refuge) - a unit of the San Luis National 

Wildlife Refuge (NWR) Complex. The Refuge is located in western Stanislaus and San 

Joaquin Counties, California. The refuge presently consists of approximately 6,500 acres 

situated along the San Joaquin River from just south of the confluence with the Tuolumne 

River north to the north bank of the Stanislaus River. The approved boundary for the 

Refuge comprises 12,887 acres; land presently not part of the Refuge is proposed for the 

conservation easement program. 

Establishing and Acquisition Authority(ies):

The San Joaquin River National Wildlife Refuge was established in 1987 to protect the, 

at the time, endangered Aleutian Canada goose, listed as endangered in 1967 and relisted 

as threatened in 1991. The Refuge was originally established under the authority of the 

Endangered Species Act. Other refuge lands were acquired under the Migratory Bird 

Conservation Act and the Fish and Wildlife Act of 1956. 

Refuge Purpose(s):

The Refuge purposes 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)

“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).

National Wildlife Refuge System Mission:

The mission of the National Wildlife Refuge System (NWRS) is “to administer a national 

network of lands and waters for the conservation, management, and where appropriate, 

restoration of the fish, wildlife, and plant resources and their habitats within the United 

States for the benefit of present and future generations of Americans.” 16 U.S.C. 668dd668ee (National Wildlife Refuge Administration Act of 1966, as amended).

Description of Use:

At the present time, public opportunities for wildlife viewing, nature interpretation and 

photography at the Refuge are limited to the wildlife observation deck off of Beckwith 

Road. However, once habitat restoration projects on the Refuge have progressed converting 
San Joaquin River NWR Comprehensive Conservation Plan 129

fallow agricultural land to native habitats, additional public use facilities will be developed 

for increased public use for wildlife observation, nature interpretation and photography 

similar to the facilities at the San Luis NWR and Merced NWR. These facilities will include 

nature trail(s), auto tour route (if feasible), interpretive panels, observation platforms, 

comfort stations, benches, waste receptacles, photography blinds and parking lots. Only 

portions of the Refuge will be open to public use, other sections will be closed to public use 

to limit disturbance to select habitats and wildlife. A public use plan will be developed to 

guide the implementation of an expanded public use program at the Refuge. This plan 

will be developed by the staff of the San Luis National Wildlife Refuge Complex working in 

conjunction with the FWS’s Regional Office along with local partners and the public. 

Once facilities are developed, access to the Refuge will be daily from 2 hour before sunrise 

to 2 hour after sunset. The current estimate of public use at the Refuge is 1,500 per 

annum, however, with the development of additional facilities, use is expected to increase 

to approximately 50,000 per annum - similar to other refuge units in the Central Valley. 

The majority of this use would occur from autumn through spring coinciding with bird 

migrations, waterfowl/waterbird use of wetland habitats, and spring vegetative green-up. 

Lesser use is expected during the summer months when conditions are dry and daytime 

temperatures are high. Visitors will have use of the facilities for wildlife observation, nature 

interpretation and photography during the approved hours and seasons which are set by the 

Refuge Manger. 

Availability of Resources:

Adequate funding and staff exist, are available or are attainable for the San Luis National 

Wildlife Refuge Complex to conduct and expand a public use program involving wildlife 

viewing, interpretation and photography at the Refuge.

Initial costs would include the preparation or construction of the following: trails, auto tour 

route (if feasible), interpretive panels, observation platforms and blinds, benches, comfort 

stations, parking lots, access gates, signage, and brochures. The project can be completed in 

phases with each phase consisting of individual trails. Annual maintenance costs will involve 

trail and parking area maintenance, entrance road maintenance, cleaning and maintenance 

of comfort stations, refuse removal, periodic maintenance of wooden structures (i.e., 

benches, platforms and blinds), and repair/replacement of signs and gates. 

Anticipated Impacts of the Use:

Short-term impacts will be associated with the establishment of the trails (and auto tour 

route if feasible) and observation platform. These short-term impacts include increased 

noise from construction activities, an increase in the number of vehicles and people on the 

Refuge, and soil disturbance where signs, posts and the observation platforms/blinds are 

situated. Wildlife will likely avoid areas where work is being conducted but are expected 

to resume normal activities and patterns when these facilities have been completed. Once 

these facilities are in place, we expect that terrestrial animals will continue to use the trail 

corridors and surrounding areas. 

Long-term impacts will be associated with the construction of a parking lot(s), observation 

platform(s), signs, and use of the trail(s)/tour route. These include loss of habitat, increase 

in manmade permanent structures, and increased use by the public, especially from autumn 

through spring. The creation of the parking lots will result in the permanent loss of less 

than two acres of introduced grasses and will not impact any sensitive, threatened, or 

endangered plant or animal species. Terrestrial and burrowing animals will be displaced 

by this action but are expected to continue to use the area. The increase in permanent 
130 San Joaquin River NWR Comprehensive Conservation Plan

structures will add a vertical and human-made component to an otherwise natural and 

relatively flat environment. Disturbance to wildlife will be increased for select species 

along the nature trail(s), observation platforms/blinds, kiosks, and parking areas. The 

major anticipated impact of these activities is disturbance of wildlife and trampling of 

plants. However, the disturbance to wildlife including migratory birds will be minimal if the 

stipulations listed below are followed. Trampling of plants and erosion of sensitive habitats 

from this activity are minimized by only allowing public access to a trail/tour route system.

Public Review and Comment:

The public was provided the opportunity to review and comment on current and potential 

Refuge programs as part of the Comprehensive Conservation Planning process for the 

Refuge. This process included three large mailings of plan updates encouraging public input 

on the development of Refuge programs as well as having the opportunity to participate at 

a public planning workshop. A main topic of public interest for many individuals was the 

opportunity for public use at the Refuge specifically wildlife viewing, nature interpretation, 

and photography. The vast majority of individuals indicated a preference for these activities 

to occur on the Refuge. Some landowners adjacent to the Refuge preferred that public use 

activities occur away from Refuge boundaries to preclude potential trespassing problems on 

private lands.

Determination (check one below):

____ Use is Not Compatible

__X_ Use is Compatible with Following Stipulations

Stipulations Necessary to Ensure Compatibility:

The following conditions apply to ensure compatibility of these activities with the Refuge’s 

primary purpose: 1) a public use plan for the Refuge with public input is completed for 

the facility along with compliance documents, 2) restoration of fallow agricultural land is 

restored to native habitats before public use facilities are developed, 3) wildlife and habitat 

surveys (with an emphasis on key trust species) are conducted and the results reviewed by 

Refuge staff to check for negative trends in wildlife/habitat use associated with public use 

activities, 4) monitoring visitor use to accurately gauge use levels, 5) periodic and random 

law enforcement patrols, 6) adequate signage indicating Service regulations and refuge 

public use policies, and 7) reduction of elements of this public use program if it is ascertained 

that wildlife or habitat is being negatively impacted.. 

Justification:

Wildlife observation, nature interpretation, and photography are public uses that will allow 

the visiting public to enjoy, experience, and learn about native wildlife, plants and habitats. 

Since the majority of the land near and adjacent to the Refuge has been highly modified and 

converted to agriculture, opening these trails/tour route on a regulated basis will provide 

wildlife-dependent recreational opportunities for the public. All three of these uses (i.e., 

wildlife observation, interpretation and photography) are considered priority public uses 

for the National Wildlife Refuge System. This program will confine the visiting public 

to designated trail systems for a quality experience while leaving the majority of Refuge 

land free from disturbance for wildlife. Concerns about the protection of native plants and 

animals, and the overall integrity of the wetland and upland habitats, require that public 

access be limited to select designated areas (i.e., contact stations, trails, parking lots, etc.) 

which will permit other portions of the Refuge to provide sanctuary areas (i.e., free of 
San Joaquin River NWR Comprehensive Conservation Plan 131

disturbance) to wildlife resources (Burger 1981). The stipulations listed above will protect 

migratory birds from disturbance on the Refuge.

Limited public access and restrictions will reduce the likelihood of adverse long-term 

impacts to plant and wildlife resources. The Refuge was established to conserve fish or 

wildlife which are listed as endangered species or threatened species or plants...; as an 

inviolate sanctuary, or for any other management purpose, for migratory birds; for the 

development, advancement, management, conservation, and protection of fish and wildlife 

resources; and for the benefit of the United States Fish and Wildlife Service, in performing 

its activities and services. A public use program featuring wildlife observation, nature 

interpretation and photography by individuals or small groups will not negatively impact the 

natural resources at the Refuge as indicated in this determination and these programs are 

deemed compatible with the purposes for which the Refuge was established.

Mandatory Re-Evaluation Date:

___2021__ Mandatory 15 year Re-Evaluation Date (for priority public uses)

_________ Mandatory 10 year Re-Evaluation Date (for all uses other than priority public uses)

NEPA Compliance for Refuge Use Decision:

_________ Categorical Exclusion without Environmental Action Statement

_________ Categorical Exclusion and Environmental Action Statement

____X____ Environmental Assessment and Finding of No Significant Impact

_________ Environmental Impact Statement and Record of Decision

Literature Cited:

Burger, J. 1981. The effect of human activity on birds at coastal bay. Biol. Conserv.; 21: 231-241).

Refuge Determination: 

Prepared by: ______________________________________________

 (Signature and Date)

Refuge Manager Approval: ______________________________________________

 (Signature and Date)

Concurrence:

Refuge Supervisor: ______________________________________________

 (Signature and Date)

Assistant Manager,

National Wildlife

Refuge System ______________________________________________

 (Signature and Date)

California/Nevada

Operations Manager _______________________________________________

 (Signature and Date)
132 San Joaquin River NWR Comprehensive Conservation Plan

COMPATIBILITY DETERMINATION for Environmental Education on the San 

Joaquin River National Wildlife Refuge

Use Considered: Environmental education programs for the public. 

Refuge Name:

San Joaquin River National Wildlife Refuge (Refuge) - a unit of the San Luis National 

Wildlife Refuge (NWR) Complex. The Refuge is located in western Stanislaus and San 

Joaquin Counties, California. The Refuge presently consists of approximately 6,500 acres 

situated along the San Joaquin River from just south of the confluence with the Tuolumne 

River north to the north bank of the Stanislaus River. The approved boundary for the 

Refuge comprises 12,887 acres; land presently not part of the Refuge is proposed for the 

conservation easement program. 

Establishing and Acquisition Authority(ies):

The San Joaquin River National Wildlife Refuge was established in 1987 to protect the, 

at the time, endangered Aleutian Canada goose, listed as endangered in 1967 and relisted 

as threatened in 1991. The Refuge was originally established under the authority of the 

Endangered Species Act. Other Refuge lands were acquired under the Migratory Bird 

Conservation Act and the Fish and Wildlife Act of 1956. 

Refuge Purpose(s):

The Refuge purposes 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)

“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).

National Wildlife Refuge System Mission:

The mission of the National Wildlife Refuge System (NWRS) is “to administer a national 

network of lands and waters for the conservation, management, and where appropriate, 

restoration of the fish, wildlife, and plant resources and their habitats within the United 

States for the benefit of present and future generations of Americans.” 16 U.S.C. 668dd668ee (National Wildlife Refuge Administration Act of 1966, as amended).

Description of Use:

Environmental education programs at a Refuge provide opportunities for the visiting 

public to learn about and experience native wildlife and their habitats. At the present 

time, environmental educational opportunities for the public at the Refuge are limited to 
San Joaquin River NWR Comprehensive Conservation Plan 133

the wildlife observation deck off of Beckwith Road. However, once habitat restoration 

projects on the Refuge have progressed in converting fallow agricultural land to native 

habitats, additional public use facilities will be developed for increased public use for 

wildlife observation, nature interpretation and photography similar to the facilities at the 

San Luis NWR and Merced NWR. These facilities will include nature trail(s), auto tour 

route (if feasible), interpretive panels, observation platforms, comfort stations, benches, 

waste receptacles, photography blinds and parking lots. These facilities will also be used 

for environmental education programs both those performed by schools and the Refuge. 

Only portions of the Refuge will be open to public use including environmental education, 

other sections will be closed to public use to limit disturbance to select habitats and wildlife. 

A public use plan including environmental education programs will be developed to guide 

the implementation of an expanded public use program at the Refuge. This plan will 

be developed by the staff of the San Luis National Wildlife Refuge Complex working in 

conjunction with the FWS’s Regional Office along with local partners and the public. 

Once facilities are developed, access to the Refuge will be daily from 2 hour before sunrise 

to 2 hour after sunset. The current estimate of public use at the Refuge is 1,500 per 

annum, however, with the development of additional facilities, use is expected to increase 

to approximately 50,000 per annum - similar to other refuge units in the Central Valley. 

It is expected that between 5,000 and 10,000 visits to the Refuge per annum will be for 

environmental education. The majority of public use would occur from autumn through 

spring coinciding with bird migrations, waterfowl/waterbird use of wetland habitats, and 

spring vegetative green-up. Lesser use is expected during the summer months when schools 

are closed and conditions are dry and daytime temperatures are high. Environmental 

education visitors will have use of the facilities developed for wildlife observation, nature 

interpretation and photography during the approved hours and seasons which are set by the 

Refuge Manger. 

Availability of Resources:

Adequate funding and staff exist, are available or are attainable for the San Luis National 

Wildlife Refuge Complex to conduct and expand an environmental education program at 

the Refuge. Initial costs for expanding the environmental education program at the Refuge 

would include the preparation or construction of the following: trails, auto tour route (if 

feasible), interpretive panels, observation platforms and blinds, benches, comfort stations, 

parking lots, access gates, signage, and brochures. The project can be completed in phases 

with each phase consisting of individual trails. Annual maintenance costs will involve trail 

and parking area maintenance, entrance road maintenance, cleaning and maintenance of 

comfort stations, refuse removal, periodic maintenance of wooden structures (i.e., benches, 

platforms and blinds), and repair/replacement of signs and gates. 

Anticipated Impacts of the Use:

Short and long-term impacts are similar to the public uses of wildlife observation, nature 

interpretation and photography as the same facilities will be used for environmental 

education programs. Short-term impacts will be associated with the establishment of the 

trails (and auto tour route if feasible) and observation platform. These short-term impacts 

include increased noise from construction activities, an increase in the number of vehicles 

and people on the Refuge, and soil disturbance where signs, posts and the observation 

platforms/blinds are situated. Wildlife will likely avoid areas where work is being conducted 

but are expected to resume normal activities and patterns when these facilities have been 

completed. Once these facilities are in place, we expect that terrestrial animals will continue 

to use the trail corridors and surrounding areas. 
134 San Joaquin River NWR Comprehensive Conservation Plan

Long-term impacts will be associated with the construction of a parking lot(s), observation 

platform(s), signs, and use of the trail(s)/tour route. These include loss of habitat, increase 

in manmade permanent structures, and increased use by the public, especially from autumn 

through spring. The creation of the parking lots will result in the permanent loss of less 

than two acres of introduced grasses and will not impact any sensitive, threatened, or 

endangered plant or animal species. Terrestrial and burrowing animals will be displaced 

by this action but are expected to continue to use the area. The increase in permanent 

structures will add a vertical and human-made component to an otherwise natural and 

relatively flat environment. Disturbance to wildlife will be increased for select species 

along the nature trail(s), observation platforms/blinds, kiosks, and parking areas. The 

major anticipated impact of these activities is disturbance of wildlife and trampling of 

plants. However, the disturbance to wildlife including migratory birds will be minimal if the 

stipulations listed below are followed. Trampling of plants and erosion of sensitive habitats 

from this activity are minimized by only allowing public access to a trail/tour route system.

Public Review and Comment:

The public was provided the opportunity to review and comment on current and potential 

Refuge programs as part of the Comprehensive Conservation Planning process for the 

Refuge. This process included three large mailings of plan updates encouraging public input 

on the development of Refuge programs as well as having the opportunity to participate at 

a public planning workshop. A main topic of public interest for many individuals was the 

opportunity for public use at the Refuge specifically wildlife viewing, nature interpretation, 

and photography. The vast majority of individuals indicated a preference for these activities 

to occur on the Refuge. Environmental educational activities were also requested to occur 

on the Refuge but to a lesser degree than wildlife observation. Some landowners adjacent 

to the Refuge preferred that public use activities occur away from Refuge boundaries to 

preclude potential trespassing problems on private lands.

Determination (check one below):

____ Use is Not Compatible

__X_ Use is Compatible with Following Stipulations

Stipulations Necessary to Ensure Compatibility:

The following conditions apply to ensure compatibility of these activities with the Refuge’s 

primary purpose: 1) a public use plan including environmental education for the Refuge with 

public input is completed for the facility along with compliance documents, 2) restoration 

of fallow agricultural land is restored to native habitats before public use facilities are 

developed, 3) wildlife and habitat surveys (with an emphasis on key trust species) are 

conducted and the results reviewed by Refuge staff to check for negative trends in wildlife/

habitat use associated with public use activities, 4) monitoring visitor use to accurately gauge 

use levels, 5) periodic and random law enforcement patrols, 6) adequate signage indicating 

Service regulations and refuge public use policies, and 7) reduction of elements of this public 

use program if it is ascertained that wildlife or habitat is being negatively impacted.. 

Justification:

Environmental education is one of six priority public uses for the National Wildlife Refuge 

System. Environmental educational activities will confine the visiting public to designated 

trail systems for a quality experience while leaving the majority of Refuge land free from 
San Joaquin River NWR Comprehensive Conservation Plan 135

disturbance for wildlife. Concerns about the protection of native plants and animals, and the 

overall integrity of the wetland and upland habitats, require that public access including for 

environmental education be limited to select designated areas (i.e., contact stations, trails, 

parking lots, etc.) which will permit other portions of the Refuge to provide sanctuary areas 

(i.e., free of disturbance) to wildlife resources (Burger 1981). The stipulations listed above 

will protect migratory birds from disturbance on the Refuge 

Limited public access and restrictions will reduce the likelihood of adverse long-term 

impacts to plant and wildlife resources. The Refuge was established to conserve fish or 

wildlife which are listed as endangered species or threatened species or plants...; as an 

inviolate sanctuary, or for any other management purpose, for migratory birds; for the 

development, advancement, management, conservation, and protection of fish and wildlife 

resources; and for the benefit of the United States Fish and Wildlife Service, in performing 

its activities and services. A public use program featuring environmental education by 

individuals or small groups will not negatively impact the natural resources at the Refuge 

as indicated in this determination and these programs are deemed compatible with the 

purposes for which the Refuge was established.

Mandatory Re-Evaluation Date:

__2021___ Mandatory 15 year Re-Evaluation Date (for priority public uses)

_________ Mandatory 10 year Re-Evaluation Date (for all uses other than priority public 

 uses)

NEPA Compliance for Refuge Use Decision:

_________ Categorical Exclusion without Environmental Action Statement

_________ Categorical Exclusion and Environmental Action Statement

____X____ Environmental Assessment and Finding of No Significant Impact

_________ Environmental Impact Statement and Record of Decision

Literature Cited:

Burger, J. 1981. The effect of human activity on birds at coastal bay. Biol. Conserv.; 21: 231-

241).

Refuge Determination: 

Prepared by: ______________________________________________

 (Signature and Date)

Refuge Manager Approval: ______________________________________________

 (Signature and Date)
136 San Joaquin River NWR Comprehensive Conservation Plan

Concurrence:

Refuge Supervisor: ______________________________________________

 (Signature and Date)

Assistant Manager,

National Wildlife

Refuge System ______________________________________________

 (Signature and Date)

California/Nevada

Operations Manager _______________________________________________

 (Signature and Date)
San Joaquin River NWR Comprehensive Conservation Plan 137

COMPATIBILITY DETERMINATION for Scientific Study on the San Joaquin River 

National Wildlife Refuge

Use Considered: Scientific Study 

Refuge Name:

San Joaquin River National Wildlife Refuge (Refuge) - a unit of the San Luis National 

Wildlife Refuge (NWR) Complex. The Refuge is located in western Stanislaus and San 

Joaquin Counties, California. The Refuge presently consists of approximately 6,500 acres 

situated along the San Joaquin River from just south of the confluence with the Tuolumne 

River north to the north bank of the Stanislaus River. The approved boundary for the 

Refuge comprises 12,887 acres; land presently not part of the Refuge is proposed for the 

conservation easement program. 

Establishing and Acquisition Authority(ies):

The San Joaquin River National Wildlife Refuge was established in 1987 to protect the, 

at the time, endangered Aleutian Canada goose, listed as endangered in 1967 and relisted 

as threatened in 1991. The Refuge was originally established under the authority of the 

Endangered Species Act. Other Refuge lands were acquired under the Migratory Bird 

Conservation Act and the Fish and Wildlife Act of 1956. 

Refuge Purpose(s):

The Refuge purposes 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)

“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).

National Wildlife Refuge System Mission:

The mission of the National Wildlife Refuge System (NWRS) is “to administer a national 

network of lands and waters for the conservation, management, and where appropriate, 

restoration of the fish, wildlife, and plant resources and their habitats within the United 

States for the benefit of present and future generations of Americans.” 16 U.S.C. 668dd668ee (National Wildlife Refuge Administration Act of 1966, as amended).

Description of Use:
138 San Joaquin River NWR Comprehensive Conservation Plan

Scientific studies concerning natural resources conducted by private individuals, groups and/

or agencies at the Refuge.

Availability of Resources:

Adequate funding and staff exist to manage scientific studies concerning natural resources 

conducted by private individuals or groups at the Refuge. Administrative staff costs 

associated with this use consists of Refuge staff time to review research proposals, collected 

data, special use permits, research summaries, and to evaluate impacts and that researchers 

are in compliance. Other staff time includes monitoring the use of the Refuge temporary 

quarters where researchers are allowed to stay during their data collection period if space 

is available. Annual monetary costs expended by the Refuge to administer this use averages 

$1,000.00. Most of the research conducted on the Refuge in the past has been funded from 

outside sources and this trend is expected to continue.

Anticipated Impacts of the Use:

The principal potential impact by this activity on the Refuge’s natural resources is 

disturbance to wildlife and habitat. However, research conducted on the natural resources 

of the Refuge can benefit the management of those resources (Leopold et al. 1968 and 

Primack 1993). To conduct research on the Refuge, an investigator needs to submit a 

research proposal on a project and indicate the purpose of the research, techniques to be 

used in the field and for analyses, time frame for the field work, and the proposed study 

area on the Refuge. If the research project is deemed valuable for the Refuge and that it 

will not negatively impact the natural resources than a Special Use Permit (SUP) is issued 

to the investigator and any controls or stipulations regarding the research are indicated on 

the permit to ensure protection of the Refuge’s natural resources. The permit is issued on 

an annual basis and an annual or final report on the research is required to be sent to the 

Refuge at the start of each year. Failure to comply with the SUP results in a revocation 

of the permit or failure to renew the annual permit. Scientific studies conducted under 

these guidelines have minimal negative impact on Refuge lands, waters and interests and 

frequently provide benefits in the information they provide on natural resource inventories 

and processes at the Refuge. 

Public Review and Comment:

The public was provided the opportunity to review and comment on current and potential 

Refuge programs as part of the Comprehensive Conservation Planning process for the 

Refuge. This process included three large mailings of plan updates encouraging public input 

on the development of Refuge programs as well as having the opportunity to participate at a 

public planning workshop. Main topics of public interest were visitor access and appropriate 

recreational or educational uses of the Refuge. No public comments addressed scientific 

research concerning natural resources conducted by private individuals or groups on the 

Refuge.

Determination (check one below):

____ Use is Not Compatible
San Joaquin River NWR Comprehensive Conservation Plan 139

_X__ Use is Compatible with Following Stipulations

Stipulations Necessary to Ensure Compatibility:

The following stipulations are required to ensure compatibility of this activity: a research 

proposal is required for any investigation, the proposal is reviewed by San Luis NWR 

Complex staff as to its potential value and impacts to the Refuge’s natural resources, a 

one year SUP is issued to approved research projects, restrictions regarding the specific 

research project are listed in the SUP, and an annual/final report are required for all 

investigations. Failure to comply with the provisions of the SUP results in revocation of 

permit privileges. Specifically all scientific studies on the Refuge will require the following:

• The principal investigator submit a study proposal for approval to the Complex. 

• All work will be coordinated with the project leader, or designated Refuge staff, and 

researcher.

• Research will adhere to current approved protocols for data collection as indicated in the 

study proposal and special use permit. 

• Proposed research methods which will adversely affect, or would have the potential 

to adversely affect Refuge resources will require the researcher to develop mitigation 

measures to minimize potential impacts; mitigation measures will be listed as a condition 

in the SUP. 

• Refuge staff will be free to accompany researchers at any time to assess potential impacts; 

to insure SUPs are adhered to; and to determine if approved research proposals and SUPs 

should be terminated because of adverse impacts. 

• All refuge rules and regulations must be followed unless otherwise excepted, in writing, by 

project leader. 

• The researcher will be responsible for acquiring all necessary permits, both from the State 

of California or U.S. Fish and Wildlife Service, if applicable, and to demonstrate that these 

permits are up to date prior to the beginning of research approval. 

Justification:

The Refuge was established to conserve fish or wildlife which are listed as endangered 

species or threatened species or plants...; as an inviolate sanctuary, or for any other 

management purpose, for migratory birds; for the development, advancement, management, 

conservation, and protection of fish and wildlife resources; and for the benefit of the United 

States Fish and Wildlife Service, in performing its activities and services. Scientific 

studies by individuals or groups on the natural resources at the Refuge as indicated in this 

determination is compatible with the purposes for which the Refuge was established.

Mandatory Re-Evaluation Date:

__________ Mandatory 15 year Re-Evaluation Date (for priority public uses)

__2016____ Mandatory 10 year Re-Evaluation Date (for all uses other than priority public 

 uses)
140 San Joaquin River NWR Comprehensive Conservation Plan

NEPA Compliance for Refuge Use Decision:

_________ Categorical Exclusion without Environmental Action Statement

_________ Categorical Exclusion and Environmental Action Statement

____X____ Environmental Assessment and Finding of No Significant Impact

_________ Environmental Impact Statement and Record of Decision

Literature Cited:

Leopold, A.S., C. Cottam, I.M. Cowan, I.N. Gabrielson and T.L. Kimball. 1968. The 

National Wildlife Refuge System-1968. Trans. N. Am. Wildl. and Nat. Res. Conf. 

33:30-53. 

Primack, R.B. 1993. Essentials of Conservation Biology. Sinauer, Mass.

Refuge Determination: 

Prepared by: ______________________________________________

 (Signature and Date)

Refuge Manager Approval: ______________________________________________

 (Signature and Date)

Concurrence:

Refuge Supervisor: ______________________________________________

 (Signature and Date)

Assistant Manager,

National Wildlife

Refuge System ______________________________________________

 (Signature and Date)

California/Nevada

Operations Manager _______________________________________________

 (Signature and Date)
San Joaquin River NWR Comprehensive Conservation Plan 141

COMPATIBILITY DETERMINATION for Grazing by Livestock on the San Joaquin 

River National Wildlife Refuge

Use Considered: Grazing by livestock (cattle and sheep) to enhance habitats for wildlife. 

Refuge Name:

San Joaquin River National Wildlife Refuge (Refuge) - a unit of the San Luis National 

Wildlife Refuge (NWR) Complex. The Refuge is located in western Stanislaus and San 

Joaquin Counties, California. The Refuge presently consists of approximately 6,500 acres 

situated along the San Joaquin River from just south of the confluence with the Tuolumne 

River north to the north bank of the Stanislaus River. The approved boundary for the 

Refuge comprises 12,887 acres; land presently not part of the Refuge is proposed for the 

conservation easement program. 

Establishing and Acquisition Authority(ies):

The Refuge was established in 1987 to protect the, at the time, endangered Aleutian Canada 

goose, listed as endangered in 1967 and relisted as threatened in 1991. The refuge was 

originally established under the authority of the Endangered Species Act. Other refuge 

lands were acquired under the Migratory Bird Conservation Act and the Fish and Wildlife 

Act of 1956. 

Refuge Purpose(s):

The Refuge purposes 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)

“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).

National Wildlife Refuge System Mission:

The mission of the National Wildlife Refuge System (NWRS) is “to administer a national 

network of lands and waters for the conservation, management, and where appropriate, 

restoration of the fish, wildlife, and plant resources and their habitats within the United 

States for the benefit of present and future generations of Americans.” 16 U.S.C. 668dd668ee (National Wildlife Refuge Administration Act of 1966, as amended).

Description of Use:

A grazing program, where sheep and cattle are used to enhance Refuge habitats for the 

benefit of wildlife and native plant communities. This Compatibility Determination is a reevaluation of a 1994 Compatibility Determination for the Refuge Biological Program which 

specifically addressed grazing on the Refuge.
142 San Joaquin River NWR Comprehensive Conservation Plan

The ongoing grazing program uses both sheep and cattle as habitat management tools. 

Cattle grazing occurs in both improved irrigated pastures and natural uplands on a longterm annual basis. Sheep grazing is currently a short-term practice used to control exotic 

invasive weeds in fallow agricultural fields until those areas are restored to riparian forest 

or wetland communities. Grazing would be used to manage habitats in a manner that is 

consistent with the Refuge System mission and the purposes for which the Refuge was 

established: 

1) In irrigated pastures, the results of grazing provide foraging habitat for wintering and 

migratory birds that require habitat characterized by short vegetation heights. These 

wildlife species include Aleutian Canada goose, white-fronted goose, snow and Ross’ 

goose, sandhill crane, white-faced ibis, and long-billed curlew.

2) In natural uplands, the results of grazing provide winter foraging habitat for the 

migratory birds listed above. It also provides foraging, denning and nesting habitat 

for species which are characteristic of Central Valley grasslands and require habitat 

characterized by short vegetation heights. Such species include California ground 

squirrel, Heermann’s kangaroo rat, American badger, burrowing owl, and long-billed 

curlew.

3) In natural uplands, grazing maintains and improves the health and integrity of native 

plant and vernal pool communities by decreasing the amount of accumulated litter (dead 

plant material) and by decreasing the competitive influence of exotic grasses and forbs.

4) In irrigated pastures, natural uplands and fallow agricultural fields, grazing reduces and 

controls the abundance and proliferation of exotic invasive weeds such as yellow star 

thistle, prickly lettuce, Russian thistle, perennial pepperweed, amongst others.

The grazing period for irrigated pastures is year-round with the objective of having 

individual pastures grazed a total of eight months out of a year. Late summer/fall grazing 

levels are managed with the objective of having the pastures in a short-cropped condition 

when geese arrive in mid-October. Projected annual stocking rates on individual fields range 

from 0.6 to 1.3 AU/acre/month for eight months depending on productivity, condition of the 

pasture and Refuge management objectives.

The grazing period for natural uplands during years with average to high precipitation 

amounts is from December 1 through June 15 with the objective of having individual 

pastures grazed for a total of four months. Projected annual stocking rates are 1 AU/acre/

month for four months. During years with below-average precipitation amounts, stocking 

levels are decreased accordingly and/or periods of use are reduced.

All livestock used in the proposed grazing program are owned and managed by local 

agricultural producers. Grazing privileges are awarded by the Refuge when a producer 

enters into a Cooperative Land Management Agreement with the Refuge. Part 29.2 of Title 

50, Code of Federal Regulations, entitled “Cooperative Land Management,” states that:

Cooperative agreements with persons for crop cultivation, haying, grazing, or the harvest 

of vegetative products, including plant life, growing with or without cultivation on wildlife 

Refuge areas may be executed on a share-in-kind basis when such agreements are in aid of 

or benefit to the wildlife management of the area.

Grazing cooperators are chosen according to the process described in the U.S. Fish and 

Wildlife Service Refuge Manual, 5 RM 17. 
San Joaquin River NWR Comprehensive Conservation Plan 143

The value of cattle grazing in both natural uplands and irrigated pastures is set at $10.00/

AUM and reflects fair-market pasture rental rates characteristic of Stanislaus County, with 

adjustments made for water and irrigation costs incurred by the Cooperator. The value of 

sheep grazing is adjusted downward from fair-market pasture rental rates to reflect costs 

associated with temporary fencing, repeated movements of animals between pastures, 

required presence of a sheep-herder, and quality of forage. The value of grazing is credited 

against the Cooperator’s cost of performing work for the Refuge, such as the planting of 

wildlife food-crops (corn and winter wheat), in lieu of cash payment.

Availability of Resources:

The grazing program is administered by Refuge staff who identify the desired objectives 

of the grazing program, prepare Cooperative Land Management Agreements and Refuge 

Grazing Plans, provide coordination for grazing Cooperators as well as compliance 

monitoring. The grazing Cooperator is responsible for the cost of installation and/or 

maintenance of all range improvements (watering facilities, cross-fencing, etc.) associated 

with grazing activities. Facilities installed primarily for Refuge purposes are constructed 

or maintained at Refuge expense. Adequate funding and staff exist to manage the grazing 

program at the Refuge.

Anticipated Impacts of the Use:

Anticipated positive impacts of the grazing program at the Refuge include the following:

• The creation and maintenance of short-cropped foraging habitat for wintering and 

migratory birds in irrigated pastures and natural uplands.

• The creation and maintenance of year-round foraging, denning and nesting habitat, 

characterized by short vegetation, in natural uplands.

• Improvement and maintenance of the health and integrity of native plant and vernal pool 

communities in natural uplands.

• A reduction in the abundance and proliferation of noxious weeds in irrigated pastures and 

natural uplands.

• A reduction in the seed bank of exotic invasive weeds in fallow agricultural fields which are 

scheduled to be restored to riparian forest communities.

Potential negative impacts of a grazing program at the Refuge include:

• Improper fence placement and rotation of livestock within pastures can result in sensitive 

areas, such as wetlands and riparian corridors, being grazed and/or trampled excessively. 

This can result in damage to desirable vegetation, soil erosion, noxious weed invasion and 

reduced water quality of streams and wetlands.

• Poor management of livestock distribution within a pasture can result in portions being 

grazed and/or trampled excessively (i.e., around watering or mineral facilities). This can 

result in the same negative impacts mentioned above. 

• Poor management of periods when livestock are present in pastures can reduce or prevent 

the use of those pastures by wildlife species that would otherwise benefit from the habitat 

enhancements provided by livestock grazing.

Positive impacts can be maximized and negative impacts can be minimized through: 

• The establishment of Cooperative Land Management Agreements and Grazing Plans 

which clearly identify Refuge goals, objectives, strategies and prescriptions.

• Continuous and effective collaboration and coordination between Refuge staff and 
144 San Joaquin River NWR Comprehensive Conservation Plan

Cooperators.

• Diligent compliance monitoring by Refuge staff.

Public Review and Comment:

The public was provided the opportunity to review and comment on current and potential 

Refuge programs as part of the Comprehensive Conservation Planning process for the 

Refuge. This process included three large mailings of plan updates encouraging public input 

on the development of Refuge programs as well as having the opportunity to participate at a 

public planning workshop. Main topics of public interest were visitor access and appropriate 

recreational or educational uses of the Refuge. No public comments addressed the topic of 

grazing on the Refuge to benefit wildlife habitat.

Determination (check one below):

____ Use is Not Compatible

_X__ Use is Compatible with Following Stipulations

Stipulations Necessary to Ensure Compatibility:

The Cooperator will operate under the terms and conditions of a Cooperative Land 

Management Agreement and a Refuge Grazing Plan. These documents provide the 

necessary information and assistance from the Refuge to determine periods of use and 

stocking rates. Refuge staff will set the value of grazing so as to reflect current fair market 

values, monitor Cooperator compliance, and maintain complete files on all grazing activities. 

Justification:

The Refuge was established to conserve fish or wildlife which are listed as endangered 

species or threatened species or plants...; as an inviolate sanctuary, or for any other 

management purpose, for migratory birds; for the development, advancement, management, 

conservation, and protection of fish and wildlife resources; and for the benefit of the 

United States Fish and Wildlife Service, in performing its activities and services. A 

grazing program to protect and enhance wildlife habitat at the Refuge as indicated in this 

determination is compatible with the purposes for which the Refuge was established.

Mandatory Re-Evaluation Date:

__________ Mandatory 15 year Re-Evaluation Date (for priority public uses)

__2016____ Mandatory 10 year Re-Evaluation Date (for all uses other than priority public 

 uses)
San Joaquin River NWR Comprehensive Conservation Plan 145

NEPA Compliance for Refuge Use Decision:

_________ Categorical Exclusion without Environmental Action Statement

_________ Categorical Exclusion and Environmental Action Statement

_____X___ Environmental Assessment and Finding of No Significant Impact

_________ Environmental Impact Statement and Record of Decision

Refuge Determination: 

Prepared by: ______________________________________________

 (Signature and Date)

Refuge Manager Approval: ______________________________________________

 (Signature and Date)

Concurrence:

Refuge Supervisor: ______________________________________________

 (Signature and Date)

Assistant Manager,

National Wildlife

Refuge System ______________________________________________

 (Signature and Date)

California/Nevada

Operations Manager _______________________________________________

 (Signature and Date)
146 San Joaquin River NWR Comprehensive Conservation Plan

COMPATIBILITY DETERMINATION for Mosquito Monitoring and Control on the San 

Joaquin River National Wildlife Refuge

Use Considered: Mosquito Monitoring and Control 

Refuge Name:

San Joaquin River National Wildlife Refuge (Refuge) - a unit of the San Luis National 

Wildlife Refuge (NWR) Complex. The Refuge is located in western Stanislaus and San 

Joaquin Counties, California. The Refuge presently consists of approximately 6,500 acres 

situated along the San Joaquin River from just south of the confluence with the Tuolumne 

River north to the north bank of the Stanislaus River. The approved boundary for the 

Refuge comprises 12,887 acres; land presently not part of the Refuge is proposed for the 

conservation easement program. 

Establishing and Acquisition Authority(ies):

The Refuge was established in 1987 to protect the, at the time, endangered Aleutian Canada 

goose, listed as endangered in 1967 and relisted as threatened in 1991. The Refuge was 

originally established under the authority of the Endangered Species Act. Other Refuge 

lands were acquired under the Migratory Bird Conservation Act and the Fish and Wildlife 

Act of 1956. 

Refuge Purpose(s):

The Refuge purposes 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)

“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).

National Wildlife Refuge System Mission:

The mission of the National Wildlife Refuge System (NWRS) is “to administer a national 

network of lands and waters for the conservation, management, and where appropriate, 

restoration of the fish, wildlife, and plant resources and their habitats within the United 

States for the benefit of present and future generations of Americans.” 16 U.S.C. 668dd668ee (National Wildlife Refuge Administration Act of 1966, as amended).

Description of Use:

The Turlock and Eastside Mosquito Vector Control Districts (Districts) propose to continue 

the monitoring and controlling of mosquitoes at the Refuge to address nuisance and human 

health concerns of neighboring communities. The Refuge is located in the San Joaquin 

Valley. 
San Joaquin River NWR Comprehensive Conservation Plan 147

While mosquitoes at certain levels are considered a nuisance because of their biting, many 

species are also known vectors of serious diseases in California. Twelve mosquito-borne 

viruses are known to occur in California, however, only western equine encephalomyelitis 

virus (WEE) and St. Louis encephalitis virus (SLE) have caused significant outbreaks of 

human disease in the past (CA Dept. of Health Services 2003). Within the last few years, 

California has also been at risk for West Nile virus (WNV) which was first detected in the 

summer of 2003. WEE tends to be most serious in very young children, whereas elderly 

people are most at risk to SLE and WNV (CA Dept. of Heath Services 2003). WEE 

and WNV can cause serious diseases in horses and emus, and WNV kills a wide variety 

of endemic and imported birds. Mosquito control is the only known practical method of 

protecting people and animals from WEE, SLE, and WNV (CA Dept. of Health Services 

2003). 

The mosquito species identified by the Districts for monitoring and control are Culex

erythrothorax, C. pipiens, C. tarsalis; Ochlerotatus dorsalis, O. melanimon, O. 

nigromaculis, and Aedes vexans. C. tarsalis is the primary vector of WEE and SLE in 

California and is also considered to be a significant vector of WNV (CA Dept. of Health 

Services 2003). C. pipiens, C. erythrothorax, O. melanimon, O. dorsalis, and A. vexans may 

also contribute to disease transmission (Goddard et al 2002).

Mosquito Monitoring

The Districts’ monitoring activities are designed to ascertain the abundance of immature 

(larvae and pupae) and adult mosquito populations. During an average mosquito monitoring 

period, typically between the months of April through October, the Districts assess larval 

mosquito populations by using the ‘dipper’ method in various wetlands, moist soil units, 

irrigated pastures, and riparian areas. Adults are monitored using carbon dioxide (CO2) and 

light traps. 

The Districts’ monitor larval stage mosquito populations and identify species using the 

dipper method. This entails using a long-handled ladle (ca 500 ml) called a dipper to collect 

water samples from water potentially serving as mosquito sources. Dipping occurs from 

every one to two weeks depending on breeding conditions. Dip counts are used to estimate 

the abundance of immature mosquitoes and to determine the need for mosquito control. 

The Districts use carbon dioxide (CO2 ) baited traps to monitor the abundance of adult 

mosquitoes and to identify species. The trap used is baited with 1-2 kg of dry ice. The use 

and placement of CO2 baited traps on the Refuge depends on perceived numbers and the 

potential disease threat. Increased use of CO2 baited traps occurs when adult numbers are 

high or the disease threat is significant. A single light trap is operated at the Refuge’s shop 

and checked weekly throughout most of the year. Light traps are cylinders with a light, fan, 

and collecting jar. The mosquitoes are attracted to the light and enter the cylinder. 

The monitoring activities described above are conducted under a Special Use Permit (SUP) 

between the Refuge and the Districts. 

Mosquito Control with larvicides: 

The Districts control mosquitoes by treating areas infested with larval stages of C.

erythrothorax, C. pipiens, C. tarsalis; O. dorsalis, O. melanimon, O. nigromaculis, and 

A. vexans. Mosquito control would be initiated with the use of larvicides when breeding 

is considered widespread in an area as determined by the larval sampling program. 

Permission needs to be given by the Refuge Manager to the Districts immediately prior 

to any application of larvicides on the Refuge. The Districts treat larval mosquitoes using 
148 San Joaquin River NWR Comprehensive Conservation Plan

Bacillus thuringiensis serovar. israelensis (Bti) and methoprene, which are applied mainly 

with ground application methods and occasionally with aerial methods. Depending on need, 

multiple treatments can be used in the same area during a season but typically are separated 

by at least a two week period.

Bti is a microbial insect pathogen used to control larval stages of mosquitoes and black flies. 

It is a naturally occurring anaerobic spore forming bacteria that is mass produced using 

modern fermentation technology. Bti produces protein endotoxins that are activated in 

the alkaline mid-gut of insect species and subsequently bind to protein specific receptors of 

susceptible insect species resulting in the lethal response (Lacey and Mulla 1990). Bti must 

be ingested by the target insect to be effective. It is most effective on younger mosquito 

larval instars. The Districts use the formulated Bti product Teknar HP-D at rates of 0.5-1.0 

pt/acre and Vectobac 12AS at rates of 0.25-1 pt/acre. 

Methoprene is a synthetic insect growth regulator that mimics juvenile hormones (Tomlin, 

1994). It interferes with the insect’s maturation stages preventing the insect from 

transforming into the adult stage, thereby precluding reproduction. Methoprene is a contact 

insecticide that does not need to be ingested. It is most effective on early larval instars 

(Extension Toxicology Network, 1996). Treated larvae will pupate, but will not emerge as 

adults. The Districts use the formulated methoprene product Altosid Liquid Larvicide 

Concentrate at a rate of 0.75-1.0 oz/acre.

During the early stages of larval growth, typically stages 2-4, Bti is most effective for control 

as larvae at these stages of life tends to feed on bacteria. Altosid is used at later stages of 

larval growth when feeding ceases. Altosid is absorbed into the bodies of larvae, inhibiting 

their growth into adults. 

Applications of larvicides may occur anywhere in wetlands, moist soil units, irrigated 

pastures and/or riparian habitat at the Refuge depending on larval abundance. The potential 

areas for mosquito breeding and consequently mosquito treatment total approximately 3,000 

acres. Mosquito control applications can occur anytime between April through November, 

depending on environmental conditions, but normally occur during August, September, and 

October when water is being added to the wetland units. 

Annual precipitation amounts can also have a direct effect on mosquito populations. 

During drought years mosquito populations tend to be low, and during wet years mosquito 

populations tend to be high. Mosquito control is consequently conducted as a response to 

seasonality and/or climatic cycles. The Districts have been controlling mosquito populations 

with larvicides on the refuge since its creation in 1987. The larvaciding activities described 

above are conducted under a SUP between the Refuge and the Districts. 

Treatment has been conducted mainly by ground application in areas where monitoring 

has documented high mosquito larval densities or high concentrations of a specific vector 

bearing mosquito species. Aerial application has been done only rarely using either 

fixed-wing or rotary aircraft flown at an altitude of 10-20 feet above the vegetation and at 

airspeeds of 130-140 miles per hour. Treatment duration would average 20 minutes, but 

would vary given the size of the treatment area. Aerial pass distance would vary depending 

on the treatment area, but would average 70 feet. The pilot would use a map of units to be 

treated as well as utilizing a GPS as an additional guide.

Mosquito control with adulticides

The preferred mosquito control technique on the refuge is the use of larvacides. However, 

in cases where a public health emergency is declared due to adult mosquitoes, permission to 

use adulticides on the refuge by the Districts will be approved through the use of a SUP. In 
San Joaquin River NWR Comprehensive Conservation Plan 149

such cases, the Districts would use the adulticides Pyrocide or Pyrenone, which have natural 

pyrethrins as their active ingredient. 

Pyrethrins are naturally occurring compounds produced by certain species of 

chrysanthemum flowers. The flowers of the plant are harvested shortly after blooming 

and are either dried and powdered, or oils within the flowers are extracted by solvents. 

Pyrethrins are non-systemic contact poisons which quickly penetrate the nerve system of 

the insect and cause paralysis and subsequent death (EXTOXNET 1994, Tomlin 1994). A 

few minutes after application, the insect cannot move or fly away. But, a “knockdown dose” 

does not mean a killing dose. Pyrethrins are swiftly detoxified by enzymes in the insect. 

Thus, some pests will recover. To delay the enzyme action so a lethal dose is assured, 

commercial products are formulated with synergists such as piperonyl butoxide, which 

inhibit detoxification (Tomlin, 1994). Both products KMVCD proposes, Pyrocide and 

Pyrenone, are composed of 5% pyrethrins and 25% piperonyl butoxide. These adulticides 

are applied as an ultra-low volume (ULV) fog at a rate of 0.1 fluid oz/ac (0.0025 lbs ai/ac 

pyrethrin) by air and/or ground.

Availability of Resources:

Adequate funding and staff exist to manage this activity. Monitoring and control will be 

conducted by the Districts and not require the direct involvement of Refuge staff with the 

exception of oversight by the Refuge Manager. Monitoring of treatments would include 

observations of sprayed areas before and after treatment and coordination of permitting, 

documentation, and record keeping.

Anticipated Impacts of the Use:

This activity has three principal potential impacts on Service lands, waters or interests. 

These include disturbance to wildlife caused by the application of Bti/Altosid, impacts to 

wildlife by the periodic elimination of mosquito larvae from the Refuge, and the impacts of 

BTI/Altosid on nontarget organisms. All three potential impacts are somewhat minimized 

by only allowing treatment of habitats when mosquito breeding has been documented 

as widespread by Refuge staff and by requiring approval for treatment by the Refuge 

Manager. Thus instead of being treated weekly, whether needed or not, like many sites, 

Refuge lands will only be treated when sampling has documented a need. Disturbance from 

the ground or by aircraft usually is of short duration for the unit being treated. 

The impacts of monitoring will be confined to pathways to shorelines where dip net samples 

will be taken. Small areas of vegetation may be crushed in transit to pools of water, but the 

vegetation will likely spring back after it has been bent under foot. There will be relatively 

little of this impact, as dipping is done at most once a week. Placing and checking of CO2 

traps might also create a transient impact from footsteps on the vegetation going to and 

from the traps. Again, this is done at most once a week. There will be no disturbance of 

habitat associated with the single light trap, as it is in the maintenance yard at headquarters.

Toxicity and Effects to Non-target Organisms 

The dominant impact of mosquito control will relate to the toxicity and effects of the 

treatments on non-target organisms. Both BTI and Altosid treatments are more target 

specific and less persistent in the environment than most chemical insecticides and thus 

impacts the Refuge biota to a lesser degree than other chemical treatments available 

(Fleming et al. 1985, Fortin et al. 1987, Lee and Scott 1989, Marten et al. 1993, Mittal et al. 

1991, Parsons and Surgeoner 1991, and Purcell 1981). The possible effects of each compound 

will be discussed individually.
150 San Joaquin River NWR Comprehensive Conservation Plan

Bacillus thuringiensis var. israelensis (Bti). Bti has practically no acute or chronic toxicity 

to mammals, birds, fish, or vascular plants (U.S. U.S. EPA, 1998). Extensive acute toxicity 

studies indicated that Bti is virtually innocuous to mammals (Siegel and Shadduck, 1992). 

These studies exposed a variety of mammalian species to Bti at moderate to high doses and 

no pathological symptoms, disease, or mortality were observed. Laboratory acute toxicity 

studies indicated that the active ingredient of Bti formulated products is not acutely toxic to 

fish, amphibians or crustacaceans (Brown et al. 2002, Brown et al. 2000, Garcia et al. 1980, 

Lee and Scott 1989, and Wipfli et al. 1994). However, other ingredients in formulated Bti 

products are potentially toxic. The acute toxicity response of fish exposed to the formulated 

Bti product Teknar® HPD was attributed to xylene (Fortin et al. 1986, Wipfli et al. 1994). 

Field studies indicated no acute toxicity to several fish species exposed to Bti (Merritt et al. 

1989, Jackson et al. 2002); no detectable adverse effects to breeding red-winged blackbirds 

using and nesting in Bti treated areas (Niemi et al. 1999, Hanowski 1997); and no detectable 

adverse effects to tadpole shrimp 48 hours post Bti treatment (Dritz et al. 2001). 

In addition to mosquitoes (Family Culicidae), Bti affects some other members of the 

suborder Nematocera within the order Diptera. Also affected are members of the Family 

Simuliidae (black flies) and some chironomids midge larvae (Boisvert and Boisvert 2000, 

Garcia et al. 1980). The most commonly observed Bti effects to non-target organisms were 

to larvae of some chironomids in laboratory settings when exposed to relatively high doses 

(Boisvert and Boisvert 2000, Lacey and Mulla 1990, Miura et al. 1980). In field studies, 

effects to target and susceptible nontarget invertebrates have been variable and difficult 

to interpret. Field study results are apparently dependent on the number, frequency, rate 

and aerial extent of Bti applications; the Bti formulation used; the sample type (e.g. benthic, 

water column or drift); the sampling interval (e.g. from 48 hrs to one or more years after 

treatment); the habitat type (e.g. lentic or lotic); the biotic (e.g. aquatic communities), and 

abiotic factors (e.g. suspended organic matter or other suspended substrates, temperature, 

water depth); the mode of feeding (e.g. filter feeder, predator, scraper or gatherer); the 

larval development stage and larval density (Ali, 1981, Boisvert and Boisvert 2000, Lacey 

and Mulla,1990). Bti activity against target and susceptible nontarget invertebrates is also 

related to Bti persistence and environmental fate which are in turn affected by the factors 

associated with field study results (Dupont and Boisvert 1986, Mulla 1992). Simulated field 

studies resulted in the suppression of two unicellular algae species, Closterium sp. and 

Chlorella sp. resulting in secondary effects to turbidity and dissolved oxygen of aquatic 

habitats, with potential trophic effects (Su and Mulla, 1999). For these reasons, Bti effects 

to target and susceptible nontarget organisms, and potential indirect trophic impacts in the 

field are difficult to predict. 

Methoprene. Methoprene has moderate acute fish toxicity, slight acute avian toxicity, 

and practically no acute mammalian toxicity (U.S. EPA 2000, and U.S. Fish and Wildlife 

Service 1984). In mallard ducks, dietary concentrations of 30 parts per million (ppm) 

caused some reproductive impairment (U.S. EPA 1991). This figure exceeds the estimated 

environmental concentration by a factor 10 (Table 1). Methoprene residues have been 

observed to bioconcentrate in fish and crayfish by factors of 457 and 75, respectively 

(U.S. EPA 1991). Up to 95 % of the residue in fish was excreted within 14 days (U.S. EPA 

1991). Risk quotients for birds, fish and mammals are below EPA levels of concern for 

endangered species indicating negligible risk to those taxa resulting from direct exposure 

using maximum labeled rates for mosquito control (Urban et al. 1986). In field studies no 

detectable adverse effects to breeding red-winged blackbirds using and nesting in areas 

treated with methoprene were observed (Niemi et al. 1999). 

Methoprene affects terrestrial and aquatic invertebrates and is used to control fleas, sciarid 

flies in mushroom houses; cigarette beetles and tobacco moths in stored tobacco; Pharaoh’s 
San Joaquin River NWR Comprehensive Conservation Plan 151

ants; leaf miners in glasshouses; and midges (Tomlin 1994). Methoprene may also be fed to 

livestock in a premix food supplement for control of hornfly (WHO, undated). Methoprene is 

highly toxic to aquatic invertebrates with a 48 hour EC50 of 0.89 ppm for Daphnia magna

(U.S. EPA, 1991). Laboratory studies show that methoprene is acutely toxic to chironomids, 

cladocerans, and some decapods, (Horst and Walker 1999, Celestial and McKenney 1994, 

McKenney and Celestial 1996, Chu et al. 1997). In field studies, significant declines of 

aquatic invertebrate, mollusk and crustacean populations have been directly correlated to 

methoprene treatments for mosquito control (Breaud et al. 1977, Miura and Takahashi 1973, 

Niemi et al. 1999, and Hershey et al., 1998). 

Methoprene has a ten day half life in soil, a photolysis half life of ten hours, and solubility 

in water is 2 ppm (Zoecon 2000). Degradation in aqueous systems is caused by microbial 

activity and photolysis (U.S. EPA 1991). Degradation rates are roughly equal in freshwater 

and saltwater systems and are positively correlated to temperature (U.S. EPA 1991). 

Pyrethroids. There are only two general classes of adulticides, organophosphates and 

pyrethroids. The pyrethroids include both natural products called pyrethrins and synthetic 

molecules that mimic the natural pyrethrins, such as permethrin, resmethrin, and sumithrin.

In general, pyrethroids have lower toxicity to terrestrial vertebrates than 

organophosphates. Although not toxic to birds and mammals, pyrethroids are very toxic to 

fish and aquatic invertebrates (Anderson 1989, Siegfried 1993, Milam et al. 2000). The actual 

toxicity of pyrethroids in aquatic habitats, however, is less than may be anticipated because 

of the propensity of these pesticides to adsorb organic particles in water (Hill et al. 1994). 

The Districts use only natural pyrethrins on Refuge lands.

Wildlife:

Anticipated impacts from mosquito monitoring and control by the Districts is expected 

to be minimal. In an extensive literature review on the effects of Bti on mammals, Siegel 

and Shadduck (1992) found the bacterium to be innocuous. These studies exposed a variety 

of mammalian species to Bti at moderate to high doses and observed no pathological 

symptoms, nor disease, or mortality. Continued use of the bacterium, Bti, at moderate rates 

is likely to have a negligible effect on mammalian species residing on the Refuge. 

Fish

Areas most likely to be treated with larvacides include irrigated pasture and seasonal 

wetland basins recently filled—both of which are unlikely to contain fish. Aquatic habitats 

which have a fish community are unlikely to be significant sources of mosquitos on the 

Refuge. Toxicity of any of these pesticides to fish populations is not likely to be an issue, 

since fish rarely occur in mosquito production areas at the Refuge.

Wetlands and Waterfowl:

The Refuge was established in part to provide habitat for migratory birds, in particular 

waterfowl which includes geese, swans, ducks, and coots. These species occur on the 

Refuge during August, September, and October when newly flooded wetlands are being 

treated to control mosquitoes, so there is a potential impact on them. There is not likely 

to be much impact on geese and swans are year round herbivores. Geese feed mainly 

on grasses and agricultural lands, while swans feed mainly on roots, tubers, stems, and 

leaves of submerged and emergent aquatic vegetation. While applications of Bti and 

Altosid would be likely to occur over areas of vegetation which may be used by geese and 
152 San Joaquin River NWR Comprehensive Conservation Plan

swans, it has been found that birds are not negatively affected by using foods exposed to 

Bti or methoprene (Niemi et al. 1999). In contrast, ducks are known to be opportunistic 

feeders on both plants and invertebrates, using the most readily available food sources. 

Invertebrates, plants, and seeds compose the majority of their diet, varying with the 

season and the geographic location. A study in California’s Sacramento Valley has shown 

that plant foods are dominant in fall diets of northern pintails, while invertebrate use 

increases in February and March (Miller 1987). Seeds of swamp timothy comprise the 

most important duck food in the summer-dry habitats of the San Joaquin Valley (Miller 

1987). Thus any food chain impacts resulting from larvicide and adulticide treatment will 

have limited impacts to the mainly seed diet of newly arriving ducks. Their diet shifts to 

invertebrates after mosquito treatments are expected to be reduced in frequency, thereby 

allowing the invertebrate populations to recover. Recent studies have shown that aquatic 

invertebrates are a dominant food of non-breeding waterfowl during the summer molt, and 

the fall and winter periods (Heitmeyer and Raveling 1988). Invertebrates are also critical 

for egg production during the spring (Swanson et al. 1979), and duckling growth during the 

summer rearing period (Krapu and Swanson 1975). Mosquitoes and chironomids make an 

important contribution to invertebrate food resources throughout the year. Other significant 

food resource contributors of the invertebrate community are Coleoptera, Odonata, and 

Trichoptera. However, during fall flood-up and peak mosquito populations, ducks tend to 

feed on seed and other plant material. Waterfowl in general tend to feed on seeds when they 

reach their wintering areas, perhaps to regain energy lost during long flights (Heitmeyer 

and Raveling 1988, Miller 1987). Thus any food chain impacts resulting from larvicide and 

adulticide treatment will have limited impacts to the mainly seed diet of newly arriving 

ducks. Their diets shift to invertebrates after treatments are expected to be reduced in 

frequency thereby allowing invertebrate populations to recover.

Shorebirds feed on a wide variety of invertebrates all year, feeding which intensifies at 

the onset of spring migration. Documentation of indirect food-chain effects have not come 

to light. Hanowski et al. (1997) studied 19 different bird species after collecting data on 

wetlands 2 years before treatment and 3 years after treatment of both Bti and methoprene 

applications and found no negative effects. Niemi et al. (1999)found the same results from 

the same study site of a 3 year study on zooplankton or breeding birds. There are primarily 

two California State Species of Concern which forage and nest on the Refuge, they are tricolored blackbirds, and white-faced ibis. Both species are associated with wetland habitats. 

While resident endangered species are limited to upland habitat on the Refuge, these 

sensitive species prefer wetland habitat or habitat bordering wetlands. While Hanowski et 

al. (1997) found no direct evidence to indicate Bti or methoprene negatively impacted the 

reproduction, growth, or foraging of red-winged blackbirds, to minimize impacts to these 

species, in particular, during their breeding season, no applications will occur where tricolored blackbirds or white-faced ibis are nesting.

While treatment on the ground may seem ideal because the impact area is small and can be 

accomplished from existing roads and levees, aerial treatment is preferred as the impacts to 

the ground are non-existent and the amount of coverage is larger, less time consuming, and 

effective over a large area. 

Low flying aircraft will undoubtedly cause disturbances to wildlife. However, the number of 

treatment days per year is low, and if the applicator (pilot or ground) follows the stipulations 

previously outlined and within the SUP, mosquito abatement practices should not materially 

interfere with or detract from the Refuge purpose or the mission of the National Wildlife 

Refuge System. If additional biological monitoring of this activity documents substantial 

negative impacts to migratory birds or other wildlife, this determination would be reanalyzed on the basis on new evidence.
San Joaquin River NWR Comprehensive Conservation Plan 153

Public Review and Comment:

The public was provided the opportunity to review and comment on current and potential 

Refuge programs as part of the Comprehensive Conservation Planning process for the 

Refuge. This process included three large mailings of plan updates encouraging public input 

on the development of Refuge programs as well as having the opportunity to participate at a 

public planning workshop. Main topics of public interest were visitor access and appropriate 

recreational or educational uses of the Refuge. No public comments addressed mosquito 

management at the Refuge. 

Determination (check one below):

____ Use is Not Compatible

_X__ Use is Compatible with Following Stipulations

Stipulations Necessary to Ensure Compatibility:

The following stipulations are required to ensure compatibility: that the Districts apply for 

and receive a SUP annually from the Refuge, that larvae control only be conducted when 

breeding is widespread as documented by sampling efforts, that only BTI and altosid may 

be applied on the Refuge as a larvacide, that the Refuge Manager has final approval for any 

larvacide treatments on the Refuge, that mosquito adulticide only be used on the Refuge 

during a declared public health emergency, that only Pyrocide or Pyrenone be used as an 

adulticide, that the Refuge Manager has final approval for any adulticide treatments on the 

Refuge, and that a final report of all control activities conducted on the by the Districts be 

sent at the end of the year to the Refuge Manager. Specifically for mosquito monitoring and 

control to occur on the Refuge will require the following:

1. All application of pesticides/biological agents must be coordinated and approved by the 

Refuge Manger to avoid conflicts with nesting birds, public use, management activities, 

etc. Prior to all larvacide applications, the Districts will provide a map and sampling 

results to the Refuge Manager and obtain verbal approval. 

2. Mosquito larvae will be widespread and abundant as documented by sampling for 

permission to be granted for the Districts to larvacide any portion of the Refuge.

3. The Districts will provide the Refuge with interim and final reports regarding mosquito 

sampling on the Refuge. 

4. Mosquito adulticides will only be allowed in cases of a declared health emergency, 

following a specific request to the Refuge and written concurrence from appropriate 

Service or Department bureaus. A human-health emergency is defined by the presence of 

human disease virus-positive mosquitoes, virus-positive birds and/or human disease at or 

by the Refuge in Stanislaus or San Joaquin Counties. 

5. Spraying of any kind will not be conducted on vernal pools or other such water basins 

resulting from rainwater accumulations in upland sites. 

6. At the end of the permitting period, the Districts will provide the Refuge Manager with a 

list of all pesticides/biological agents used, and the quantities of each that were applied. 

7. Application of mosquito control measures is to be conducted in accordance with approved 

Pesticide Use Proposals and labels.
154 San Joaquin River NWR Comprehensive Conservation Plan

8. Mosquito control will be authorized on an annual basis by a SUP. SUP condition will 

stipulate that all mosquito control work will be carried out under the guidance of preapproved Pesticide Use Proposals.

Justification:

The Refuge was established to conserve fish or wildlife which are listed as endangered 

species or threatened species or plants...; as an inviolate sanctuary, or for any other 

management purpose, for migratory birds; for the development, advancement, management, 

conservation, and protection of fish and wildlife resources; and for the benefit of the United 

States Fish and Wildlife Service, in performing its activities and services. Mosquito 

monitoring and control by the Districts at the Refuge as indicated in this determination 

is compatible with the purposes for which the Refuge was established. For many years 

the Refuge has worked cooperatively with these two Districts and their mosquito control 

activities. After a review of these activities, the Refuge has determined that allowing these 

uses to continue would not interfere with the purposes for which the Refuge was established, 

nor the mission of the National Wildlife Refuge System.

Mandatory Re-Evaluation Date:

__________ Mandatory 15 year Re-Evaluation Date (for priority public uses)

__2016____ Mandatory 10 year Re-Evaluation Date (for all uses other than priority public 

 uses)

NEPA Compliance for Refuge Use Decision:

_________ Categorical Exclusion without Environmental Action Statement

_________ Categorical Exclusion and Environmental Action Statement

____X____ Environmental Assessment and Finding of No Significant Impact

_________ Environmental Impact Statement and Record of Decision

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Boisvert, M., and J. Boisvert. 2000. Effects of Bacillus thuringiensis var. israelensis 

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San Joaquin River NWR Comprehensive Conservation Plan 155

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and Soil Pollution 29:425-438.

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teal wintering in California. Journal of Wildlife Management 51(4): 724-732.

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http://ace.ace.orst.edu/info/extoxnet/pips/methopre.htm

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mallard ducklings and the influence of cold. Environ. Toxicology and Chemistry 4:193-

200. 

Fortin, C.; Marie, A.; and Leclair, R. 1987. The residual effect of Abate on nontarget 

 communities. J. Am. Mosquito Control Assoication 3:282-288. 

Fortin, C, D. Lapointe, and G. Charpentier. 1986. Susceptibility of brook trout (Salvelinus 

fontinalis) fry to a liquid formulation of Bacillus thuringiensis serovar. Israelensis

(Teknar®) used for blackfly control. Canadian Journal of Fisheries and Aquatic 

Science 43:1667-1670.

Garcia, R., B. Des Rochers, amd W. Tozer. 1980. Studies on the toxicity of Bacillus 

thuringiensis var. israelensis against organisms found in association with mosquito 

larvae. California Mosquito and Vector Control Association Proceedings and Papers 

48:33-36. 
156 San Joaquin River NWR Comprehensive Conservation Plan

Goddard, L.B., A.E. Roth, W.K Reisen, and T.W. Scott. 2002. Vector competence of California 

mosquitoes for West Nile virus. Emerging Infectious Diseases 8/12 1385-1391.

Hanowski, J. M., G. J. Niemi, A. R. Lima, and R. R. Regal. 1997. Do mosquito control 

treatments of wetlands affect red-winged blackbird (Agelaius phoeniceus) growth, 

reproduction, or behavior? Environmental Toxicology and Chemistry 16( 5):1014-1019. 

Hershey, A. E., A. R. Lima, G. J. Niemi, and R R. Regal. 1998. Effects of Bacillus 

thuringiensis israelensis (Bti) and methoprene on non-target macroinvertebrates in 

Minnesota wetlands. Ecological Applications 8:41-60. 

Heitmeyer, M. E. and D. G. Raveling. 1988. Winter resource use by three species of dabbling 

ducks in California. Delta Waterfowl and Wetlands Research Station, Portage la 

Prairie, Man., Can.

Horst, M.N., and A.N. Walker. 1999. Effects of the pesticide methoprene on morphogenesis 

and shell formation in the blue crap Callinectues sapidus. Journal of Crustacean 

Biology 19: 699-707. 

Jackson, J. K., R.J. Horowitz, and B.W. Sweeny. 2002. Effects of Bacillus thuringiensis 

israelensis on black flies and nontarget macroinvertebratess and fish in a large river. 

Transactions of the American Fisheries Society 131:910-930.

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nesting pintails. Journal of Wildlife Management 39:156-162.

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Bacillus sphaericus to non-target organisms in the aquatic environment. In Laird, M., 

L.A. Lacey, E.W. Davidson, eds. Safety of microbial insecticides. CRC Press.

Lee, B. M. And G. I. Scott. 1989. Acute toxicity of temephos, fenoxycarb, diflubenzuron, and 

methoprene and Bacillus thuringiensis var. israelensis to the mummichog (Fundulus

heteroclitus). Bulletin of Environmental Contamination and Toxicology 43:827-832.

Marten, G.G.; Che, W.; and Bordes, E.S. 1993. Compatibility of cyclopoid copepods with 

mosquito insecticides. J. Am. Mosquito Control Association 9:150-154. 

McKenney, C.L., Jr., and D.M. Celestial. 1996. Modified survival, growth, and reproduction 

in an estuarine mysid (Mysidoposis bahia) exposed to a juvenile hormone analogue 

through a complete life cycle. Aquatic Toxicology 35:11-20. 

Merritt, R. W., E. D. Walker, M. A. Wilzbach, K. W. Cummings, and W. T. Morgan. 1989. 

A broad evaluation of Bti for black fly (Diptera: Simuliidae) control in a Michigan 

River: Efficacy, carry, and non-target effects on invertebrates and fish. Journal of the 

American Mosquito Control Association 5:397-415.

Millam, D.C., J.L. Farris, and J.D. Wilhide. 2000. Evaluating mosquito control pesticides 

for effect on target and nontarget organisms. Mosquito News 40:619-622.

Miller, M. R. 1987. Fall and winter foods of northern pintails in the Sacramento Valley, 

California. Journal of Wildlife Management. 51:405-414.

Mittal, P.K.; Adak, T.; and Sharma, V.P. 1991. Acute toxicity of certain organochlorine, 

organophosphorus, synthetic pyrethroid and microbial insecticides to the mosquito 
San Joaquin River NWR Comprehensive Conservation Plan 157

fish. Indian J. of Malariology 28:167-170. 

Miura, T., and R.M. Takahashi. 1973. Insect development inhibitors. 3. Effects on nontarget 

aquatic organisms. Journal of Economic Entomology. 66(4):917-922.

Miura, T.; Takahashi, R. M.; and Mulligan, F.S. 1980. Effects of the bacterial mosquito 

larvicide Bacillus thuringiensis stereotype H-14 on selected aquatic organisms. 

Mosquito News. 40:619-622.

Mulla, M.S. 1992. Activity, Field Efficacy, and Use of Bacillus thuringiensis israelensis

against Mosquitoes. Pp. 134-160 in de Barjac, Hugette and Donald J. Sutherland, 

eds. Bacterial Control of Mosquitoes and Blackflies: Biochemistry, Genetics, and 

Applications of Bacillus thuringiensis israelensis and Bacillus sphaericus. Kluwer 

Academic.

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Birds. Environmental Toxicology and Chemistry, 18(3):549-559.

Parsons, J.T. and Surgeoner, G.A. 1991. Acute toxicities of permethrin, fenitrothion, 

carbaryl and carbofuran to mosquito larvae during sing pulse or multiple pulse 

exposures. Environ. Toxicology and Chemistry 10:1229-1233. 

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nontarget organisms in the salt marsh. Mosq. News 41:476-484).

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virus in the Southern San Joaquin Valley of California. Entomological Society of 

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Kluwer Academic.

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Bacillus sphaericus suppress eutrophication, enhance water quality, and control 

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pesticide Programs. Special Review and Registration Division.
158 San Joaquin River NWR Comprehensive Conservation Plan

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Prevention, Pesticides and Toxic Substances. EPA738-R-98-004.

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Bacillus thuringiensis var. israelensis to early stages of brook trout (Salvelinus 

fontinalis), brown trout (Salmo trutta), and steelhead trout (Oncorhynchus mykiss) 

following direct and indirect exposure. Canadian Journal of Fisheries and Aquatic 

Science 41:1451-1458. 

Zoecon. 2000. MSDS Altosid Liquid Larvicide Concentrate

Refuge Determination: 

Prepared by: ______________________________________________

 (Signature and Date)

Refuge Manager Approval: ______________________________________________

 (Signature and Date)

Concurrence:

Refuge Supervisor: ______________________________________________

 (Signature and Date)

Assistant Manager,

National Wildlife

Refuge System ______________________________________________

 (Signature and Date)

California/Nevada

Operations Manager _______________________________________________

 (Signature and Date)
San Joaquin River NWR Comprehensive Conservation Plan 159

Appendix E: Species List

Invertebrates

Artemia franciscana brine shrimp

Branchinecta coloradensis Colorado fairy shrimp

Branchinecta conservatio Conservancy fairy shrimp (E)

Branchinecta lindahli (no common name)

Branchinecta longiantenna longhorn fairy shrimp (E)

Branchinecta lynchi vernal pool fairy shrimp (T)

Branchinecta mackini (no common name)

Branchinecta mesovallensis midvalley fairy shrimp

Lepidurus packardi vernal pool tadpole shrimp (E)

Linderiella occidentalis California linderiella

Anticus antiochensis Antioch Dunes anthicid beetle (CS)

Anticus sacramento Sacramento anthicid beetle (CS)

Desmocerus californicus dimorphus Valley elderberry longhorn beetle (T)

Hygrotus curvipes curved-foot hygrotus diving beetle (CS)

Lytta moesta moestan blister beetle (CS)

Lytta molesta molestan blister beetle (CS)

Vertebrates

Amphibia

Caudata:

Ambystomatidae Ambystoma californiense California tiger salamander (CP, CS)

Anura:

Pelobatidae Spea hammondii western spadefoot (CP, CS)

Bufonidae Bufo boreas western toad

Hylidae Hyla regilla Pacific treefrog

Ranidae Rana aurora red-legged frog (FT, CP, CS)

 Rana boylii foothill yellow-legged frog (CP,CS, FS)

 Rana catesbeiana bullfrog (H)

Reptilia

Testudines:

Emydidae Clemmys marmorota western pond turtle (CP, CS, FS)

 Trachemys scripta slider

Squamata:

Iguanidae Gambelia sila blunt-nosed leopard lizard (FE, CE, CP)

 Sceloporus occidentalis western fence lizard

 Uta stansburiana side-blotched lizard

 Phrynosoma coronatum coast horned lizard (CP, CS)

Scincidae Eumeces gilbertii Gilbert’s skink

Teiidae Cnemidophorus tigris western whiptail

Anguidae Elgaria multicarinatus southern alligator lizard

 Elgaria coerulea northern alligator lizard

Anniellidae Anniella pulchra California legless lizard
160 San Joaquin River NWR Comprehensive Conservation Plan

Colubridae Coluber constrictor racer

 Masticophis flagellum coachwhip (CP, CS)

Arizona elegans glossy snake

Pituophis melanoleucus Pacific gopher snake

 Lampropeltis getula common kingsnake

 Rhinochielus lecontei long-nosed snake

 Thamnophis sirtalis common garter snake 

 Thamnophis gigas giant garter snake (FT, CT, CP)

Viperidae Crotalus viridis western rattlesnake

Fish

Petromyzontidae Lampetra tridentata Pacific Lamprey*

Acipenseridae Acipenser transmontanus white sturgeon*

Clupeidae Alosa sapidissima American shad

 Dorosoma petenese threadfin shad 

Cyprinidae Cyprinus carpio common carp

 Carassius auratus goldfish

 Notemigonus crysoleucas golden shiner

 Lavinia exilicauda hitch*

 Orthodon microlepidotus Sacramento blackfish*

 Pogonichthys macrolepidotus Sacramento splittail**

 Ptychocheilus grandis Sacramento pikeminnow*

 Cyprinella lutrensis red shiner

 Pimephales promelas fathead minnow

Catostomidaeca Catostomus occidedntalis Sacramento sucker*

Ictaluridae Ameiurus catus white catfish

 Ameiurus nebulosus broun bullhead

 Ameiurus melas black bullhead

 Ictalurus punctatus channel catfish

Salmonidae Oncorhynchus tshawytscha chinook salmon**

 Oncorhynchus mykiss rainbow trout*

Poeciliidae Gambusia affinis western mosquitofish

Atherinidae Menidia beryllina inland silverside

Cottidae Cottus asper prickly sculpin*

Percichthyidae Morone saxatilis striped bass

Centrarchidae Pomoxis migromaculatus black crappie

 Pomoxis annularis white crappie

 Lopomis gulosus warmouth

 Lopomis cyanellus green sunfish

 Lopomis macrochirus bluegill

 Lopomis microlophus redear sunfish

 Micropterus salmoides largemouth bass

 Micropterus dolomieu smallmouth bass

Percidae Percina macrolepida bigscale logperch

Embiotocidae Hysterocarpus traski tule perch*

Aves

Podicipediformes:

Podicipedidae Aechomophorus clarkii Clark’s grebe

 Aechomophorus occidentalis western grebe

 Podiceps auritus horned grebe
San Joaquin River NWR Comprehensive Conservation Plan 161

 Podiceps nigricollis eared grebe

 Podilymbus podiceps pied-billed grebe

Pelecaniformes:

Pelecanidae Pelecanus erythrorynchos American white pelican

Phalacrocoracidae Phalacrocorax auritus double-crested cormorant

Ciconiiformes:

Ardeidae Ixobrychus exilis least bittern

 Botaurus lentiginosus American bittern

 Nycticorax nycticorax black-crowned night heron

 Butorides striatus green-backed heron

 Bubulcus ibis cattle egret

 Egretta thula snowy egret

 Ardea alba great egret

 Ardea herodias great blue heron

Threskiornithidae Plegadis chihi white-faced ibis

Anseriformes:

Anatidae Cygnus columbianus tundra swan

 Anser albifrons greater white-fronted goose

 Chen caerulescens snow goose

 Chen rossii Ross’ goose

 Branta canadensis leucopareia Aleutian Canada goose (T)

 Branta canadensis minima cackling Canada goose

 Branta canadensis moffitti Great Basin Canada goose

 Branta canadensis parvipes lesser Canada goose

 Branta bernicla brant

 Anas platyrhynchos mallard

 Anas strepera gadwall

 Anas crecca green-winged teal

 Anas americana American wigeon

 Anas penelope Eurasian wigeon

 Anas acuta northern pintail

 Anas clypeata northern shoveler

 Anas discors blue-winged teal

 Anas cyanoptera cinnamon teal

 Oxyura jamaicensis ruddy duck

 Aix sponsa wood duck

 Aythya valisineria canvasback

 Aythya americana redhead

 Aythya collaris ring-necked duck

 Aythya marila greater scaup

 Athya affinis lesser scaup

 Bucephala clangula common goldeneye

 Bucephola albeola bufflehead

 Mergus merganser common merganser

 Lophodytes cucullatus hooded merganser

 Aix galericulata Mandarin duck

 Branta rufficollis red-breasted goose (accidental)

Gruiformes:

Rallidae Rallus limicola Virginia rail

 Porzana carolina sora

 Gallinula chloropus common moorhen

 Fulica americana American coot
162 San Joaquin River NWR Comprehensive Conservation Plan

Charadriiformes:

Recurvirostridae Recurvirostra americana American avocet

 Himantopus mexicanus black-necked stilt

Charadriidae Charadrius alexandrinus snowy plover

 Charadrius semipalmatus semipalmated plover

 Charadrius vociferus killdeer

 Charadrius montanus mountain plover

 Pluvialis squatarola black-bellied plover

 Pluvialis dominica American golden plover

Scolopacidae Limosa fedoa marbled godwit

 Newmenius phaeopus whimbrel

 Newmenius americanus long-billed curlew

 Catoptrophorus semipalmatus willet

 Tringa melanoleuca greater yellowlegs

 Tringa flavipes lesser yellowlegs

 Tringa solitaria solitary sandpiper

 Actitis macularia spotted sandpiper

 Phalaropus tricolor Wilson’s phalarope

 Phalaropus lobatus red-necked phalarope

 Limnodromus griseus short-billed dowitcher

 Limnodromus scolopaceus long-billed dowitcher

 Gallinago gallinago common snipe

 Calidris alpina dunlin

 Calidris mauri western sandpiper

 Calidris minutilla least sandpiper

 Calidris bairdii Baird’s sandpiper

 Calidris melanotos pectoral sandpiper

Laridae Larus philidelphia Bonaparte’s gull

 Larus delawarensis ring-billed gull

 Larus argentatus herring gull

 Larus californicus California gull

 Larus glaucescens glaucous-winged gull

 Sterna forsteri Forster’s tern

 Chlidonias niger black tern

 Sterna caspia Caspian tern

Falconiformes:

Cathartidae Cathartes aura turkey vulture

Accipitridae Aquila chrysaetos golden eagle

 Haliaeetus leucocephalus bald eagle (T)

 Elanus leucurus white-tailed kite

 Circus cyaneus northern harrier

 Accipiter striatus sharp-shinned hawk

 Accipiter cooperii Cooper’s hawk

 Buteo lineatus red-shouldered hawk

 Buteo jamaicensis red-tailed hawk

 Buteo swainsoni Swainson’s hawk

 Buteo lagopus rough-legged hawk

 Buteo regalis ferruginous hawk

 Pandion haliaetus osprey

Falconidae Falco sparverius American kestrel

 Falco columbarius merlin

 Falco mexicanus prairie falcon

 Falco peregrinus peregrine falcon (E)
San Joaquin River NWR Comprehensive Conservation Plan 163

Galliformes:

Phasianidae Callipepla californica California quail

 Phasianus colchicus ring-necked pheasant

Columbiformes:

Columbidae Columba livia rock dove

 Zenaida macroura mourning dove

Cuculiformes:

Cuculidae Coccyzus americanus yellow-billed cuckoo

Strigiformes:

Tytonidae Tyto alba barn owl

Strigidae Asio flammeus short-eared owl

 Asio otus long-eared owl

 Bubo virginianus great horned owl

 Otus kennicottii western screech owl

 Athene cunicularia burrowing owl

Caprimulgiformes:

Caprimulgidae Chordeiles acutipennis lesser nighthawk

Apodiformes:

Apodidae Chaetura vauxi Vaux’s swift

 Aeronautes saxatalis White-throated swift

Trochilidae Archilochus alexandri black-chinned hummingbird

 Calypte anna Anna’s hummingbird

 Selasphorus rufus rufous hummingbird

Coraciiformes:

Alcedinidae Ceryle alcyon belted kingfisher

Piciformes:

Picidae Colaptes auratus northern flicker

 Melanerpes formicivorus acorn woodpecker

 Melanerpes lewis Lewis’ woodpecker

 Picoides pubescens downy woodpecker

 Picoides nuttallii Nuttall’s woodpecker

Passeriformes:

Tyrannidae Tyrannus verticalis western kingbird

 Tyrranus vociferans Cassin’s kingbird

 Myiarchus cinerascens ash-throated flycatcher

 Contopus sordidulus western wood-pewee

 Sayornis nigricans black phoebe

 Sayornis saya Say’s phoebe

 Empidonax oberholseri dusky flycatcher

 Empidonax traillii willow flycatcher

 Empidonax difficilis Pacific-slope flycatcher

Alaudidae Eremophila alpestris horned lark

Hirundinidae Tachycineta bicolor tree swallow

 Tachycineta thalassina violet-green swallow

 Progne subis purple martin

 Riparia riparia bank swallow

 Stelgidopteryx serripennis northern rough-winged swallow

 Petrochelidon pyrrhonata cliff swallow

 Hirundo rustica barn swallow

Corvidae Aphelocoma californica western scrub jay

 Pica nuttalli yellow-billed magpie

 Corvus brachyrynchos American crow

 Corvus corax common raven
164 San Joaquin River NWR Comprehensive Conservation Plan

Regulidae Regulus satrapa golden-crowned kinglet

 Regulus calendula ruby-crowned kinglet

Muscicapidae Chamaea fasciata wrentit

 Sialia mexicana western bluebird

 Catharus ustulatus Swainson’s thrush

 Catharus guttatus hermit thrush

 Ixoreus naevius varied thrush

 Turdus migratorius American robin

Paridae Baeolophus inornatus oak titmouse

Aegithalidae Psaltriparus minimus bushtit

Certhiidae Certhia americana brown creeper

Sittidae Sitta carolinensis white-breasted nuthatch

 Sitta canadensis red-breasted nuthatch

Troglodytidae Troglodytes aedon house wren

 Troglodytes troglodytes winter wren

 Thyromanes bewickii Bewick’s wren

 Cistothorus palustris marsh wren

 Salpinctes obsoletus rock wren

Laniidae Lanius ludovicianus loggerhead shrike

Mimidae Mimus polyglottos northern mockingbird

 Toxostoma redivivum California thrasher

Motacillidae Anthus rubescens American pipit

Bombycillidae Bombycilla cedrorum cedar waxwing

Sturnidae Sturnus vulgaris European starling

Vireonidae Vireo cassinii Cassin’s vireo

 Vireo gilvus warbling vireo

 Vireo bellii pusillus least Bell’s vireo (E)

Emberizidae Vermivora celata orange-crowned warbler

 Vermivora ruficapilla Nashville warbler

 Dendroica coronata yellow-rumped warbler

 Dendroica nigriscens black-throated gray warbler

 Dendroica townsendi Townsend’s warbler

 Dendroica occidentalis Hermit warbler

 Dendroica petechia yellow warbler

 Oporornis tolmiei MacGillivray’s warbler

 Wilsonia pusilla Wilson’s warbler

 Geothlypis trichas common yellowthroat

 Icteria virens yellow-breasted chat

 Pheucticus melanocephalus black-headed grosbeak

 Guiraca caerulea blue grosbeak

 Passerina amoena lazuli bunting

 Pipilo maculatus spotted towhee

 Pipilo crissalis California towhee

 Ammodramus savannarum grasshopper sparrow

 Pooecetes gramineus vesper sparrow

 Passerculus sandwichensis savannah sparrow

 Melospiza melodia song sparrow

 Chondestes grammacus lark sparrow

 Amphispiza belli sage sparrow

 Spizella passerina chipping sparrow

 Junco hyemalis dark-eyed junco

 Zonotrichia leucophrys white-crowned sparrow

 Zonotrichia atricapilla golden-crowned sparrow
San Joaquin River NWR Comprehensive Conservation Plan 165

 Passerella iliaca fox sparrow

 Melospiza lincolnii Lincoln’s sparrow

 Sturnella neglecta western meadowlark

 Xanthocephalus xanthocephalus yellow-headed blackbird

 Agelaius phoeniceus red-winged blackbird

 Agelaius tricolor tricolored blackbird

 Euphagus cyanocephalus Brewer’s blackbird

 Molothrus ater brown-headed cowbird

 Icterus bullockii Bullock’s oriole

 Icterus cucullatus hooded oriole

 Piranga ludoviciana western tanager

Passeridae Passer domesticus house sparrow

Fringillidae Carduelis pinus pine siskin

 Carduelis tristis American goldfinch

 Carduelis psaltria lesser goldfinch

 Carduelis lawrencei Lawrence’s goldfinch

 Carpodacus purpureus purple finch

 Carpodacus mexicanus house finch

Mammalia Mammals

Marsupia1ia:

Didelphidae Didelphis virginiana Virginia opossum (H)

Insectivora:

Soricidae Sorex ornatus ornate shrew (CS)

Talpidae Scapanus latimanus broad-footed mole (CS)

Chiroptera:

Vespertilionidae Myotis lucifugus little brown myotis (CS)

 Antrozous pallidus pallid bat (CS)

 Myotis ciliolabrum western small-footed myotis

 Myotis evotis long-eared myotis

 Myotis thysanodes fringed myotis

 Myotis volans long-legged myotis

 Myotis yumanensis Yuma myotis

 Plecotus townsendii Townsend’s big-eared bat (CS)

Molossidae Tadarida brasiliensis Brazilian free-tailed bat

 Eumops perotis western mastiff bat (CS)

Carnivora:

Canidae Canis latrans coyote (H)

 Canus domesticus domestic dog

 Urocyon cinereoargenteus gray fox (H)

 Vulpes vulpes red fox (H)

 Vulpes macrotis mutica San Joaquin kit fox (FE, CT)

Procyonidae Procyon lotor raccoon (H)

Mustelidae Lutra canadensis northern river otter (CS)

 Mephitis mephitis striped skunk (H)

 Spilogale gracilis western spotted skunk (CS)

 Mustela frenata long-tailed weasel (H)

 Mustela vison mink (H)

 Taxidea taxus badger (H)

Felidae Felis catus housecat

 Lynx rufus bobcat (H)

Perissodactyla:

Equidae Equus caballus domestic horse
166 San Joaquin River NWR Comprehensive Conservation Plan

Artiodactyla:

Suidae Sus scrofa wild pig (H)

Cervidae Odocoileus hemionus mule deer (H)

Bovidae Bos taurus domestic cattle

 Ovis aries domestic sheep

Rodentia:

Sciuridae Spermophilus beecheyi California ground squirrel

Geomyidae Thomomys bottae Botta’s pocket gopher

Heteromyidae Dipodomys heermanni Heerman’s kangaroo rat (FE, CE, CP)

 Perognathus inornatus San Joaquin pocket mouse (CS)

Castoridae Castor canadensis beaver (H)

Cricetidae Neotoma fuscipes riparia San Joaquin Valley woodrat (FE, CE)

 Peromyscus boylii brush mouse

 Peromyscus maniculatus deer mouse (CS)

 Reithrodontomys megalotis western harvest mouse

Arvicolidae Microtus californicus California vole

 Ondatra zibethicus muskrat

Muridae Mus musculus house mouse

 Rattus norvegicus Norway rat

 Rattus rattus black rat

Lagomorpha:

Leporidae Lepus californicus black-tailed hare (CS, H)

 Sylvilagus audubonii Desert cottontail (H)

 Sylvilagus bachmanii riparius riparian brush rabbit (CE)

Source of statuses: www.dfg.ca.gov/wmd/cwhr/natives.html

FE: federally endangered

FT: federally threatened

CE: California endangered

CT: California threatened

CP: California protected

CS: Callifornia special concern

FS: Forest Service sensitive

BS: BLM sensitive

H: harvest

Note:

1. Confirmed species appear in bold print

2. List from San Joaquin River National Wildlife Refuge Riparian Habitat Protection and Flood Restoration 

Project, Biological Inventory and Monitoring 1998, USFWS, August
San Joaquin River NWR Comprehensive Conservation Plan 167

Appendix F: Intra-Service Section 7 Consultation

Originating Refuge: San Luis NWRC 

Telephone Number: (209) 826-3508 

Date: August 3, 2006 

I.	 Region:	 CA/Nevada Operations Office

II.	 Service Activity (Program): Riparian/Wetland/Upland Restoration (Refuge Management), San Joaquin

River NWR Comprehensive Conservation Plan

III.	 Pertinent Species:

A. Listed species and/or their critical habitat within the action area:

Bald eagle (Haliaeetus leucocephalus) (T)

Willow flycatcher (Epidonax trailli extimus) (E)

Least Bell’s vireo (Vireo bellii pusillus) (E)

Fresno kangaroo rat (Dipodomys nitratoides exilis) (E)

San Joaquin kit fox (Vulpes macrotis mutica) (E)

Riparian brush rabbit (Sylvilagus bachmani riparius) (E)

San Joaquin Valley woodrat (Neotoma fuscipes riparia) (E)

Giant garter snake (Thamnophis gigas) (T)

Blunt-nosed leopard lizard (Gambelia sila) (E)

Conservancy fairy shrimp (Branchinecta conservatio) (E)

Vernal pool fairy shrimp (Branchinecta lynchi) (T) (CH)

Vernal pool tadpole shrimp (Lepidurus packardi) (E)

Valley elderberry longhorn beetle (Desmocerus californicus dimorphus) (T)

California tiger salamander, central pop. (Ambystoma californiense) (T)

	 	 Delta smelt (Hypomesus transpacificus) (T) (CH)

	 	 California red-legged frog (Rana aurora draytonii) (T)

B. Proposed species within the action area:

 None

C. Candidate species within the action area:

 None

D. Include species/habitat occurrence on a map: 

	 	 See species narrative accounts section VII A

IV.	 Geographic area or station name and action:

The San Joaquin River National Wildlife Refuge (Refuge) was established in 1987 as part of the San Luis NWR

Complex. The main focus of the management of the refuge over the years has been to protect and manage

wintering habitat for Aleutian Canada geese, a Federally listed endangered species. This management has been

instrumental in the recovery of the Aleutian Canada goose and its removal in 2001 from the Threatened and

Endangered Species list. In recent years, as staffing and funding increased, Refuge management focus has been
168 San Joaquin River NWR Comprehensive Conservation Plan

expanded. In 1999 a major initiative was launched to protect floodplain lands through acquisition and to restore

floodplain habitats and function on those lands. In 2002 a project to re-establish the federally endangered riparian

brush rabbit onto the Refuge was initiated as part of the recovery program for that species. 

V. Location:

	 A.	 Ecoregion Number and Name:	 	 San Joaquin Valley

	 B.	 County and State:	 	 	 Stanislaus County, California

	 C.	 Latitude and longitude: 	 	 37 4’ x 121 1’

	 D.	 Distance and direction to nearest town: 	 Modesto, 9 miles west

	 E.	 Species/habitat occurrence:	 	 See species narrative accounts section VIIA

VI. Description of proposed action:

The U.S. Fish and Wildlife Service (Service) is developing a Comprehensive Conservation Plan (CCP) to

guide management and resource use at the Refuge. This plan for the San Joaquin National Wildlife Refuge

is a management tool to be used by the Refuge staff. It describes how the purposes for which the Refuge was

established are to be pursued over a 15 year period. The plan sets Refuge goals and objectives, and provides

strategies for achieving these goals and objectives based on Refuge purposes, other Federal laws, National

Wildlife Refuge System goals, and Fish and Wildlife Service policies. 	 	 	 	 	 	

 

The plan is comprehensive in the sense that it addresses all activities that occur on the Refuge. . The stated

Refuge goals, objectives and management strategies are intended to guide wildlife and other natural resource

management and public use for the next 15 years. The effects of these management actions will be monitored

to provide information for future managers and managers of other refuges. The plan has flexibility; it will be

reviewed periodically to ensure that its goals, objectives and implementation strategies and timetables are still

valid. 

Five broad goals are proposed for the Refuge that are consistent with the Refuge purpose, ecoregion goals, NWRS

goals, the National Wildlife Refuge System Improvement Act of 1997, Service Policy, and international treaties. 

One of these goals specifically addresses conservation and recovery of threatened and endangered species, and

outlines actions to be taken by the Refuge to assist in recovery efforts for those species. Special emphasis will be

given to recovery efforts for the riparian brush rabbit, San Joaquin Valley woodrat, and listed anadromous fish.

Another goal addresses the Refuge role and the management actions necessary to maintain continued recovery of

the recently delisted Aleutian Canada goose. 

The Refuge goals with stepped down objectives and the management strategies to implement them are presented

in Chapter 5 of the CCP. 

Determination of effects:

Species occurrence provided below are compiled from data in the refuge biological files, and include information

from operational refuge surveys and monitoring, special surveys and inventories, special studies, and observations

during refuge operations. Projected species effects (Both beneficial and adverse) are based on the biology of

individual species and their habitat needs as documented in literature and agency documents, discussions with

species experts, and refuge personnel observations of species response to similar restoration and management
San Joaquin River NWR Comprehensive Conservation Plan 169

activities. Actual species effects will be evaluated through regular surveys and habitat monitoring conducted by

refuge personnel and cooperators.

2.	 Explanation of effects of action on species and critical habitats in items III. A, B, and C:

Bald Eagle: This species does not nest in the area but is periodically observed preying on geese (including

Aleutian Canada goose) and other waterfowl on refuge lands during the winter and spring months. It has been 

seen most frequently at roost ponds and goose foraging areas on the east side of the Refuge but probably also

occurs on the west units, especially during high water events. The wetland habitat to be restored, enhanced, and

managed under this action will provide additional foraging areas for the bald eagle. The effects of this action

would potentially benefit this species by enhancing prey populations (waterfowl and fish) which may lead to an

increase in winter survival and reproductive fitness.

Willow Flycatcher: This species has been documented on the Refuge during spring and fall banding efforts. The

riparian forest to be restored and enhanced under this action will provide additional habitat for this species. The

effects of this action would potentially benefit this species by restoring and managing riparian habitat necessary

for this species during migration stopovers.

Least Bell’s Vireo: This species was documented as breeding on the Refuge for the first time in the past year. The

species used newly restored riparian vegetation as breeding habitat. The efforts to restore significant amounts of

riparian habitat at the Refuge will benefit this species.

Fresno Kangaroo Rat: The San Joaquin River NWR is within the historical range of this species. However,

extensive landscape changes in the San Joaquin Valley have reduced their present range, and the closest recent

record of Fresno kangaroo rat is from the south end of Merced County in 1972. There are currently no known

populations in or near the Refuge. Due to the fact that most of the Refuge land base is floodplain with heavy

soils, native arid grassland habitat is limited. The species has not been documented by Refuge biologists during

biological inventories in 1998, nor during operational Refuge activities conducted since 1987. The existing

and proposed (wetland and riparian restoration) habitats within the Refuge are not suitable for this arid uplands 

associated species. There would be no effects of this project upon the species due to a lack of presence.

San Joaquin Kit Fox: The San Joaquin River NWR is within the historical range of this species. However, there

have been no recent observations by species experts or Refuge staff that would indicate the species are present

on the Refuge. Kit fox have been recorded in recent years in the Coast Range about 20 miles west of the Refuge. 

The periodic flooding of the Refuge and intensity of agricultural operations on surrounding lands limits suitability

of the area for Kit Fox. No evidence of Kit Fox nor their burrows has ever been observed during operational

activities conducted on the refuge since its establishment in 1987, nor on surveys conducted as part of a biological

inventory in 1998. There would be no effects of this project upon the species due to a lack of presence. 

Riparian Brush Rabbit: The project area is within the historic range of this subspecies. Two small existing

populations of Riparian Brush Rabbit had previously been known to occur at Caswell State Park northwest of the

Refuge and near Paradise Cut in San Joaquin County. Past surveys by Refuge staff, CSU-Stanislaus Endangered

Species Recovery Program (ESRP), and other research personnel staff found no evidence that brush rabbits

were present on the Refuge in recent years. It was believed that the lack of rabbits was due to construction of

flood control levees along the San Joaquin River and land conversion to agriculture, prior to establishment of

the Refuge, which had altered the vegetative communities and hydrology thus making the floodplain unsuitable

for the species. Management activities proposed under this CCP include breaching existing flood control levees

to restore natural floodplain function, replanting former agricultural lands back to riparian and floodplain plant

communities, and building and vegetating mounds to provide refugia during flood events. The Refuge was

selected as a re-establishment site for riparian brush rabbit as part of the species recovery program. A total of
170 San Joaquin River NWR Comprehensive Conservation Plan

134 captive-reared rabbits were released on the Refuge in summers 2002 and 2003, and are being intensively

monitored through radio telemetry. Although unquantified, multiple litters of riparian brush rabbits have been

born on the Refuge. Releases have been made on the refuge in 2003 and 2004. This recovery effort is being

implemented by ESRP, and closely coordinated with the Sacramento FWO Endangered Species Program, the

Refuge, California Dept. of Fish and Game, and U.S. Bureau of Reclamation. Major funding is being provided by

the U.S. Bureau of Reclamation and the FWS. The Refuge staff is actively participating in the re-establishment

effort and is coordinating with species experts to ensure that habitat restoration and subsequent management

maximizes benefits to riparian brush rabbits. Avoidance measures during the habitat restoration/management, as

well as other Refuge programs such as public use, are being implemented. The effects of the actions proposed

under this CCP will greatly benefit riparian brush rabbits and contribute to recovery goals.

San Joaquin Valley Woodrat: The project area is within the historic range of the species. Existing populations

are known to occur at Caswell State Park northwest of the Refuge and along the riparian corridor of the San

Joaquin River on private land north of the refuge. Surveys prior to 2003 by Refuge and ESRP staff, as well as

other researchers found no evidence that San Joaquin Valley woodrats were present on the Refuge in recent years.

However, 5 woodrats, including a lactating female were documented in summer 2003 by ESRP staff during

riparian brush rabbit monitoring activities. Actual size and status of the population is not known at this time. 

Suitability of the area for woodrats has been degraded due to reduction of floodplain riparian habitat through past

construction of flood control levees along the river and land conversion to agriculture, altered river hydrology, and

competition by non-native black rats.

Management activities proposed under this CCP include breaching existing flood control levees to restore natural

floodplain function, and replanting former agricultural lands back to riparian and floodplain plant communities. 

Management activities being conducted for riparian brush rabbit recovery, such as building and vegetating

mounds to provide refugia during flood events, will provide direct benefits to San Joaquin Valley woodrats.

When a specific recovery plan is developed and funded, the Refuge will work closely with the Sacramento FWO

Endangered Species Program, ESRP, and other partners to assist in species recovery activities. Refuge staff are

currently coordinating with species experts so that ongoing restoration and subsequent management maximizes

benefits to woodrats, and that avoidance measures during that restoration/management, as well as other Refuge

programs such as public use, are implemented. The effects of the actions proposed under this CCP will greatly

benefit San Joaquin Valley woodrat populations. 

Giant Garter Snake: The San Joaquin River NWR is within the historical range of this species and is part of the

San Joaquin Valley Recovery Unit of the draft FWS Recovery Plan. However, limited surveys in recent years

have not documented any occurrence on or near the Refuge. Part of the wetlands and sloughs appear to be

suitable habitat for the species. The wetlands restoration proposed by this CCP, primarily consisting of contouring

dry basins in former agricultural fields, constructing water control structures, and connecting the basins to

delivery system, will take place on dry uplands away from potential habitat. Subsequent management of these

restored wetlands will beneficially impact giant garter snakes by increasing potential habitat for the species. In

addition, giant garter snake surveys on the Refuge, as directed in the monitoring component of the CCP will add

to the knowledge of distribution of the species and potentially contribute to recovery efforts. 

Blunt-nosed Leopard Lizard: The historic range of this species includes the San Joaquin NWR but it has not been

documented as present on or near the Refuge. The existing floodplain and riparian habitats are not suitable habitat

for this arid uplands associated species. There would be no effects of this action upon the species due to a lack of

presence. 

Conservancy Fairy Shrimp; Vernal Pool Fairy Shrimp; Vernal Pool Tadpole Shrimp: Less than a dozen small

vernal pools are present on the refuge and are limited to two areas east of the San Joaquin River that had not been

altered prior to Refuge ownership. The Vernal Pool Fairy Shrimp and Tadpole Shrimp have been documented to
San Joaquin River NWR Comprehensive Conservation Plan 171

occur within the refuge vernal pools. The other two species are considered as potentially present based on habitat

availability and presence of other vernal pool obligate species. The San Luis NWR Complex has a long-standing

policy to avoid any actions that adversely impact vernal pools. All the vernal pools within the Refuge are located

away from the construction areas and would not be directly impacted by any restoration/ enhancement activities. 

Subsequent water levels of nearby existing wetlands will continue to be managed to avoid adversely impacting

any of the vernal pools. Vernal pool habitat will be subject to seasonal cattle grazing as part of the Refuge grazing

program. The effects of the actions proposed under this CCP, specifically continuation of the existing grazing

program, will have positive impacts by maintaining short grassland communities and limiting the growth of

invasive plants in and around the vernal pools.

Valley Elderberry Longhorn Beetle: The historic range of this species includes the San Joaquin River NWR;

however, the beetle has not been documented to occur on or near the Refuge. Habitat (elderberry shrubs) is

relatively abundant on the Refuge east of the San Joaquin River, but limited west of the river. Large quantities

of elderberry seedlings are being planted on the west side of the Refuge as part of an ongoing 800-acre riparian

restoration effort. Additional plantings are planned dependent on funding. The effects of the actions proposed

under this CCP, specifically the riparian restoration, would benefit the species by increasing native habitat (i.e.,

elderberry shrubs).

California Tiger Salamander: California tiger salamanders are relatively abundant in suitable vernal pool

communities throughout the San Joaquin Valley. Less than a dozen small vernal pools are present on the refuge

and are limited to two areas east of the San Joaquin River that had not been altered prior to Refuge ownership. 

The presence of California tiger salamanders have been documented by Refuge staff during surveys of these

vernal pools. The San Luis NWR Complex has a long-standing policy to avoid any actions that adversely impact

vernal pools. All the vernal pools and associated ground squirrel burrows are located away from any areas that

would be subject to restoration/enhancement related earth moving activities or management related disturbance

such a farming and wetland rehabilitation. Subsequent water levels of existing wetlands will be managed to avoid

impacting any of the vernal pools communities. Vernal pool habitat will be subject to seasonal cattle grazing as

part of the Refuge grazing program. The effects of the actions proposed under this CCP, specifically continuation

of the existing grazing program, will have positive impacts by maintaining short grassland communities,

promoting ground squirrel habitat, and limiting the growth of invasive plants in and around the vernal pools.

3. Explanation of actions to be implemented to reduce adverse effects: 

The San Joaquin River NWR is not included in the Central Valley Project Improvement Act and does not

receive water as mandated by the legislation. However, if a listed species has been documented to occur within

the proposed action boundaries, all precautions and avoidance measures will be taken during restoration and

operational management activities consistent with the Programmatic Biological Opinion on National Wildlife

Refuge and Wildlife Area Water Conveyance Projects within Tulare, Kern, Fresno, Madera and Merced Counties. 

For instance, any restoration associated earth moving activities or operational canal maintenance along or adjacent

to existing wetlands or potential giant garter snake habitat will be conducted only during the May to November

period, and the site will be surveyed by a qualified FWS biologist prior to any construction. Also, no native

uplands or vernal pools will be modified and we will restrict/avoid equipment use in these areas.

	 In the case of riparian brush rabbits and San Joaquin Valley woodrats, current Refuge management

practices limit potential for adverse impacts or take in existing habitat. There is very little habitat manipulation,

mowing, or earth-moving conducted within the currently forested riparian corridor. Earth-moving to restore

floodplain wetlands, and the disking, site preparation, planting, mowing, irrigating, and herbicide application to

re-establish riparian forest is being conducted on former agricultural fields which are currently unsuitable habitat

for either species. Radio-telemetry of brush rabbits during 2002 and 2003, and woodrats in 2003 indicate that

those species are not using the restoration sites. The intensive floodplain restoration activities will be
172 San Joaquin River NWR Comprehensive Conservation Plan
San Joaquin River NWR Comprehensive Conservation Plan 173
174 San Joaquin River NWR Comprehensive Conservation Plan

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San Joaquin River NWR Comprehensive Conservation Plan 175

Appendix G: Step-Down and Other Plans Pertaining to the San 

Joaquin River National Wildlife Refuge—a Unit of 

the San Luis National Wildlife Refuge Complex

Title of Plan Status Purpose

–Station Plans–

Fire Management Plan Completed 

(2001)

Provides the proper procedures for all management 

activities involving fire on the Refuge including wildfire 

presuppression activities, wildfire suppression, and the 

use of prescribed fire. Step-down portions of this plan 

include the wildfire dispatch plan and step-up plan.

Disease Management Plan Completed 

(1983)

Outlines procedures for the prevention and control of 

disease in migratory birds.

Chronic Wasting Disease 

Surveillance and Response 

Plan

Completed 

(2005)

Provides guidelines for dealing with chronic wasting 

disease issues with mule deer on the Refuge Complex.

Water Management Plan Needs to be 

Completed

Provides guidelines for the management of wetlands on 

the Refuge.

Law Enforcement Plan Needs to be 

Completed

Plan provides guidance for the law enforcement 

program on the Refuge.

Emergency Management 

Plan

Completed

(1993)

Provides the protocol for the Complex when dealing 

with disaster and emergency situations.

Public Use Management Plan Needs to be 

Completed

Describes and provides the procedures/guidance for all 

aspects of the Refuge’s public use program.

Hunt Management Plan Needs to be 

Completed

Documents the waterfowl resource and associated 

recreational waterfowl hunt program on the Refuge.

Upland Management Plan Needs to be 

Completed

Document provides the upland management goals and 

implementation procedures for upland habitats on the 

Refuge.

Spill Response Plan Completed

(1973)

Outlines procedures for the prevention, handling and 

cleanup of hazardous materials and oil spills.

Safety Management Plan Completed

(1970)

Safety procedures outline for the San Luis National 

Wildlife Refuge Complex.

Fisheries Management Plan Needs to be 

Completed

Documents the fisheries resource and associated aquatic 

management activities on the Refuge.

Biological Inventory Plan Needs to be 

Completed

Procedures for documenting, monitoring and analyses of 

biological resources on the Refuge.
176 San Joaquin River NWR Comprehensive Conservation Plan

Title of Plan Status Purpose

Invasive Exotic Plant Control 

Plan

Needs to be 

Completed

Documents goals and techniques/procedures for 

controlling invasive, exotic plants on the Refuge.

–FWS Region 1 Plans–

FWS Migratory Bird Disease 

Contingency Plan - Region 1

Completed 

(1984)

Documents the procedures and responsibilities for 

prevention and management of migratory bird diseases.

FWS Recovery Plan for 

Upland Species of the San 

Joaquin Valley, California–

Region 1

Completed

(1998)

Includes recovery plans for threatened and endangered 

species in the San Joaquin Valley including San Joaquin 

kit fox, riparian brush rabbit and riparian woodrat.

FWS Recovery Plan for the 

Sacramento-San Joaquin 

Delta Native Fishes–Region 1

Completed

(1995)

Includes recovery plans for threatened and endangered 

native fish species of the Sacramento-San Joaquin Delta 

including the chinook salmon, Sacramento splittail and 

Sacramento perch.

–FWS National or Other Regional Plans–

FWS Director’s Priorities Completed

(1999)

Provides goals and action items for the management of 

the National Wildlife Refuge System.

FWS Energy Management 

Plan

Completed

(1986)

Outlines procedures and responsibilities for the FWS to 

reduce energy use and costs on its facilities.

FWS Aleutian Canada Goose 

Recovery Plan–Region 7

Completed

(1982)

Plan outlines the efforts needed for the recovery of the 

Aleutian Canada Goose in North America.

–Other Plans–

U.S. Shorebird Conservation 

Plan–Southern Pacific Region

Completed

(1999)

Provides a review of issues and regional goals 

concerning the management of shorebirds.

California Partners in 

Flight. Riparian Bird 

Conservation Plan: A 

Strategy for Reversing the 

Decline of Birds Associated 

with Riparian Habitats in 

California

Completed

(1998)

Outlines migratory birds of special concern which 

use Californian riparian habitats and provides 

recommendations for their monitoring, preservation and 

management.
San Joaquin River NWR Comprehensive Conservation Plan 177

Appendix H: Levee Breach Study

San Joaquin River National Wildlife Refuge—Phase l

Analysis of the Proposed Levee Breaches 

CONTEXT AND RATIONALE FOR THE PWA (Phil Williams & Assoc.) STUDY

As a result of the January 1997 floods several levees failed along the west side of the 

San Joaquin River in the vicinity of the Tuolumne River confluence. After the flood, 

the levees were partially repaired; however, the San Joaquin River National Wildlife 

Refuge (SJRNWR) worked with the US Army Corps of Engineers (USACE) to plan a 

non-structural flood management alternative (NSA). This alternative includes breaching 

existing mainstream San Joaquin River levees on recently acquired Refuge land to restore 

wetland and riparian habitat. The proposed NSA will provide floodplain inundation behind 

project levees of up to 3,100 acres of Refuge land in some years.

The focus of this study is to examine habitat effects of proposed levee breaches and NSA 

refinements with particular emphasis on the needs of fish. The primary analysis tool used 

in this study was a one dimensional, looped network hydrodynamic model, MIKE ll. Model 

results include depth and time of inundation as well as simulated flow on reactivated 

floodplain at the Refuge.

The PWA report describes the historical setting of the site, the hydrodynamic modeling, 

evaluation criteria being used to assess the results and finally, the challenges of the project. 

Evaluation criteria being used include: frequency, duration, depth and area of flooding; 

potential for fish stranding; and potential for creation of non-native or predator fish species 

habitat. In addition, potential refinements of the currently proposed NSA are identified. 

LIMITATIONS OF THE STUDY

Phase 1 of the present study (PWA phase one) represents an initial overview of the proposed 

non-structural flood management alternative proposed by the USACE. Refinements to the 

proposed alternative will be made in Phase 2 of the project. The results contained in the 

report represent the potential conditions of the Refuge under the existing topographical 

conditions and flow regimes. Modifications to these parameters are likely under proposed 

Phase 2 alternatives to improve potential habitat conditions at the Refuge.

No hydrodynamic model calibration or validation data were available at the time of the 

Phase One study and therefore the results should be considered with this in mind. In 

addition, no sensitivity analysis has been conducted in this Phase of the study.

 

FINDINGS 

1. The floodplains outside the project levees at the SJRNWR (i.e. Lara, Hagemann, and 

Vierra properties) are likely to flood at approximately 16,000 cfs if breaches are made as 

proposed in the USACE NSA, and are cut to the depth of the adjoining ground elevation. 

2. Implementation of the NSA is expected to cause flooding of this SJRNWR floodplain 

every two to three years, on average; this frequency is appropriate to achieve anadromous 

fish habitat enhancement goals.

Additional work has been funded by AFRP in concert with the Refuge to conduct a more 

detailed study which includes design recommendations. The results of this work are 

anticipated shortly after completion of the Refuge CCP.
178 San Joaquin River NWR Comprehensive Conservation Plan

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San Joaquin River NWR Comprehensive Conservation Plan 179

Appendix I: References & Resources

Reports and Studies

DRAFT SAN JOAQUIN RIVER NWR, PRE-RESTORATION REPORT, USFWS, 18 Oct 

1999 Phase III Basin Project Information Report

Final Emergency Levee Repairs, San Joaquin River Basin

Reclamation Districts 2100 and 2102, Stanislaus County, California USACE

NORTHERN CALIFORNIA STREAMS: TUOLUMNE RIVER, CALIFORNIA, 

RECONNAISSANCE STUDY, Section 905 (b) (WRDA 86) Analysis, Division: South 

Pacific District: Sacramento Date: 30 September 1998

Project Study Plan TUOLUMNE RIVER, CALIFORNIA

Modesto, California, U.S. Army Corps of Engineers Sacramento District July 1999

San Joaquin River National Wildlife Refuge—Phase 1, Analysis of the Proposed Levee 

Breaches, Phillip Williams & Associates, May 2001.

Report of Recommended Alternatives, Refuge Water Supply and San Joaquin Basin action 

Plan Lands, Bureau of Reclamation-Mid-Pacific Region and Fish and Wildlife Service, 

April 1995

The Grasslands Water Summary, Grasslands Water District, Jayne Philport Casey, 1962, 

Reprint.

References

Arkley, R. J. 1964. Soil Survey - Eastern Stanislaus area, California. Series 1957, 

No. 20. USDA, Soil Conservation Service, in cooperation with University of 

California Agricultural Experiment Station. 210pp. 

Anderson, B. and A. DeGange. 2001. Final rule to remove the Aleutian Canada goose from 

the federal list of endangered and threatened wildlife. 50 Code Fed. Reg. Part 17, 

66:15643-15656.

Barbour, M.G. and W.D. Billings. North American Terrestrial Vegetation. Cambridge 

University Press, New York, New York. 434pp.

Bonnicksen, T.M. 2000. America’s Ancient Forests. John Wiley and Sons, Inc. 594pp.

California Regional Water Quality Control Board. 1998. Water Quality of the Lower San 

Joaquin River: Lander Avenue to Vernalis October 1995 through September 1997. 

Staff Report. 80 pp.

Claudill, James, and Andrew Laughland. 1998. 1996 National and State Economic Impacts 

of Wildlife Watching: Based on the 1996 National Survey of Fishing, Hunting and 

Wildlife-Associated Recreation. US Department of the Interior, USFWS, Division of 

Economics, Arlington, Virginia.
180 San Joaquin River NWR Comprehensive Conservation Plan

Ferren, W. R., Jr., and D. A. Pritchett. 1988. Enhancement, restoration, and creation of 

vernal pools at Del Sol Open Space and Vernal Pool Reserve, Santa Barbara County, 

California. Environmental Report No. 13, University of California, Santa Barbara. 

169pp. 

Fisher, R. In Press. Protocol for Herp study field personnel. USGS Biological Resource 

Division, San Diego, California.

Flannery, T. 2001. The Eternal Frontier, An Ecological History of North American and its 

Peoples. Atlantic Montly Press, New York, New York. 404pp. 

Gains, B. and S. Laymon. 1984. Decline, status and preservation of the yellow-billed cuckoo. 

Western Birds 15:49-80.

Hansen, G. E. 1988. Review of the status of the giant garter snake (Thamnophis couchi 

gigas) and its supporting habitat during 1986-1987. Final Report for California Dept. 

Fish and Game.

Hansen, G.E. and J.M. Brode. 1980. Status of the giant garter snake, Thamnophis 

couchi gigas (Fitch). Special Publication 80-5, Inland Fisheries Endangered Species 

Program, Dept. of Fish and Game. 

Heitmeyer, M.E., D.P. Connelly and R.L. Pedersen. 1989. The Central, Imperial, and 

Coachella Valleys of California. Pp 475-506 IN Habitat Management for Migrating 

and Wintering Waterfowl in North America. Texas Tech University Press, Lubbock. 

560 pp.

Holland, R. F. 1986. Preliminary descriptions of the terrestrial natural communities of 

California. Non-game Heritage Program, Dept. of Fish and Game, Sacramento, 

California. 155pp.

Isola, C.R., M.A. Colwell, O.W. Taft and R.J. Safran. 2000. Interspecific differences in 

habitat use of shorebirds and waterfowl foraging in managed wetlands of California’s 

San Joaquin Valley. Waterbirds 23(2):196-203.

Iverson, G. C., and T. C. Tacha. 1982. Food contents of Sandhill Cranes during winter and 

spring. P. 95-98 in J. C. Lewis [ed.], Proc. 1981 Crane Workshop, Nat. Audubon Soc., 

Tavernier, FL.

Jain, S., and P. Moyle. 1981. Vernal Pools and Intermittent Streams. Symposium of the 

Institute of Ecology University of California, Davis. Institute of Ecology Publication 

No. 28. 280 pp.

Jensen, P.M. 1996 Archaeological Survey Report (ASR)–Negative. Proposed Fresno-Tracy 

Fiberoptics Data Transmission Line. CALTRANS’ Rights-Of-Way at Six State 

Highway Crossings. Caltrans District 3, Portions of Fresno, Madera, Merced, 

Stanislaus, and San Joaquin Counties, California. Jensen and Associates, Durham, 

California.

Johnson, D.H., D.E. Timm, and P.F. Springer. 1979. Morphological characterisitics of 

Canada geese in the Pacific Flyway. Pp. 56-80 in R.L. Jarvis and J.C. Bartonek, eds. 

Management and Biology of Pacific Flyway Geese: A Symposium. Oregon State Univ. 

Book Stores, Inc., Corvallis.
San Joaquin River NWR Comprehensive Conservation Plan 181

Katibah, E. F. 1984. A brief history of riparian forests in the Central Valley of California 

in California Riparian Systems: Ecology, Conservation, and Productive Management. 

Edited by R. E. Warner and K. M. Hendrix. Univ. of Cal. Press, California. Pages 23-

29.

Laymon, S. A. 1998. Partners in Flight bird conservation plan: yellow-billed cuckoo 

(Coccyzus americanus). Admin. Rept. to California Partners in Flight. 

Levy, R.S., et al. 1995. Archaeological Survey Report for the Proposed Seismic Retrofit of

 California State Highway Bridge #38-45 on Route 132 over the San Joaquin River, 

East of Venalis in Stanislaus County, California 10-Sta-132, PM $2.43. Department of

 Transportation District 10.

Lewis, J. C., G. W. Archibald, R. C. Drewien, C. R. Frith, E. A. Gluessing, R. D. Klataske, C. 

D. Littlefield, J. Sands, W. J. D. Stephen, and L. E. Williams. 1977. Sandhill Cranes, p. 

5-43 inG. C. Sanderson [ed.], Management of migratory, shore, and upland game birds 

in North America. Intl. Assoc. Fish. And Wildl. Agency.

McLaughlin, J.C. and G.L. Huntington. 1968. Soils of Westside Stanislaus Area California. 

University of California, Davis.

McShea, W.J. and W.M. Healy, 2002. Oak Forest Ecosystems. John Hopkins University 

Press, Baltimore. 432pp.

Mitsch, W.J. And G.G. Gosselink. 2000. Wetlands. John Wiley & Sons, Inc. New York. 

920pp.

MBMO (Migratory Bird Management Office, U. S. Fish and Wildlife Service). 1997. 

Equipment and Techniques for Observing Neckbanded Canada Geese. Non-pub. 8pp.

Modesto Irrigation District. 1998. Modesto, California.

Moyle, P.B. 2002. Inland fishes of California: revised and expanded. University of California 

Press, Ltd. London England.

Ornduff, R. 1974. Introduction to California Plant Life. University of California Press, 

Berkeley. 152pp.

Orr, R.T. 1940. The Rabbits of California. Occasional Papers of the California Academy of 

Sciences, San Francisco, California. 227pp.

Page, P. J. 1970. San Joaquin River rookery study. State of California Department of Fish 

and Game, Wildlife Management Branch.

Pogson, T. H. and S. M. Lindstedt. 1991. Distribution and abundance of large sandhill 

cranes, Grus canadensis, wintering in California’s Central Valley. Condor 93:266-278.

Root, T. 1988. Atlas of Wintering North American Birds. University of Chicago Press, 

Chicago. 312pp.

Schoenherr, A.A. 1992. A Natural History of California. University of California Press, 

Berkley. 772pp.
182 San Joaquin River NWR Comprehensive Conservation Plan

Shuford, W.P., G.W. Page and J.E. Kjelmyr. 1998. Patterns and dynamics of shorebird use of 

California’s Central Valley. Condor 100:227-244.

Silverstein, M. 1978. Yokuts: Introduction. Handbook of North American Indians. Vol. 8

 California. Heizer, Robert F. Volume Editor; Sturtevant, William C. General Editor. Pp 

446-447.

Speulda, Lou Ann. 1999. USFWS. Historic Properties Identification and Evaluation Report 

of the Vierra Dairy. 22.

Swernoff, Michael. 1982. Archeological Investigations at the Lower Stanislaus River 

Recreation Areas, Calaveras, Tuolumne, Stanislaus, and San Joaquin Counties, 

California. Final Report submitted to Interagency Agency Archeological Services, 

National Park Service. Prepared under the supervision of Dr. Elliott A. Gehr. 

Professional Analysts, Eugene, Oregon.

True, D.L., et al. 1981. Archaeological Survey of the Proposed San Luis Drain Project:

 Kesterson Reservoir to the Sacramento-San Joaquin Delta, California.

U.S. Fish and Wildlife Service. 1987. Aleutian Canada Goose Disease and Contamination 

Hazard Contingency Plan. Unpubl. report-updated 1995. Fish Wildl. Serv., U.S. Dep 

Int., Anchorage, AK. 26 pp.

U.S. Fish and Wildlife Service. 1991. Aleutian Goose Recovery Plan.

U.S. Fish and Wildlife Service. 1991. San Luis NWR/Grasslands Wildlife Management 

Area Disease Contingency Plan. Unpubl. report. Fish Wildl. Serv., U.S. Dep Int., Los 

Banos, CA. 42 pp.

Werner, R. H. 1984. Archaeological Record Search and Field Survey Lower San Joaquin 

River and Tributaries Channel Clearing Project. Archaeological Services, Clearlake, 

California.

Willliams, D.F., P.A. Kelly and L.P. Hamilton. 2002. Controlled propagation and 

reintroduction plan for the riparian brush rabbit (Sylvilagus bachmani riparius). 

Endangered Species Recovery Program, California State University, Stanislaus. 75pp.

Woolington, D.W., P.F. Springer, and D.R. Yparraguirre. Migration and wintering ecology 

of Aleutian Canada geese. Pages 299-309 in R.L. Jarvis and J.C. Bartonek, eds. 

Management of Pacific Flyway Geese. Ore. St. Univ. Corvallis. 346pp. 

Websites:

EDD. http://www.edd.ca.gov/

http:cache.census.gov/hhes/www/saipe/estimate/cty/cty06077.htm

http://www.Cathedralcity.org/sa6.htm

http://www.Cathedralcity.org/st1.htm

hhtp:cache.census.gov/hhes/www/saipe/estimate/cty/cty06077.htm
San Joaquin River NWR Comprehensive Conservation Plan 183

hhtp:cache.census.gov/hhes/www/saipe/estimate/cty/cty06099.htm

http://gocalif.ca.gov/research/county.html

Scedco.org. Stanislaus County Economic Development Corporation. http://www.scedco.org

SJPNET. San Joaquin Partnership. Http://www.sjpnet.org

USFWS. 1998. USFWS Economic Study Shows Wildlife Watching is Big Business. Luary 

Parramore. June 10, 1998. http://www.fws.gov/r9extaff/pr9833.html
184 San Joaquin River NWR Comprehensive Conservation Plan

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Appendix J: Relevant Federal Laws and Mandates 

American Indian Religious Freedom Act (1978):

Directs agencies to consult with native traditional religious leaders to determine appropriate 

policy changes necessary to protect and preserve Native American religious cultural rights 

and practices.

Americans With Disabilities Act (1992):

Prohibits discrimination in public accommodations and services.

Architectural Barriers Act (1968): 

Requires federally owned, leased, or funded buildings and facilities to be accessible to 

persons with disabilities.

Clean Water Act (1977): 

Requires consultation with the Corps of Engineers (404 permits) for major wetland 

modifications.

Emergency Wetland Resources Act of 1986:

This Act authorized the purchase of wetlands from Land and Water Conservation Fund 

moneys, removing a prior prohibition on such acquisitions. The Act also requires the 

Secretary to establish a National Wetlands Priority Conservation Plan, requires the States 

to include wetlands in their Comprehensive Outdoor Recreation Plans, and transfers to the 

Migratory Bird Conservation Fund amount equal to import duties on arms and ammunition. 

Endangered Species Act of 1973:

 (16 U.S.C. 1531-1544, 87 Stat. 884), as amended

Public Law 93-205, approved December 28, 1973, repealed the Endangered Species 

Conservation Act of December 5, 1969 (P.L. 91-135, 83 Stat. 275). The 1969 act had amended 

the Endangered Species Preservation Act of October 15, 1966 (P.L. 89-669, 80 Stat. 926). 

The 1973 Endangered Species Act provided for the conservation of ecosystems upon which 

threatened and endangered species of fish, wildlife, and plants depend, both through Federal 

action and by encouraging the establishment of State programs. The Act:

• Authorizes the determination and listing of species as endangered and threatened;

• Prohibits unauthorized taking, possession, sale, and transport of endangered species;

• Provides authority to acquire land for the conservation of listed species, using land and 

water conservation funds;

• Authorizes establishment of cooperative agreements and grants‐in‐aid to States that 

establish and maintain active and adequate programs for endangered and threatened 

wildlife and plants;

• Authorizes the assessment of civil and criminal penalties for violating the Act or 

regulations; and

• Authorizes the payment of rewards to anyone furnishing information leading to arrest and 

conviction for any violation of the Act of any regulation issued thereunder.

Environmental Education Act of 1990:

(20 USC 5501-5510; 104 Stat. 3325)

Public Law 101-619, signed November 16, 1990, established the Office of Environmental 

Education within the Environmental Protection Agency to develop and administer a Federal 

environmental education program.
186 San Joaquin River NWR Comprehensive Conservation Plan

Responsibilities of the Office include developing and supporting programs to improve 

understanding of the natural and developed environment, and the relationships between 

humans and their environment; supporting the dissemination of educational materials; 

developing and supporting training programs and environmental education seminars; 

managing a Federal grant program; and administering an environmental internship and 

fellowship program. The Office is required to develop and support environmental programs 

in consultation with other Federal natural resource management agencies, including the 

Fish and Wildlife Service.

Executive Order 11988, Floodplain Management:

The purpose of this Executive Order, signed May 24, 1977, is to prevent Federal agencies 

from contributing to the “adverse impacts associated with occupancy and modification of 

floodplains” and the “direct or indirect support of floodplain development.” In the course of 

fulfilling their respective authorities, Federal agencies Ashall take action to reduce the risk 

of flood loss, to minimize the impact of floods on human safety, health and welfare, and to 

restore and preserve the natural and beneficial values served by floodplains.

Executive Order 11990:

E.O. 11990 directs Federal agencies to (1) minimize destruction, loss, or degradation of 

wetlands and (2) preserve and enhance the natural and beneficial values of wetlands when a 

practical alternative exists. 

Executive Order 12372:

(Intergovernmental Review of Federal Programs):

Directs the Service to send copies of the Environmental Assessment to Iowa State Planning 

Agencies for review.

Executive Order 12898 (1994):

Establishes environmental justice as a Federal government priority and directs all Federal 

agencies to make environmental justice part of their mission. Environmental justice calls for 

fair distribution of environmental hazards.

Executive Order 12996 Management and General Public Use of the National 

Wildlife Refuge System (1996): 

Defines the mission, purpose, and priority public uses of the National Wildlife Refuge 

System. It also presents four principles to guide management of the System.

Executive Order 13006 Locating Federal Facilities on Historic Properties in Our 

Nation’s Central Cities:

Directs Federal agencies to select, utilize and maintain historic properties and districts, 

especially those located in cities’ central business districts, whenever operationally 

appropriate and economically prudent.

Executive Order 13007 Indian Sacred Sites (1996):

Directs Federal land management agencies to accommodate access to and ceremonial use of 

Indian sacred sites by Indian religious practitioners, avoid adversely affecting the physical 

integrity of such sacred sites, and where appropriate, maintain the confidentiality of sacred 

sites.

Executive Order 13112, Invasive Species (1999):

Directs federal agencies to prevent introduction and provide control of invasive species. 

Executive Order 13186, of Jan. 10, 2001: 

Responsibilities of Federal Agencies to Protect Migratory Birds. FR 66(11), Jan. 17, 2001.
San Joaquin River NWR Comprehensive Conservation Plan 187

Federal Farmland Protection Policy Act (1979) 

as amended: Minimizes the extent to which Federal programs contribute to the unnecessary 

and irreversible conversion of farmland to nonagricultural uses.

Federal List of Birds of Conservation Concern: 

Draft Region 1and BCR 32 Birds of Conservation Concern.

Federal Noxious Weed Act (1990):

Requires the use of integrated management systems to control or contain undesirable plant 

species, and an interdisciplinary approach with the cooperation of other Federal and State 

agencies.

Federal Records Act (1950):

Directs preservation of evidence of the government’s organization, functions, policies, 

decisions, operations, and activities, as well as basic historical and other information.

Fish and Wildlife Act of 1956: 

(16 U.S.C. 742a-742j, not including 742 d-l; 70 Stat. 1119), as amended: 

The Act of August 8, 1956, as frequently amended, establishes a comprehensive national fish, 

shellfish, and wildlife resources policy with emphasis on the commercial fishing industry but 

also with a direction to administer the Act with regard to the inherent right of every citizen 

and resident to fish for pleasure, enjoyment, and betterment and to maintain and increase 

public opportunities for recreational use of fish and wildlife resources. Among other things, 

it directs a program of continuing research, extension, and information services on fish and 

wildlife matters, both domestically and internationally.

Section 7(a) of the Act (16 U.S.C. 742f; 70 Stat. 1122) requires the Secretary of the Interior 

to: 1) develop measures for “maximum sustainable production of fish”; 2) make economic 

studies of the industry and recommend measures to insure stability of the domestic 

fisheries; 3) undertake promotional and information activities to stimulate consumption of 

fishery products; 4) take steps “required for the development, advancement, management, 

conservation, and protection of the fisheries resources,” and take steps “required for the 

development, management, advancement, conservation, and protection of fish and 

wildlife resources” through research, acquisition of land and water or interests therein, 

development of existing facilities, and other means. (Note: subsection 5 was amended 

and combined into subsection 4 by P.L. 95-616, November 8, 1978.).

Fish and Wildlife Conservation Act, 1988: 

Amendment. Requires the Service to identify species, subspecies, and populations of all 

migratory nongame birds that, without additional conservation actions, likely to become 

candidates for listing under the Endangered Species Act of 1973”. The Act also requires 

the Service monitor and assess migratory nongame birds and track efferts of environmental 

changes on these species. Report every 5 years to Congress. The Services’ list of Birds of 

Conservation Concern derives from this legislation.

Fish and Wildlife Coordination Act (1934):

as amended: Requires that the Fish and Wildlife Service and State Fish and Wildlife 

agencies be consulted whenever water is to be impounded, diverted or modified under a 

Federal permit or license. The Service and State agency recommend measures to prevent 

the loss of biological resources, or to mitigate or compensate for the damage. The project 

proponent must take biological resource values into account and adopt justifiable protection 

measures to obtain maximum overall project benefits. A 1958 amendment added provisions 

to recognize the vital contribution of wildlife resources to the Nation and to require 

equal consideration and coordination of wildlife conservation with other water resources 
188 San Joaquin River NWR Comprehensive Conservation Plan

development programs. It also authorized the Secretary of Interior to provide public fishing 

areas and accept donations of lands and funds.

Fish and Wildlife Improvement Act of 1978:

This act was passed to improve the administration of fish and wildlife programs and amends 

several earlier laws, including the Refuge Recreation Act, the National Wildlife Refuge 

Administration Act, and the Fish and Wildlife Act of 1956. It authorizes the Secretary to 

accept gifts and bequests of real and personal property on behalf of the United States. It 

also authorizes the use of volunteers on Service projects and appropriations to carry out 

volunteer programs.

Historic Preservation Acts: 

There are various laws for the preservation of historic sites and objects.

Antiquities Act: (16 USC 431–433)—The Act of June 8, 1906, (34 Stat. 225) authorizes 

the President to designate as National Monuments objects or areas of historic or scientific 

interest on lands owned or controlled by the United States. The Act required that a permit 

be obtained for examination of ruins, excavation of archaeological sites and the gathering 

of objects of antiquity on lands under the jurisdiction of the Secretaries of Interior, 

Agriculture, and Army, and provided penalties for violations.

Archeological and Historic Preservation Act: (16 U.S.C. 469-469c)—Public Law 

86-523, approved June 27, 1960, (74 Stat. 220) as amended by Public Law 93-291, approved 

May 24, 1974, (88 Stat. 174) to carry out the policy established by the Historic Sites Act 

(see below), directed Federal agencies to notify the Secretary of the Interior whenever 

they find a Federal or Federally assisted, licensed or permitted project may cause loss or 

destruction of significant scientific, prehistoric or archaeologic data. The Act authorized 

use of appropriated, donated and/or transferred funds for the recovery, protection and 

preservation of such data.

Archaeological Resources Protection Act: (16 U.S.C. 470aa–470ll)—Public Law 

96-95, approved October 31, 1979, (93 Stat. 721) largely supplanted the resource protection 

provisions of the Antiquities Act for archaeological items.

This Act established detailed requirements for issuance of permits for any excavation for 

or removal of archaeological resources from Federal or Indian lands. It also established 

civil and criminal penalties for the unauthorized excavation, removal, or damage of any such 

resoruces; for any trafficking in such resources removed from Federal or Indian land in 

violation of any provision of Federal law; and for interstate and foreign commerce in such 

resources acquired, transported or received in violation of any State or local law.

Historic Sites, Buildings and Antiquities Act: (16 USC 461-462, 464-467)—The Act 

of August 21, 1935, (49 Stat. 666) popularly known as the Historic Sites Act, as amended 

by Public Law 89-249, approved October 9, 1965, (79 Stat. 971) declared it a national policy 

to preserve historic sites and objects of national significance, including those located on 

refuges. It provided procedures for designation, acquisition, administration and protection 

of such sites. Among other things, National Historic and Natural Landmarks are designated 

under authority of this Act. As of January, 1989, 31 national wildlife refuges contained such 

sites.

National Historic Preservation Act of 1966: (16 U.S.C. 470-470b, 470c-470n)—Public 

Law 89-665, approved October 15, 1966, (80 Stat. 915) and repeatedly amended, provided 

for preservation of significant historical features (buildings, objects and sites) through a 

grant-in-aid program to the States. It established a National Register of Historic Places and 

a program of matching grants under the existing National Trust for Historic Preservation 
San Joaquin River NWR Comprehensive Conservation Plan 189

(16 U.S.C. 468-468d). The Act established an Advisory Council on Historic Preservation, 

which was made a permanent independent agency in Public Law 94-422, approved 

September 28, 1976 (90 Stat. 1319). That Act also created the Historic Preservation Fund. 

Federal agencies are directed to take into account the effects of their actions on items or 

sites listed or eligible for listing in the National Register. As of January, 1989, 91 historic 

sites on national wildlife refuges have been placed on the National Register.

Public Law 100-588:

approved November 3, 1988, (102 Stat. 2983) lowered the threshold value of artifacts 

triggering the felony provisions of the Act from $5,000 to $500, made attempting to commit 

an action prohibited by the Act a violation, and required the land managing agencies to 

establish public awareness programs regarding the value of archaeological resources to the 

Nation.

Land and Water Conservation Fund Act of 1948:

(1965) This act provides funding through receipts from the sale of surplus federal land, 

appropriations from oil and gas receipts from the outer continental shelf, and other sources 

of for land acquisition under several authorities. Appropriations from the fund may be used 

for matching grants to states for outdoor recreation projects and for land acquisition by 

various federal agencies, including the Fish and Wildlife Service.

Migratory Bird Conservation Act of 1929:

(16 U.S.C. 715-715d, 715e,715f-715r)

This Act established the Migratory Bird Conservation Commission which consists of the 

Secretaries of the Interior (chairman), Agriculture, and Transportation, two members from 

the House of Representatives, and an ex-officio member from the state in which a project 

is located. The Commission approves acquisition of land and water, or interests therein, 

and sets the priorities for acquisition of lands by the Secretary for sanctuaries or for other 

management purposes. Under this Act, to acquire lands, or interests therein, the state 

concerned must consent to such acquisition by legislation. Such legislation has been enacted 

by most states. 

Migratory Bird Hunting and Conservation Stamp Act:

(16 U.S.C. 718-718j, 48 Stat. 452), as amended:

The “Duck Stamp Act,” as this March 16, 1934, authority is commonly called, requires 

each waterfowl hunter 16 years of age or older to possess a valid Federal hunting stamp. 

Receipts from the sale of the stamp are deposited in a special Treasury account known as the 

Migratory Bird Conservation Fund and are not subject to appropriations.

Migratory Bird Treaty Act (1918): 

Designates the protection of migratory birds as a Federal responsibility. This Act enables 

the setting of seasons, and other regulation including the closing of areas, Federal or nonFederal, to the hunting of migratory birds.

National and Community Service Act:

Will make grants to States for the creation of full-time and/or part-time programs for 

citizens over 17 years of age. Programs must be designed to fill unmet educational, human, 

environmental, and public safety needs. Initially, participants will receive post-employment 

benefits of up to $1000 per year for part-time and $2500 for full-time participants.

Thousand Points of Light B 

Creates a non-profit Points of Light Foundation to administer programs to encourage 

citizens and institutions to volunteer in order to solve critical social issues, and to discover 

new leaders and develop institutions committed to serving others.
190 San Joaquin River NWR Comprehensive Conservation Plan

National and Community Service Act of 1990: 

(42 U.S.C. 12401; 104 Stat. 3127)

Public Law 101-610, signed November 16, 1990, authorizes several programs to engage 

citizens of the U.S. in full- and/or part-time projects designed to combat illiteracy and 

poverty, provide job skills, enhance educational skills, and fulfill environmental needs. 

Several provisions are of particular interest to the U.S. Fish and Wildlife Service.

American Conservation and Youth Service Corps B As a Federal grant program established 

under Subtitle C of the law, the Corps offers an opportunity for young adults between the 

ages of 16-25, or in the case of summer programs, 15-21,to engage in approved human and 

natural resources projects which benefit the public or are carried out on Federal or Indian 

lands.

To be eligible for assistance, natural resources programs will focus on improvement of 

wildlife habitat and recreational areas, fish culture, fishery assistance, erosion, wetlands 

protection, pollution control and similar projects. A stipend of not more than 100 percent of 

the poverty level will be paid to participants. A Commission established to administer the 

Youth Service Corps will make grants to States, the Secretaries of Agriculture and Interior 

and the Director of ACTION to carry out these responsibilities.

National Environmental Policy Act of 1969: 

(P. L. 91-190, 42 U.S.C. 4321-4347, January 1, 1970, 83 Stat. 852) as amended by P. L. 94-52, 

July 3, 1975, 89 Stat. 258, and P. L. 94-83, August 9, 1975, 89 Stat. 424).

Title I of the 1969 National Environmental Policy Act (NEPA) requires that all Federal 

agencies prepare detailed environmental impact statements for “every recommendation or 

report on proposals for legislation and other major Federal actions significantly affecting the 

quality of the human environment.”

The 1969 statute stipulated the factors to be considered in environmental impact statements, 

and required that Federal agencies employ an interdisciplinary approach in related 

decision-making and develop means to ensure that unquantified environmental values are 

given appropriate consideration, along with economic and technical considerations.

Title II of this statute requires annual reports on environmental quality from the President 

to the Congress, and established a Council on Environmental Quality in the Executive Office 

of the President with specific duties and functions.

National Trails System Act: 

Assigns responsibility to the Secretary of Interior and thus the Service to protect the 

historic and recreational values of congressionally designated National Historic Trail sites.

National Wildlife Refuge System Administration Act of 1966:

(16 U.S.C. 668dd-668ee) -- as amended:

This Act, derived from sections 4 and 5 of Public Law 89-669 (October 15, 1966; 80 Stat. 

927), provides guidelines and directives for administration and management of all areas 

in the system, including “wildlife refuges, areas for the protection and conservation 

of fish and wildlife that are threatened with extinction, wildlife ranges, game ranges, 

wildlife management areas, or waterfowl production areas.” The Secretary is authorized 

to permit by regulations the use of any area within the system provided “such uses are 

compatible with the major purposes for which such areas were established.” The purchase 

consideration for rights-of way go into the Migratory Bird Conservation Fund for the 

acquisition of lands. By regulation, up to 40% of an area acquired for a migratory bird 

sanctuary may be opened to migratory bird hunting unless the Secretary finds that the 

taking of any species of migratory game birds in more than 40% of such area would be 

beneficial to the species. The Act requires an Act of Congress for the divestiture of lands 

in the system, except (1) lands acquired with Migratory Bird Conservation Commission 
San Joaquin River NWR Comprehensive Conservation Plan 191

funds, and (2) lands can be removed from the system by land exchange, or if brought into the 

system by a cooperative agreement, then pursuant to the terms of the agreement.

National Wildlife Refuge System Improvement Act of 1997:

Public Law 105-57, amends the National Wildlife System Act of 1966 (16 U.S.C. 668ddee), providing guidance for management and public use of the Refuge System. The Act 

mandates that the Refuge System be consistently directed and managed as a national 

system of lands and waters devoted to wildlife conservation and management.

The Act establishes priorities for recreational uses of the Refuge System. Six wildlifedependent uses are specifically named in the Act: hunting, fishing, wildlife observation 

and photography, and environmental education and interpretation. These activities are 

to be promoted on the Refuge System, while all non-wildlife dependant uses are subject 

to compatibility determinations. A compatible use is one which, in the sound professional 

judgement of the Refuge Manger, will not materially interfere with or detract from 

fulfillment of the Refuge System Mission or refuge purpose(s).

As stated in the Act, “The mission of the System is to administer a national network of lands 

and waters for the conservation, management, and where appropriate, restoration of the 

fish, wildlife, and plant resources and their habitats within the United States for the benefit 

of present and future generations of Americans.”

The Act also requires development of a comprehensive conservation plan for each refuge 

and management of each refuge consistent with the plan. When writing CCP, planning 

for expanded or new refuges, and when making management decisions, the Act requires 

effective coordination with other Federal agencies, state fish and wildlife or conservation 

agencies, and refuge neighbors. A refuge must also provide opportunities for public 

involvement when making a compatibility determination or developing a CCP.

National Wildlife Refuge System Volunteer and Community Partnership 

Enhancement Act (1998):

Amends the Fish and Wildlife Act of 1956 to promote volunteer programs and community 

partnerships for the benefit of national wildlife refuges, and for other purposes.

Native American Graves Protection and Repatriation Act (1990):

Requires Federal agencies and museums to inventory, determine ownership of, and 

repatriate cultural items under their control or possession.

North American Wetlands Conservation Act:

(103 Stat. 1968; 16 U.S.C. 4401-4412)

Public Law 101-233, enacted December 13, 1989, provides funding and administrative 

direction for implementation of the North American Waterfowl Management Plan and the 

Tripartite Agreement on wetlands between Canada, U.S. and Mexico.

The Act converts the Pitman-Robertson account into a trust fund, with the interest available 

without appropriation through the year 2006 to carry out the programs authorized by the 

Act, along with an authorization for annual appropriation of $15 million plus an amount equal 

to the fines and forfeitures collected under the Migratory Bird Treaty Act.

Available funds may be expended, upon approval of the Migratory Bird Conservation 

Commission, for payment of not to exceed 50 percent of the United States share of the cost 

of wetlands conservation projects in Canada, Mexico, or the United States (or 100 percent 

of the cost of projects on Federal lands). At least 50 percent and no more than 70 percent of 

the funds received are to go to Canada and Mexico each year.

A North American Wetlands Conservation Council is created to recommend projects to 

be funded under the Act to the Migratory Bird Conservation Commission. The Council 
192 San Joaquin River NWR Comprehensive Conservation Plan

is to be composed of the Director of the Service, the Secretary of the National Fish and 

Wildlife Foundation, a State fish and game agency director from each Flyway, and three 

representatives of different non-profit organizations participating in projects under the 

Plan or the Act. The Chairman of the Council and one other member serve ex officio on the 

Commission for consideration of the Council’s recommendations.

The Commission must justify in writing to the Council and, annually, to Congress, any 

decisions not to accept Council recommendations.

Oil Pollution Act of 1990:

Public Law 101-380 (33 U.S.C. 2701et. seq.; 104 Stat. 484) established new requirements and 

extensively amended the Federal Water Pollution Control Act (33 U.S.C. 1301 et. seq.) To 

provide enhanced capabilities for oil spill response and natural resource damage assessment 

by the Service. It required Service consultation on developing a fish and wildlife response 

plan for the National Contingency Plan, input to Area Contingency Plans, review of Facility 

and Tank Vessel Contingency Plans, and to conduct damage assessments associated with oil 

spills. The following are the pertinent provisions.

Title I, section 1006, provided that Federal trustees shall assess natural resource damages 

for natural resources under their trusteeship. Federal trustees may, upon request from a 

State or Indian tribe, assess damages to natural resources for them as well. Trustees shall 

develop and implement a plan for the restoration, rehabilitation, replacement, or acquisition 

of the equivalent of natural resources under their trusteeship. 

Title I, section 1011, provides that trustees are to be consulted on the appropriate removal 

action to be taken in connection with any discharge of oil.

Title I, section 1012, provided for the uses of the oil pollution fund. In addition to response 

costs, the fund may be used without appropriations to pay the costs of assessments, as well 

as to pay claims for natural resource damages if there are no funds or insufficient funds 

from a responsible party. (A claims procedure was to be developed under section 1013.) 

This section also stipulated deadlines for the submission of removal cost claims and damage 

claims.

Title IV, section 4202, amended subsection 311(j) of the Federal Water Pollution Control act 

with respect to the National Planning and Response System. It defined area committees 

and area contingency plans, and requirements and deadlines for agencies. Under this 

section, the Service is required to generate a list of all equipment, including fire fighting 

equipment, as well as personnel and any other equipment and supplies that could be used to 

expedite the removal of oil or mitigation of a spill.

One aspect of particular interest to the Service involves the identification of ecologically 

sensitive areas and the preparation of scientific monitoring and evaluation plans. Research 

conducted by the Service is to be directed and coordinated by the National Wetland 

Research Center.

Public Law 98-293: 

approved May 22, 1984 (98. Stat. 207)

Renamed the Brigantine National Wildlife Refuge and Barnegat National Wildlife Refuge, 

collectively, as the Edwin B. Forsythe National Wildlife Refuge, in memory of the late 

Congressman Forsythe of New Jersey, ranking member of the House Merchant Marine and 

Fisheries Committee for many years.

Refuge Recreation Act of 1962:

This Act authorizes the Secretary of the Interior to administer refuges, hatcheries, and 

other conservation areas for recreational use, when such uses do not interfere with the 

area’s primary purposes. It authorizes construction and maintenance of recreational 
San Joaquin River NWR Comprehensive Conservation Plan 193

facilities and the acquisition of land for incidental fish and wildlife oriented recreational 

development or protection of natural resources. It also authorizes the charging of fees for 

public uses.

Refuge Revenue Sharing Act:

(16 U.S.C. 715s)

Section 401 of the Act of June 15, 1935, (49 Stat. 383) provided for payments to counties in 

lieu of taxes, using revenues derived from the sale of products from refuges.

Public Law 93-509, approved December 3, 1974, (88 Stat. 1603) required that moneys 

remaining in the fund after payments be transferred to the Migratory Bird Conservation 

Fund for land acquisition under provisions of the Migratory Bird Conservation Act.

Public Law 95-469, approved October 17, 1978, (92 Stat. 1319) expanded the revenue 

sharing system to include National Fish Hatcheries and Service research stations. It also 

included in the Refuge Revenue Sharing Fund receipts from the sale of salmonid carcasses. 

Payments to counties were established as:

1) on acquired land, the greatest amount calculated on the basis of 75 cents per acre, 

three-fourths of one percent of the appraised value, or 25 percent of the net receipts 

produced from the land; and

2) on land withdrawn from the public domain, 25 percent of net receipts and basic payments 

under Public Law 94-565 (31 U.S.C. 1601-1607, 90 Stat. 2662), payment in lieu of taxes on 

public lands.

This amendment also authorized appropriations to make up any difference between the 

amount in the Fund and the amount scheduled for payment in any year. The stipulation that 

payments be used for schools and roads was removed, but counties were required to pass 

payments along to other units of local government within the county which suffer losses in 

revenues due to the establishment of Service areas.

Rehabilitation Act of 1973:

 (29 U.S.C. 794)as amended:

Title 5 of P. L. 93-112 (87 Stat. 355), signed October 1, 1973, prohibits discrimination on the 

basis of handicap under any program or activity receiving Federal financial assistance.

Rivers and Harbor Act (1899):

(33 U.S.C. 403): Section 10 of this Act requires the authorization by the U.S. Army Corps of 

Engineers prior to any work in, on, over, or under a navigable water of the United States.

Surface Mining Control and Reclamation Act (1977):

(Public Law 95-87) (SMCRA):as amended:

Regulates surface mining activities and reclamation of coal-mined lands. Further regulates 

the coal industry by designating certain areas as unsuitable for coal mining operations.

Transfer of Certain Real Property for Wildlife Conservation purposes Act of 1948:

This Act provides that upon determination by the Administrator of the General Services 

Administration, real property no longer needed by a Federal agency can be transferred, 

without reimbursement, to the Secretary of the Interior if the land has particular value for 

migratory birds, or to a State agency for other wildlife conservation purposes.

Uniform Relocation and Assistance and Real Property Acquisition Policies Act 

(1970):

as amended:

Provides for uniform and equitable treatment of persons who sell their homes, businesses, 

or farms to the Service. The Act requires that any purchase offer be no less than the fair 

market value of the property.
194 San Joaquin River NWR Comprehensive Conservation Plan

Wilderness Act of 1964:

(16 U.S.C. 1131-1136; 78 Stat. 890)

Public Law 88-577, approved September 3, 1964, The Wilderness Act of 1964 directs the 

Secretary of the Interior to review, within ten years, every roadless area of 5,000 acres 

or more and every roadless island regardless of size within the National Wildlife Refuge 

System and to recommend suitability of each such area. The Act permits certain activities 

within designated Wilderness Areas that do not alter natural processes. Wilderness 

values are preserved through a “minimum Tool” management approach which requires 

refuge managers to use the least intrusive methods, equipment and facilities necessary for 

administering the areas.

Youth Conservation Corps Act:

(16 U.S.C. 1701-1706, 84 Stat. 794)as amended:

Public Law 91-378, approved August 13, 1970, declares the YCC pilot program a success 

and establishes permanent programs within the Department of Interior and Agriculture for 

young adults who have attained the age of 15, but not the age of 19, to perform specific tasks 

on lands and waters administered under jurisdiction of these Secretaries. Within the Fish 

and Wildlife Service, YCC participants perform various tasks on National Wildlife Refuges, 

National Fish Hatcheries, research stations, and other facilities.

The legislation also authorizes the Secretary of Interior and the Secretary of Agriculture 

to establish a joint grant program to assist States employing young adults on non-Federal 

public lands and waters throughout the U.S.

Requires the Secretaries of Interior and Agriculture to prepare a joint report to the 

President and Congress prior to April 1 of each year. 
San Joaquin River NWR Comprehensive Conservation Plan 195

Appendix K: Mailing List

Elected Federal Officials

U.S. Senator Feinstein

U.S. Senator Boxer

U.S. Representative Condit

Federal Agencies

USDA/Natural Resource Conservation Service

USDI/Fish and Wildlife Service, Region 1 (Portland, Oregon), Region 2 (Albuquerque, 

New Mexico), Region 3 (Fort Snelling, Minnesota), Region 4 (Atlanta, Georgia), Region 

5 (Hadley, Massachusetts), Region 6 (Denver, Colorado), Region 7 (Anchorage, Alaska), 

National Conservation Training Center (Shepherdstown, West Virginia)

U.S. Army Corps of Engineers

U.S. Department of Agriculture

Bureau of Reclamation

Cooperative Alliance for Refuges

Fish and Wildlife Service–CVPIA Implementation Team

Fish and Wildlife Service–CA/NV Operations Office

Fish and Wildlife Service–Central Valley Habitat Joint Venture

Fish and Wildlife Service–Realty, Sacramento

U.S. Environmental Protection Agency

Farm Bureau

Elected State Officials

Governor Arnold Schwarzenegger 

State Representative Monteith

State Assemblyman Cordoza

State Assemblyman Frusetta

State Agencies

Tuolumne River Restoration Center - DFG

CALTRANS

California Reclamation Board

California Department of Fish and Game

California Department of Conservation

State Water Resources Control Board-Delta Unit

California Department of Food & Agriculture

California Department of Parks & Recreation 

California State Clearinghouse

California Department of Water Resources

Resources Agency–Water Policy and Science Advisor

CALFED Bay-Delta Program

ESRP–Endangered Species Recovery Program

Tribes

Me-Wuk Tribe

Ione Band of Miwork Indians

American Indian Council of Mariposa County

Table Mountain Rancheria

Picayune Rancheria

Tuolumne Rancheria
196 San Joaquin River NWR Comprehensive Conservation Plan

Santa Rosa Rancheria

Tuolumne Band of Me-Wuk

Native American Heritage Commission 

American Indian Council of Mariposa County

City/County/Local Governments

City of Atwater

City of Modesto

San Joaquin County Board of Supervisors

Stanislaus County Board of Supervisors

City of Ripon Fire Department

El Solyo Water District

San Joaquin Valley-Southern Sierra Region

City of Patterson

Stanislaus County Parks

Stanislaus County Farm Bureau Board

Stanislaus County Fish and Wildlife Committee

City of Ripon

City of Oakdale

Turlock Mosquito Abatement District

Farm Bureau Stanislaus County

Farm Bureau Modesto

Sacramento/San Joaquin Estuary FRO

Turlock Irrigation District

Department of Planning and Community Development, Stanislaus County

Stanislaus County

Fire Chief, City of Patterson

City of Merced

Stanislaus Area Ass. of Governments

White Lake Mutual Water Dist.

Resources Agency, Water Policy and Science Advisor

West Stanislaus Irrigation District 

City of Modesto, Community Development Dept.

Grasslands Water District

AICP-City of Modesto, Community Development Dept.

City of Tracy

City of Stockton

Resource Conservation District-West Stanislaus County

East Side Mosquito Abatement District-Modesto

Public Libraries

Modesto Public Library

Atwater Public Library

Tracy Public Library

Stockton Public Library

Stanislaus Public Library

Organizations

Defenders of Wildlife

Ducks Unlimited

National Audubon Society

National Wildlife Refuge Association

Sierra Club
San Joaquin River NWR Comprehensive Conservation Plan 197

The Conservation Fund

The Nature Conservancy

Wilderness Watch

Wildlife Management Institute

Sacramento/San Joaquin Estuary FRO

California Striped Bass Association

San Joaquin Audubon Society

California Farm Bureau Federation

Golden Gate Audubon Society

Napa-Solano Audubon Society

Central Sierra Audubon Society

Morro Coast Audubon Society

National Marine Fisheries Service

All Pro Environmental Corporation

CAFF 

Stanislaus Audubon Society

Sacramento River Partners

American Farmland Trust

Trust for Public Land

Stanislaus Stakeholders Group

Tulare Audubon Society

Yokuts Group of the Sierra Club

EDAW

Yosemite Audubon Society–Field Trip Chair

American Farmland Trust

Mt. Diablo Audubon Society

Sacramento Audubon Society

Ecology Action

Community Resource Center, Modesto

Friends of the Tuolumne

Sutter Basin Corporation

Jones & Stokes Associates, Inc.

Stanislaus Connections

Point Reyes Bird Observatory

Stillwater Sciences

Tuolumne River Preservation Trust

Yolo Audubon Society-Field Trip Chair

James J. Stevinson Corp.

Old Fisherman’s Club

David Evans & Associates, Inc.

Rocky Mountain Elk Foundation

Beveridge & Diamond

Stanislaus Fly Fisherman

Fresno Audubon Society

Cal Trout

Central Sierra Audubon Society

Pacific Institution

Friends of the River-Senior Policy Advocate

William and Flora Hewlett Foundation

Riparian Habitat Joint Venture/CA Audubon Society

Dry Creek Homeowners Association

Great Valley Center

Wolfe & Associates
198 San Joaquin River NWR Comprehensive Conservation Plan

Office of Historic Preservation

National Wildlife Federation

Natural Heritage Institute

Great Valley Center

Native American Heritage Comm.

California Waterfowl Association

Marjal Corp.

California Native Plant Society

Sacramento River Partners

Natural Resources Defense Council

National Fish and Wildlife Foundation

Sierra Club-Tehipite Chapter

San Joaquin Wildlife Rescue Center

Trust for Public Land

Environmental Defense Fund

Colleges/Universities

Modesto Junior College

Stanislaus State University

California State University, Stanislaus

Local Landowners

Faith Ranch

G&H Farms

PMZ Ranch RE

The Orchard RV Park

Chicken Ranch Rancheria of Me-Wuk

Joseph Gallo Farm

El Solyo Dairy

Collier Farms Inc.

Maring Farms, Inc.

Newspapers

The Modesto Bee

Stockton Record

Others

Individuals who participated in open house session or focus group or who requested to be on 

the mailing list

National Wildlife Refuge, planning team members, other agencies

Note: This list includes individuals and organizations who were mailed the Draft and/or 

Final CCPs upon their release. Others were made aware of these documents’ availability 

through notices, the World Wide Web, word of mouth, etc, and/or requested copies.
San Joaquin River NWR Comprehensive Conservation Plan 199

Appendix L: List of Preparers

 

CCP Core Team:

Tina Chouinard, Refuge Biologist–San Luis NWR Complex

Scott Fraser, Refuge Operations Specialist–San Luis NWR Complex

Miki Fujitsubo, Refuge Planner–FWS CNO Office

Leslie Lew, Refuge Planner–FWS CNO Office

Dennis Woolington, Supervisory Wildlife Biologist–San Luis NWR Complex

CCP Expanded Team:

John Beam, Biologist–California Department of Fish and Game

Mike Chouinard, Easement Program Manager–San Luis NWR Complex

Tina Chouinard, Refuge Biologist–San Luis NWR Complex

Scott Frazer, Refuge Operations Specialist–San Luis NWR Complex

Miki Fujitsubo, Refuge Planner–FWS CNO Office

John Fulton, Refuge Operations Specialist, Visitor Services–San Luis NWR Complex

Leslie Lew, Refuge Planner–FWS CNO Office

Mark Pelz, Refuge Planner–FWS CNO Office

Dennis Woolington, Supervisory Wildlife Biologist–San Luis NWR Complex

Gary Zahm–Independent Consultant

CCP Contributors:

Richard Albers, Assistant Refuge Manager–San Luis NWR Complex

Sharon Bakeman, Refuge Biologist–San Luis NWR Complex

Penny Beale, Secretary–FWS CNO Office

John Castellano, Land Planner–FWS CNO Office

Kim Forrest, Project Leader–San Luis NWR Complex

Kenneth Griggs, Refuge Biologist–San Luis NWR Complex

Eric Hopson, Assistant Refuge Manager–San Luis NWR Complex

Tim Keldsen, Refuge Biologist–San Luis NWR Complex

Yvette Laredo, Refuge Biologist–San Luis NWR Complex 

Victor Lyon, Refuge Biologist–San Luis NWR Complex

Loretta McCorkle, Writer/Editor–FWS CNO Office

Jeff McLain, Biologist–FWS AFRP

Anthony Merrill, Park Ranger–San Luis NWR Complex

Shawn Milar, Refuge Biologist–San Luis NWR Complex

R.W. Parris, Deputy Project Leader–San Luis NWR Complex

Brian Paul, Prescribed Fire Specialist–San Luis NWR Complex

Rhonda Reed, AFRP Biologist–California Department of Fish and Game

Chris Schoneman, Assistant Refuge Manager–San Luis NWR Complex

Scott Spaulding, Biologist–FWS AFRP

Todd Williams, Refuge Biologist–San Luis NWR Complex

Note: During the CCP process numerous changes and transitions in personnel and team 

make up occurred.
200 San Joaquin River NWR Comprehensive Conservation Plan

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San Joaquin River NWR Comprehensive Conservation Plan 201

Appendix M: Wilderness Review

Introduction

The purpose of a wilderness review is to identify and recommend for Congressional 

designation National Wildlife Refuge System (System) lands and waters that merit inclusion 

in the National Wilderness Preservation System (NWPS). Wilderness reviews are a 

required element of comprehensive conservation plans (CCPs) and conducted in accordance 

with the refuge planning process outlined in 602 FW 1 and 3, including public involvement 

and the National Environmental Policy Act (NEPA) compliance.

There are three phases to the wilderness review: 1) inventory, 2) study; and 3) 

recommendation. Lands and waters that meet the minimum criteria for wilderness are 

identified in the inventory phase. These areas are called wilderness study areas (WSAs). 

WSAs are evaluated through the CCP process to determine their suitability for wilderness 

designation. In the study phase, a range of management alternatives are evaluated to 

determine if a WSA is suitable for wilderness designation or management under an 

alternate set of goals and objectives that do not involve wilderness designation. The 

recommendation phase consists of forwarding or reporting recommendations for wilderness 

designation from the Director through the Secretary and the President to Congress in a 

wilderness study report.

If the inventory does not identify any areas that meet the WSA criteria, we document our 

findings in the administrative record for the CCP, fulfilling the planning requirement for a 

wilderness review. We inventoried Service lands and waters within the San Joaquin River 

NWR and found no areas that meet the eligibility criteria for a WSA as defined by the 

Wilderness Act. This appendix summarizes the wilderness inventory

for the San Joaquin River NWR.

Inventory Criteria

The wilderness inventory is a broad look at the planning area to identify WSAs. These are

roadless areas that meet the minimum criteria for wilderness identified in Section 2(c) of the

Wilderness Act.

“A wilderness, in contrast with those areas where man and his works dominate 

the landscape, is hereby recognized as an area where the earth and its community 

of life are untrammeled by man, where man himself is a visitor who does not 

remain. An area of wilderness is further defined to mean in this Act an area of 

undeveloped Federal land retaining its primeval character and influence, without 

permanent improvements or human habitation, which is protected and managed 

so as to preserve its natural conditions, and which: (1) generally appears to have 

been affected primarily by the forces of nature, with the imprint of man’s work 

substantially unnoticeable; (2) has outstanding opportunities for solitude or a 

primitive and unconfined type of recreation; (3) has at least five thousand acres 

of land or is of sufficient size as to make practicable its preservation and use in 

an unimpaired condition; and (4) may also contain ecological, geological or other 

features of scientific, educational, scenic, or historical value.”

A WSA must be a roadless area or island, meet the size criteria, appear natural, and provide

outstanding opportunities for solitude or primitive recreation. The process for identification 

of roadless areas and islands in the San Joaquin River NWR and application of the 

wilderness criteria are described in the following sections.
202 San Joaquin River NWR Comprehensive Conservation Plan

Identification of Roadless Areas and Roadless Islands

Identification of roadless areas and roadless islands required gathering and evaluating land 

status maps, land use and road inventory data, and aerial photographs for the San Joaquin 

River NWR. “Roadless” refers to the absence of improved roads suitable and maintained for 

public travel by means of motorized vehicles primarily intended for highway use. Only lands 

currently owned by the Service in fee title were evaluated.

Evaluation of the Size Criteria

Roadless areas or roadless islands meet the size criteria if any one of the following standards

apply:

Q An area with over 5,000 contiguous acres. State and private lands are not included in 

making this acreage determination.

Q A roadless island of any size. A roadless island is defined as an area surrounded by 

permanent waters or that is markedly distinguished from the surrounding lands by 

topographical or ecological features.

Q An area of less than 5,000 contiguous Federal acres that is of sufficient size as to make 

practicable its preservation and use in an unimpaired condition, and of a size suitable for 

wilderness management.

Q An area of less than 5,000 contiguous Federal acres that is contiguous with a designated 

wilderness, recommended wilderness, or area under wilderness review by another 

Federal wilderness managing agency such as the Forest Service, National Park Service, 

or Bureau of Land Management.

Evaluation of the Naturalness Criteria

In addition to being roadless, a WSA must meet the naturalness criteria. Section 2(c) defines

wilderness as an area that “... generally appears to have been affected primarily by the 

forces of nature with the imprint of man’s work substantially unnoticeable.” The area 

must appear natural to the average visitor rather than “pristine.” The presence of historic 

landscape conditions is not required. An area may include some human impacts provided 

they are substantially unnoticeable in the unit as a whole. Significant human-caused hazards, 

such as the presence of unexploded ordnance from military activity, and the physical impacts 

of refuge management facilities and activities are also considered in evaluation of the 

naturalness criteria. An area may not be considered unnatural in appearance solely on the 

basis of the “sights and sounds” of human impacts and activities outside the boundary of the

unit.

Evaluation of Outstanding Opportunities for Solitude or Primitive and 

Unconfined Recreation

In addition to meeting the size and naturalness criteria, a WSA must provide outstanding

opportunities for solitude or primitive recreation. The area does not have to possess 

outstanding opportunities for both solitude and primitive and unconfined recreation, and 

does not need to have outstanding opportunities on every acre. Further, an area does 

not have to be open to public use and access to qualify under this criteria; Congress has 

designated a number of wilderness areas in the Refuge System that are closed to public 

access to protect resource values.

Opportunities for solitude refer to the ability of a visitor to be alone and secluded from other 

visitors in the area. Primitive and unconfined recreation means non-motorized, dispersed 

outdoor recreation activities that are compatible and do not require developed facilities or 

mechanical transport. These primitive recreation activities may provide opportunities to 

experience challenge and risk; self reliance; and adventure.
San Joaquin River NWR Comprehensive Conservation Plan 203

These two “opportunity elements” are not well defined by the Wilderness Act but, in most 

cases, can be expected to occur together. However, an outstanding opportunity for solitude 

may be present in an area offering only limited primitive recreation potential. Conversely, an 

area may be so attractive for recreation use that experiencing solitude is not an option.

Evaluation of Supplemental Values

Supplemental values are defined by the Wilderness Act as “...ecological, geological, or other 

features of scientific, educational, scenic, or historic value.” These values are not required for 

wilderness but their presence should be documented.

Inventory Findings

As documented below, none of the parcels in the San Joaquin River NWR meet the criteria 

necessary for a WSA.

Roadless Areas and Roadless Islands

The San Joaquin River NWR is bisected by numerous roads including both paved countymaintained roads and gravel access roads. One exception is the Christman Island unit which 

is bound by the San Joaquin River on the east and a abandoned river meander on the west. 

However, the abandoned river meander which forms the western boundary of the Christman 

Island unit is not continuous so is not technically an island. 

Size Criteria

San Joaquin River NWR contains no units which meet the size criteria for a wilderness 

study area. The Refuge is bisected by numerous paved county roads and gravel access 

roads into relatively small (averaging less than 100 acres) management units. The 720-acre 

Christman Island unit is the largest roadless unit on the Refuge.

Naturalness Criteria

The riparian habitat on the Christman Island and Gardner’s Cove units would appear 

natural to the average visitor. However, the rest of the units are either currently intensive 

managed wetlands or croplands or contain evidence of these past agricultural activities 

including roads, canals, water structures, levees, and other signs of development.

Outstanding Opportunities for Solitude or Primitive and Unconfined Recreation

Both the Christman Island and Gardner’s cove units are adjacent the the heavily used State 

Highway 132. The units are also adjacent to parcels with active agricultural operations. 

Although the Refuge does provide opportunities for escape from the developed environment, 

the sites and sounds of vehicular traffic and agricultural operations are always present just 

beyond the unit boundaries. 

Supplemental Values

The abundant wildlife and wetlaned and riparian habitats on San Joaquin River NWR 

provides significant scenic value to visitors of the Refuge. The Refuge’s expansive riparian 

corridors and managed wetlands also provides regionally significant ecological value for 

migratory birds and other wildlife.
204 San Joaquin River NWR Comprehensive Conservation Plan

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San Joaquin River NWR Comprehensive Conservation Plan 205

Appendix N—Estimate of Refuge Water Needs

9-10-01, rev. 9/18

Land use Areas

1. Wetlands

Permanent units require 10 acre feet (AF) per year

Semi-permanent units require 8 AF per year

Seasonal units require 6.5 AF per year

East units Size Water Regime Consumptive Use

Upper Miller Lake 16 ac. permanent 160 AF

Nelson Lake 56 ac. semi-perm. 448

Goose Lake 80 ac. seasonal 520

Page Lake 70 ac. seasonal 455

Ringneck Slough 100ac. seasonal 650

Colwell Roost 80 ac. seasonal 520

Subtotal 402 ac. 2753 AF / year

West Units

River Bend 95 ac. seasonal 618

Creekside 5 ac. seasonal 32

Lower White Lake 367 ac. permanent 3670

Upper White Lake 182 ac. semi-perm 1456

Subtotal 649 ac. 5776 AF /year

Total Wetland use 8,529 AF/ year

2. Irrigated pasture 467 ac. 3736 AF

• 8 AF per year gross application (as per NRCS pers. comm. Dan Johnson 9-11-01)

List of Irrigated Pastures 

90 acre field 97 ac.

Beet field 48 ac.

Johnson field 102 ac.

South Johnson field 68 ac.

Lower 34 17 ac.

Maze Bottom 105 ac.

Quresma field 30 ac.

 467 acres 
206 San Joaquin River NWR Comprehensive Conservation Plan

3. Irrigated cropland 700 ac. 3325 AF

• 4.75 AF per year with double cropping corn and winter wheat

• Consider alternative use of alfalfa (alfalfa uses 41.85 inches of water (3.5 AF) per year, 

as per NRCS, Modesto Field Office)

 

• Riparian restoration planting varies each year of implementation. Assume 700 acre 

maximum irrigation at full development and water requirement assumed to be same 

as a mature orchard at 5.5 AF per acre. Total: 3,850 AF

List of Irrigated Crop Fields

Page field 65 ac.

Dairy field 205 ac.

Colwell new 150 ac.

Arambel hay 130 ac.

Hagemann food plot 150 ac.

 700 acres

Grand total, all water requirements 19,440 AF/YR

4. Water Delivery “System”

Water sources for the Refuge are varied by field location. Some portions of the Refuge 

have combinations of the following water sources; wells, Modesto Irrigation District 

canal, riparian lift pump, and agricultural tail water. The reliability, cost and quality of 

water varies within a wide range of variation. The dry upland sites on the Refuge are in 

close proximity to wetland or irrigated fields. Therefore habitat quality and conditions 

are closely associated with the type of water available.

Generally the East units have water sources that were used by the previous landowner 

for agricultural operations. These sources are intertwined with the continuing operation 

of neighboring ranches. Distribution of Refuge water sources is accomplished as 

part of the Cooperative Land Management Agreement with the Mapes Ranch. A new 

ground water well was installed in 2000 in the Dairy field.

Water sources for the West units consist primarily of riparian diversions and tail 

water. Three lift pump stations have been abandoned due to concerns of fish screen 

installation, maintenance cost and flood damage. Selected lift pump stations will be 

retained for continued use. The Refuge is conducting a consultation with the National 

Marine Fisheries Service as required by section seven of the endangered species act 

on the potential impact of lift pumps on salmon and steelhead. Additional consultations 

are anticipated to consider potential impacts to other listed fish species (ie. Sacramento 

splittail). Well water quality and cost has prohibited sustained use to meet Refuge 

requirements from ground water sources.